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1

Flavivirus reverse genetic systems, construction techniques and applications: a historical perspective.  

PubMed

The study of flaviviruses, which cause some of the most important emerging tropical and sub-tropical human arbovirus diseases, has greatly benefited from the use of reverse genetic systems since its first development for yellow fever virus in 1989. Reverse genetics technology has completely revolutionized the study of these viruses, making it possible to manipulate their genomes and evaluate the direct effects of these changes on their biology and pathogenesis. The most commonly used reverse genetics system is the infectious clone technology. Whilst flavivirus infectious clones provide a powerful tool, their construction as full-length cDNA molecules in bacterial vectors can be problematic, laborious and time consuming, because they are often unstable, contain unwanted induced substitutions and may be toxic for bacteria due to viral protein expression. The incredible technological advances that have been made during the past 30years, such as the use of PCR or new sequencing methods, have allowed the development of new approaches to improve preexisting systems or elaborate new strategies that overcome these problems. This review summarizes the evolution and major technical breakthroughs in the development of flavivirus reverse genetics technologies and their application to the further understanding and control of these viruses and their diseases. PMID:25512228

Aubry, Fabien; Nougairède, Antoine; Gould, Ernest A; de Lamballerie, Xavier

2015-02-01

2

Reverse genetics for mammalian reovirus  

Microsoft Academic Search

Mammalian orthoreoviruses (reoviruses) are highly tractable models for studies of viral replication and pathogenesis. The versatility of reovirus as an experimental model has been enhanced by development of a plasmid-based reverse genetics system. Infectious reovirus can be recovered from cells transfected with plasmids encoding cDNAs of each reovirus gene segment using a strategy that does not require helper virus and

Karl W. Boehme; Mine´ Ikizler; Takeshi Kobayashi; Terence S. Dermody

2011-01-01

3

Genetic Programming for Reverse Engineering Mark Harman, William B. Langdon and Westley Weimer  

E-print Network

Genetic Programming for Reverse Engineering Mark Harman, William B. Langdon and Westley Weimer of Genetic Programming (GP) and Genetic Improvement (GI) to reverse engineering. Section II presents that form part of a `GP4RE' research agenda; genetic programming applications for reverse engineering. II

Harman, Mark

4

RNA Virus Reverse Genetics and Vaccine Design  

PubMed Central

RNA viruses are capable of rapid spread and severe or potentially lethal disease in both animals and humans. The development of reverse genetics systems for manipulation and study of RNA virus genomes has provided platforms for designing and optimizing viral mutants for vaccine development. Here, we review the impact of RNA virus reverse genetics systems on past and current efforts to design effective and safe viral therapeutics and vaccines. PMID:24967693

Stobart, Christopher C.; Moore, Martin L.

2014-01-01

5

Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals  

PubMed Central

With the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequencing efficiency and accuracy, many species of animals, plants, and microbes have annotated genomic information publicly available. The focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. Reverse genetic approaches have been used for many years to advance from sequence data to the resulting phenotype in an effort to deduce the function of a gene in the species of interest. Many of the currently used approaches (RNAi, gene knockout, site-directed mutagenesis, transposon tagging) rely on the creation of transgenic material, the development of which is not always feasible for many plant or animal species. TILLING is a non-transgenic reverse genetics approach that is applicable to all animal and plant species which can be mutagenized, regardless of its mating / pollinating system, ploidy level, or genome size. This approach requires prior DNA sequence information and takes advantage of a mismatch endonuclease to locate and detect induced mutations. Ultimately, it can provide an allelic series of silent, missense, nonsense, and splice site mutations to examine the effect of various mutations in a gene. TILLING has proven to be a practical, efficient, and an effective approach for functional genomic studies in numerous plant and animal species. EcoTILLING, which is a variant of TILLING, examines natural genetic variation in populations and has been successfully utilized in animals and plants to discover SNPs including rare ones. In this review, TILLING and EcoTILLING techniques, beneficial applications and limitations from plant and animal studies are discussed. PMID:19452039

Barkley, N.A; Wang, M.L

2008-01-01

6

Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals  

Microsoft Academic Search

With the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequenc- ing efficiency and accuracy, many species of animals, plants, and microbes have annotated genomic information publicly available. The focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. Reverse genetic approaches have been used for

N. A. Barkley; M. L. Wang

2008-01-01

7

Establishment of Canine RNA Polymerase I-Driven Reverse Genetics for Influenza A Virus: Its Application for H5N1 Vaccine Production  

Microsoft Academic Search

In the event of a new influenza pandemic, vaccines whose antigenicities match those of circulating strains must be rapidly produced. Here, we established an alternative reverse genetics system for influenza virus using the canine polymerase I (PolI) promoter sequence that works efficiently in the Madin-Darby canine kidney cell line, a cell line approved for human vaccine production. Using this system,

Shin Murakami; Taisuke Horimoto; Shinya Yamada; Satoshi Kakugawa; Hideo Goto; Yoshihiro Kawaoka

2008-01-01

8

Biol Cell . Author manuscript Reverse genetics in eukaryotes  

E-print Network

Biol Cell . Author manuscript Page /1 20 Reverse genetics in eukaryotes Serge Hardy , Vincent Abstract Reverse genetics consists in the modification of the activity and will help decipher gene functions in the post-genome era. MESH Keywords Animals ; Animals, Genetically

Paris-Sud XI, Université de

9

Towards Reverse Engineering of Genetic Regulatory Networks Zelmina Lubovac  

E-print Network

1 Towards Reverse Engineering of Genetic Regulatory Networks Zelmina Lubovac , Björn Olsson understanding of reverse engineering of regulatory networks. One of the aspects that have not been considered to a great extent in the development of reverse engineering approaches is combinatorial regulation

Chang, Joseph T.

10

Reversible gelation of genetically engineered macromolecules  

NASA Astrophysics Data System (ADS)

Genetic engineering of protein-based polymers offers distinct advantages over conventional synthesis of polymers. Microorganisms can synthesize high molecular weight materials, in relatively large quantities, that are inherently stereoregular, monodisperse, and of controlled sequence. In addition, specific secondary and higher order structures are determined by this protein sequence. As a result, scientists can design polymers to have unique structural features found in natural protein materials and functional properties that are inherent in certain peptide sequences. For this reason, genetic engineering principles were used to create a set of artificial genes that encode twelve macromolecules having both alpha-helical and disordered coil protein sequences with the last amino acid being cysteine (cys) or tryptophan (trp). Triblock copolymer sequences having coiled-coil protein ends, A or B, where A and B represent alpha-helical acidic and basic leucine zipper proteins, separated by a water soluble flexible spacer coil protein, C, where C represents ((AG)sb3PEG) sbn (n = 10 or 28), showed reversible physical gelation behavior. This behavior is believed to result from the aggregation of two or more helices that form physical crosslinks with the disordered coil domain retaining solvent and preventing precipitation of the chain. Diffising wave spectroscopy was used to investigate the gelation behavior of ACsb{10}Acys in buffer when environmental conditions such as pH, temperature, and concentration were varied. The dynamic intensity autocorrelation function recorded over time for 5% (w/v) ACsb{10}Acys showed that the protein behaved as a gel at pH 6.7-8.0 and that the melting point was between 40sp°C and 48sp°C. In addition to the triblock results, the incorporation of 5sp',5sp',5sp'-trifluoroleucine (Tfl) in place of leucine (Leu) in the A and B blocks was accomplished by synthesizing proteins in bacterial hosts auxotrophic for Leu. The substitution of Tfl for Leu in A and B was confirmed by electrospray mass spectrometry. Amino acid analyses performed on purified Tfl A and Tfl B populations suggested 66% and 38% levels of Tfl substitution, respectively. Thermal denaturation temperatures measured by circular dichroism of the Tfl containing helices were higher than those of the corresponding Leu containing helices by 8sp°C and 13sp°C for A and B respectively.

Petka, Wendy Ann

11

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling  

E-print Network

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling Jesper contained in the genetic circuit. A natural plan of attack is to use a forward engineering approach, wherebyDynamics and Department of Biomedical Engineering, Boston University, Boston, MA 02215; Division of Computational Biology

Babu, M. Madan

12

Bayesian Networks Applications in Genetics  

E-print Network

Bayesian Networks Applications in Genetics Segregation, IBD and Linkage from the Perspective the Perspective of BNT #12;Bayesian Networks Applications in Genetics Outline 1 Bayesian Networks Model and Notations Belief Propagation Exact Inference 2 Applications in Genetics Segregation IBD Linkage G. NUEL

Nuel, Gregory

13

The reverse genetics applied to fish RNA viruses  

PubMed Central

Aquaculture has expanded rapidly to become a major economic and food-producing sector worldwide these last 30 years. In parallel, viral diseases have emerged and rapidly spread from farm to farm causing enormous economic losses. The most problematic viruses encountered in the field are mainly, but not exclusively, RNA viruses belonging to the Novirhabdovirus, Aquabirnavirus, Alphavirus and Betanodavirus genera. The recent establishment of reverse genetics systems to recover infectious fish RNA viruses entirely from cDNA has made possible to genetically manipulate the viral genome. These systems have provided powerful tools to study all aspects of the virus biology and virus-host interactions but also gave the opportunity to use these viruses as live vaccines or as gene vectors. This review provides an overview on the recent breakthroughs achieved by using these reverse genetics systems in terms of viral protein function, virulence and host-specificity factor, vaccine development and vector design. PMID:21314978

2011-01-01

14

Reprint of: Coronavirus reverse genetic systems: infectious clones and replicons.  

PubMed

Coronaviruses (CoVs) infect humans and many animal species, and are associated with respiratory, enteric, hepatic, and central nervous system diseases. The large size of the CoV genome and the instability of some CoV replicase gene sequences during its propagation in bacteria, represent serious obstacles for the development of reverse genetic systems similar to those used for smaller positive sense RNA viruses. To overcome these limitations, several alternatives to more conventional plasmid-based approaches have been established in the last 13 years. In this report, we briefly review and discuss the different reverse genetic systems developed for CoVs, paying special attention to the severe acute respiratory syndrome CoV (SARS-CoV). PMID:25261606

Almazán, Fernando; Sola, Isabel; Zuñiga, Sonia; Marquez-Jurado, Silvia; Morales, Lucia; Becares, Martina; Enjuanes, Luis

2014-12-19

15

Coronavirus reverse genetic systems: infectious clones and replicons.  

PubMed

Coronaviruses (CoVs) infect humans and many animal species, and are associated with respiratory, enteric, hepatic, and central nervous system diseases. The large size of the CoV genome and the instability of some CoV replicase gene sequences during its propagation in bacteria, represent serious obstacles for the development of reverse genetic systems similar to those used for smaller positive sense RNA viruses. To overcome these limitations, several alternatives to more conventional plasmid-based approaches have been established in the last 13 years. In this report, we briefly review and discuss the different reverse genetic systems developed for CoVs, paying special attention to the severe acute respiratory syndrome CoV (SARS-CoV). PMID:24930446

Almazán, Fernando; Sola, Isabel; Zuñiga, Sonia; Marquez-Jurado, Silvia; Morales, Lucia; Becares, Martina; Enjuanes, Luis

2014-08-30

16

An improved reverse genetics system for mammalian orthoreoviruses  

Microsoft Academic Search

Mammalian orthoreoviruses (reoviruses) are highly useful models for studies of double-stranded RNA virus replication and pathogenesis. We previously developed a strategy to recover prototype reovirus strain T3D from cloned cDNAs transfected into murine L929 fibroblast cells. Here, we report the development of a second-generation reovirus reverse genetics system featuring several major improvements: (1) the capacity to rescue prototype reovirus strain

Takeshi Kobayashi; Laura S. Ooms; Mine Ikizler; James D. Chappell; Terence S. Dermody

2010-01-01

17

Reverse genetics system for studying human rhinovirus infections.  

PubMed

Human rhinovirus (HRV) contains a 7.2 kb messenger-sense RNA genome which is the template for reproducing progeny viruses after it enters the cytoplasm of a host cell. Reverse genetics refers to the regeneration of progeny viruses from an artificial cDNA copy of the RNA genome of an RNA virus. It has been a powerful molecular genetic tool for studying HRV and other RNA viruses because the artificial DNA stage makes it practical to introduce specific mutations into the viral RNA genome. This chapter uses HRV-16 as the model virus to illustrate the strategy and methods for constructing and cloning the artificial cDNA copy of a full-length HRV genome, identifying the infectious cDNA clone isolates, and selecting the most vigorous cDNA clone isolate to serve as the standard parental clone for future molecular genetic study of the virus. PMID:25261313

Lee, Wai-Ming; Wang, Wensheng; Bochkov, Yury A; Lee, Iris

2015-01-01

18

Chloroquine Susceptibility and Reversibility in a Plasmodium falciparum Genetic Cross  

PubMed Central

Summary Mutations in the Plasmodium falciparum chloroquine (CQ) resistance transporter (PfCRT), are major determinants of verapamil (VP)-reversible CQ resistance (CQR). In the presence of mutant PfCRT, additional genes contribute to the wide range of CQ susceptibilities observed. It is not known if these genes influence mechanisms of chemosensitization by CQR reversal agents. Using quantitative trait locus (QTL) mapping of progeny clones from the HB3 × Dd2 cross, we show that the P. falciparum multidrug resistance gene 1 (pfmdr1) interacts with the Southeast Asia-derived mutant pfcrt haplotype to modulate CQR levels. A novel chromosome 7 locus is predicted to contribute with the pfcrt and pfmdr1 loci to influence CQR levels. Chemoreversal via a wide range of chemical structures operates through a direct pfcrt-based mechanism. Direct inhibition of parasite growth by these reversal agents is influenced by pfcrt mutations and additional loci. Direct labeling of purified recombinant PfMDR1 protein with a highly specific photoaffinity CQ analogue, and lack of competition for photolabeling by VP, supports our QTL predictions. We find no evidence that pfmdr1 copy number affects CQ response in the progeny, however, inheritance patterns indicate that an allele-specific interaction between pfmdr1 and pfcrt is part of the complex genetic background of CQR. PMID:20807203

Patel, Jigar J.; Thacker, Drew; Tan, John C.; Pleeter, Perri; Checkley, Lisa; Gonzales, Joseph M.; Deng, Bingbing; Roepe, Paul D.; Cooper, Roland A.; Ferdig, Michael T.

2011-01-01

19

REVERSE ENGINEERING OF METABOLIC PATHWAYS FROM OBSERVED DATA USING GENETIC PROGRAMMING  

E-print Network

REVERSE ENGINEERING OF METABOLIC PATHWAYS FROM OBSERVED DATA USING GENETIC PROGRAMMING John R. Koza Biomedical Informatics, Department of Medicine Department of Electrical Engineering Stanford University, Stanford, California, koza@stanford.edu William Mydlowec Genetic Programming Inc., Los Altos, California

Fernandez, Thomas

20

REVERSE ENGINEERING BY MEANS OF GENETIC PROGRAMMING OF METABOLIC PATHWAYS FROM OBSERVED DATA  

E-print Network

REVERSE ENGINEERING BY MEANS OF GENETIC PROGRAMMING OF METABOLIC PATHWAYS FROM OBSERVED DATA John R, to automatically reverse engineer the network from the data. Genetic programming (Koza, Bennett, Andre, and Keane. Koza Biomedical Informatics, Department of Medicine Department of Electrical Engineering Stanford

Fernandez, Thomas

21

Genetic algorithms and their applications  

Microsoft Academic Search

This article introduces the genetic algorithm (GA) as an emerging optimization algorithm for signal processing. After a discussion of traditional optimization techniques, it reviews the fundamental operations of a simple GA and discusses procedures to improve its functionality. The properties of the GA that relate to signal processing are summarized, and a number of applications, such as IIR adaptive filtering,

K. S. Tang; K. F. Man; S. Kwong; Q. He

1996-01-01

22

Reversible Hydrogels from Self-Assembling Genetically Engineered Protein Block Copolymers  

E-print Network

Reversible Hydrogels from Self-Assembling Genetically Engineered Protein Block Copolymers Chunyu Xu-soluble polyelectrolyte segment flanked by two coiled-coil domains was synthesized by genetic engineering methods antibodies that can form complexes with antigens,20 and genetically engineered proteins containing coiled

Breedveld, Victor

23

Live vaccines for human metapneumovirus designed by reverse genetics.  

PubMed

Human metapneumovirus (HMPV) was first described in 2001 and has quickly become recognized as an important cause of respiratory tract disease worldwide, especially in the pediatric population. A vaccine against HMPV is required to prevent severe disease associated with infection in infancy. The primary strategy is to develop a live-attenuated virus for intranasal immunization, which is particularly well suited against a respiratory virus. Reverse genetics provides a means of developing highly characterized 'designer' attenuated vaccine candidates. To date, several promising vaccine candidates have been developed, each using a different mode of attenuation. One candidate involves deletion of the G glycoprotein, providing attenuation that is probably based on reduced efficiency of attachment. A second candidate involves deletion of the M2-2 protein, which participates in regulating RNA synthesis and whose deletion has the advantageous property of upregulating transcription and increasing antigen synthesis. A third candidate involves replacing the P protein gene of HMPV with its counterpart from the related avian metapneumovirus, thereby introducing attenuation owing to its chimeric nature and host range restriction. Another live vaccine strategy involves using an attenuated parainfluenza virus as a vector to express HMPV protective antigens, providing a bivalent pediatric vaccine. Additional modifications to provide improved vaccines will also be discussed. PMID:17181442

Buchholz, Ursula J; Nagashima, Kunio; Murphy, Brian R; Collins, Peter L

2006-10-01

24

Allele-specific chemical genetics: concept, strategies, and applications.  

PubMed

The relationship between DNA and protein sequences is well understood, yet because the members of a protein family/subfamily often carry out the same biochemical reaction, elucidating their individual role in cellular processes presents a challenge. Forward and reverse genetics have traditionally been employed to understand protein functions with considerable success. A fundamentally different approach that has gained widespread application is the use of small organic molecules, known as chemical genetics. However, the slow time-scale of genetics and inherent lack of specificity of small molecules used in chemical genetics have limited the applicability of these methods in deconvoluting the role of individual proteins involved in fast, dynamic biological events. Combining the advantages of both the techniques, the specificity achieved with genetics along with the reversibility and tunability of chemical genetics, has led to the development of a powerful approach to uncover protein functions in complex biological processes. This technique is known as allele-specific chemical genetics and is rapidly becoming an essential toolkit to shed light on proteins and their mechanism of action. The current review attempts to provide a comprehensive description of this approach by discussing the underlying principles, strategies, and successful case studies. Potential future implications of this technology in expanding the frontiers of modern biology are discussed. PMID:25436868

Islam, Kabirul

2015-02-20

25

Reversibility conditions for quantum channels and their applications  

SciTech Connect

Conditions for a quantum channel (noncommutative Markov operator) to be reversible with respect to complete families of quantum states with bounded rank are obtained. A description of all quantum channels reversible with respect to a given (orthogonal or nonorthogonal) complete family of pure states is given. Some applications in quantum information theory are considered. Bibliography: 20 titles.

Shirokov, M E [Steklov Mathematical Institute of the Russian Academy of Sciences (Russian Federation)

2013-08-31

26

Molecular genetic etiology of twin reversed arterial perfusion sequence  

Microsoft Academic Search

OBJECTIVE: Our purpose was to determine whether the twin reversed arterial perfusion sequence (acardiac anomaly) results from fertilization of the first or second polar body. STUDY DESIGN: Placental or fetal tissue was obtained from nine twin sets discordant for twin reversed arterial perfusion. After deoxyribonucleic acid extraction, the polymerase chain reaction was used to amplify five polymorphic microsatellite repeats. The

Nicholas M. Fisk; Mark Ware; Philip Stanier; Gudrun Moore; Phillip Bennett

1996-01-01

27

Industry application of marbling genetics  

E-print Network

Abstract. Improved marbling performance has been recognised for many years as an important objective for the “high quality ” export sector of the Australian beef industry. Over the last 5 years there have been several developments that have provided breeders with significantly better information on which to base breeding decisions aimed at improved marbling performance. These include the application of real-time ultrasound scanning for intramuscular fat percentage (IMF%); the derivation of genetic parameters involving IMF%; the enhancement of BREEDPLAN to incorporate IMF % in multi-trait genetic evaluation; and, the industry adoption of selection index technology (via BREEDOBJECT) to assist in optimal multi-trait selection including marbling performance. It is argued that a major constraint to the genetic improvement in beef palatability traits, including marbling performance, has been the inadequate communication of effective market signals and poor information flow through the beef supply chain. This situation is unlikely to change unless the industry achieves a greater degree of vertical co-ordination and improved linkage across the supply chain from the producer to the consumer. There is a need for the implementation of genuine value based marketing systems that provide an appropriate financial incentive for seedstock and commercial beef producers to adopt breeding and management strategies that emphasise the improvement of beef palatability and marbling. The application of gene marker technology will provide future opportunities, as well as additional challenges, in the quest for achieving improved marbling performance.

Peter F. Parnell

28

An efficient reverse genetics platform in the model legume Medicago truncatula.  

PubMed

Medicago truncatula is one of the model species for legume studies. In an effort to develop legume genetics resources, > 21 700 Tnt1 retrotransposon insertion lines have been generated. To facilitate fast-growing needs in functional genomics, two reverse genetics approaches have been established: web-based database searching and PCR-based reverse screening. More than 840 genes have been reverse screened using the PCR-based approach over the past 6 yr to identify mutants in these genes. Overall, c. 84% (705 genes) success rate was achieved in identifying mutants with at least one Tnt1 insertion, of which c. 50% (358 genes) had three or more alleles. To demonstrate the utility of the two reverse genetics platforms, two mutant alleles were isolated for each of the two floral homeotic MADS-box genes, MtPISTILATA and MtAGAMOUS. Molecular and genetic analyses indicate that Tnt1 insertions in exons of both genes are responsible for the defects in floral organ development. In summary, we have developed two efficient reverse genetics platforms to facilitate functional characterization of M. truncatula genes. PMID:24206427

Cheng, Xiaofei; Wang, Mingyi; Lee, Hee-Kyung; Tadege, Million; Ratet, Pascal; Udvardi, Michael; Mysore, Kirankumar S; Wen, Jiangqi

2014-02-01

29

Yeast Genetics and Biotechnological Applications  

NASA Astrophysics Data System (ADS)

Yeast can be recognized as one of the very important groups of microorganisms on account of its extensive use in the fermentation industry and as a basic eukaryotic model cellular system. The yeast Saccharomyces cerevisiae has been extensively used to elucidate the genetics and regulation of several key functions in the cell such as cell mating, electron transport chain, protein trafficking, cell cycle events and others. Even before the genome sequence of the yeast was out, the structural organization and function of several of its genes was known. With the availability of the origin of replication from the 2 ?m plasmid and the development of transformation system, it became the host of choice for expression of a number of important proteins. A large number of episomal and integrative shuttle vectors are available for expression of mammalian proteins. The latest developments in genomics and micro-array technology have allowed investigations of individual gene function by site-specific deletion method. The application of metabolic profiling has also assisted in understanding the cellular network operating in this yeast. This chapter is aimed at reviewing the use of this system as an experimental tool for conducting classical genetics. Various vector systems available, foreign genes expressed and the limitations as a host will be discussed. Finally, the use of various yeast enzymes in biotechnology sector will be reviewed.

Mishra, Saroj; Baranwal, Richa

30

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling  

PubMed Central

While the fundamental building blocks of biology are being tabulated by the various genome projects, microarray technology is setting the stage for the task of deducing the connectivity of large-scale gene networks. We show how the perturbation of carefully chosen genes in a microarray experiment can be used in conjunction with a reverse engineering algorithm to reveal the architecture of an underlying gene regulatory network. Our iterative scheme identifies the network topology by analyzing the steady-state changes in gene expression resulting from the systematic perturbation of a particular node in the network. We highlight the validity of our reverse engineering approach through the successful deduction of the topology of a linear in numero gene network and a recently reported model for the segmentation polarity network in Drosophila melanogaster. Our method may prove useful in identifying and validating specific drug targets and in deconvolving the effects of chemical compounds. PMID:12730377

Tegnér, Jesper; Yeung, M. K. Stephen; Hasty, Jeff; Collins, James J.

2003-01-01

31

Reverse engineering Web applications: the WARE approach  

Microsoft Academic Search

The rapid, progressive diffusion of Web applications in several productive contexts of our modern society is laying the foundations of a renewed scenario of software development, where one of the emerging problems is that of defining and validating cost-effective approaches for maintaining and evolving these software systems.Due to several factors, the solution to this problem is not straightforward. The heterogeneous

Giuseppe Antonio Di Lucca; Anna Rita Fasolino; Porfirio Tramontana

2004-01-01

32

Experimental implementation of reverse time migration for nondestructive evaluation applications.  

PubMed

Reverse time migration (RTM) is a commonly employed imaging technique in seismic applications (e.g., to image reservoirs of oil). Its standard implementation cannot account for multiple scattering/reverberation. For this reason it has not yet found application in nondestructive evaluation (NDE). This paper applies RTM imaging to NDE applications in bounded samples, where reverberation is always present. This paper presents a fully experimental implementation of RTM, whereas in seismic applications, only part of the procedure is done experimentally. A modified RTM imaging condition is able to localize scatterers and locations of disbonding. Experiments are conducted on aluminum samples with controlled scatterers. PMID:21302980

Anderson, Brian E; Griffa, Michele; Bas, Pierre-Yves Le; Ulrich, Timothy J; Johnson, Paul A

2011-01-01

33

A High Through-Put Reverse Genetic Screen Identifies Two Genes Involved in Remote Memory in Mice  

E-print Network

A High Through-Put Reverse Genetic Screen Identifies Two Genes Involved in Remote Memory in Mice Through-Put Reverse Genetic Screen Identifies Two Genes Involved in Remote Memory in Mice. PLoS ONE 3 required for remote memory, we screened randomly selected mouse strains harboring known mutations. In our

Anagnostaras, Stephan

34

Establishment of a Reverse Genetics System for Studying Human Bocavirus in Human Airway Epithelia  

E-print Network

, CuFi-8 (originally derived from a cystic fibrosis patient), also supported productive infection of HBoV1. Thus, we have established a reverse genetics system and generated the first cell line-based culture system for the study of HBoV1 infection...

Huang, Qinfeng; Deng, Xuefeng; Yan, Ziying; Cheng, Fang; Lou, Yong; Shen, Weiran; Lei-Butters, Diana C. M.; Chen, Aaron Yun; Li, Yi; Tang, Liang; Sö derlund-Venermo, Maria; Englehardt, John F.; Qiu, Jianming

2012-08-30

35

Genetic evidence for extreme polyandry and extraordinary sex-role reversal in a pipe sh  

E-print Network

Genetic evidence for extreme polyandry and extraordinary sex-role reversal in a pipe sh Adam G, USA Due to the phenomenon of male pregnancy, the ¢sh family Syngnathidae (seahorses and pipe¢shes) has assemblage of pipe¢shes or seahorses in order to demonstrate conclusively that sexual selection acts most

Avise, John

36

Reverse genetics by loss-of-function mosaic analysis in Drosophila.  

PubMed

Genetic mosaics in Drosophila typically involve derivation of homozygous daughter cells from heterozygous precursors through mitotic recombination. MARCM (mosaic analysis with a repressible cell marker) couples loss of heterozygosity with derepression of a marker gene, permitting unique labeling of specific homozygous daughter cells. The generation of GAL80-minus homozygous daughter cells in otherwise heterozygous tissues allows GAL4-dependent activation of upstream activation sequence (UAS)-reporter specifically in the homozygous cells of interest. To make MARCM clones, organisms must carry at least five genetic elements (flippase [FLP], flippase recognition targets [FRTs], tubP-GAL80, GAL4, and UAS-marker) in specific configurations. One major application of MARCM, as described here, is to study cell-autonomous function(s) of a gene within single cells or a group of cells in otherwise unperturbed organisms. A mutation of interest distal to one FRT site is put in trans to a tubP-GAL80-containing chromosome arm that carries the same FRT. The resulting MARCM clones, which are negative for tubP-GAL80 and thus specifically marked, will become homozygous for the mutation in otherwise heterozygous organisms. By including a UAS-transgene, one can perform rescue experiments in the mutant MARCM clones. Conversely, if the mutation is placed on the same chromosome arm as tubP-GAL80, MARCM-labeled cells will be homozygous wild-type and may lie adjacent to sister cells that are homozygous mutant. This variant, called reverse MARCM, allows one to determine non-cell-autonomous effects of a mutation. PMID:23282632

Kao, Chih-Fei; Lee, Tzumin

2013-01-01

37

Construction of a Sonchus Yellow Net Virus minireplicon: a step toward reverse genetic analysis of plant negative-strand RNA viruses.  

PubMed

Reverse genetic analyses of negative-strand RNA (NSR) viruses have provided enormous advances in our understanding of animal viruses over the past 20 years, but technical difficulties have hampered application to plant NSR viruses. To develop a reverse genetic approach for analysis of plant NSR viruses, we have engineered Sonchus yellow net nucleorhabdovirus (SYNV) minireplicon (MR) reporter cassettes for Agrobacterium tumefaciens expression in Nicotiana benthamiana leaves. Fluorescent reporter genes substituted for the SYNV N and P protein open reading frames (ORFs) exhibited intense single-cell foci throughout regions of infiltrated leaves expressing the SYNV MR derivatives and the SYNV nucleocapsid (N), phosphoprotein (P), and polymerase (L) proteins. Genomic RNA and mRNA transcription was detected for reporter genes substituted for both the SYNV N and P ORFs. These activities required expression of the N, P, and L core proteins in trans and were enhanced by codelivery of viral suppressor proteins that interfere with host RNA silencing. As is the case with other members of the Mononegavirales, we detected polar expression of fluorescent proteins and chloramphenicol acetyltransferase substitutions for the N and P protein ORFs. We also demonstrated the utility of the SYNV MR system for functional analysis of SYNV core proteins in trans and the cis-acting leader and trailer sequence requirements for transcription and replication. This work provides a platform for construction of more complex SYNV reverse genetic derivatives and presents a general strategy for reverse genetic applications with other plant NSR viruses. PMID:23885070

Ganesan, Uma; Bragg, Jennifer N; Deng, Min; Marr, Sharon; Lee, Mi Yeon; Qian, Shasha; Shi, Manling; Kappel, Justin; Peters, Cole; Lee, Yeon; Goodin, Michael M; Dietzgen, Ralf G; Li, Zhenghe; Jackson, Andrew O

2013-10-01

38

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

NASA Technical Reports Server (NTRS)

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

Liang, Shoudan; Fuhrman, Stefanie; Somogyi, Roland

1998-01-01

39

The human genome project--some implications of extensive "reverse genetic" medicine.  

PubMed Central

Impressive progress has been made during the past several decades in understanding the pathogenesis of human genetic disease. The tools of molecular biology have allowed the isolation of many disease-related genes by forward and a few by reverse genetics, and the imminent completion of a complete human genetic linkage map will accelerate the genetic characterization of many more genetic diseases. The major impacts of the molecular characterization of human genetic diseases will be 1. To increase markedly the number of human diseases that we recognize to have major genetic components. We already understand that genetic diseases are not rare medical curiosities with negligible societal impact, but rather constitute a wide spectrum of both rare and extremely common diseases responsible for an immense amount of suffering in all human societies. The characterization of the human genome will lead to the identification of genetic factors in many more human diseases, even those that now seem too multifactorial or polygenic for ready understanding. 2. To allow the development of powerful new approaches to diagnosis, detection, screening and even therapy of these disorders aimed directly at the mutant genes rather than at the gene products. This should eventually allow much more accurate and specific management of human genetic disease and the genetic factors in many human maladies. The preparation of a fine-structure physical map of the entire human genome together with an overlapping contiguous set of clones spanning entire chromosomes or large portions of chromosomes is rapidly becoming feasible, and the information that will flow from this effort promises eventually to affect the management of many important genetic diseases.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2309696

Friedmann, T

1990-01-01

40

Prospects for fusion applications of reversed-field pinches  

SciTech Connect

The applicability of the Reversed-Field Pinch (RFP) as a source of fusion neutrons for use in developing key fusion nuclear technologies is examined. This Fusion Test Facility (FTF) would emphasize high neutron wall loading, small plasma volume, low fusion and driver powers, and steady-state operation. Both parametric tradeoffs based on present-day physics understanding and a conceptual design based on an approx.1-MW/mS (neutron) driven operation are reported. 10 refs.

Bathke, C.G.; Krakowski, R.A.; Hagenson, R.L.

1985-01-01

41

A high-throughput cloning system for reverse genetics in Trypanosoma cruzi  

PubMed Central

Background The three trypanosomatids pathogenic to men, Trypanosoma cruzi, Trypanosoma brucei and Leishmania major, are etiological agents of Chagas disease, African sleeping sickness and cutaneous leishmaniasis, respectively. The complete sequencing of these trypanosomatid genomes represented a breakthrough in the understanding of these organisms. Genome sequencing is a step towards solving the parasite biology puzzle, as there are a high percentage of genes encoding proteins without functional annotation. Also, technical limitations in protein expression in heterologous systems reinforce the evident need for the development of a high-throughput reverse genetics platform. Ideally, such platform would lead to efficient cloning and compatibility with various approaches. Thus, we aimed to construct a highly efficient cloning platform compatible with plasmid vectors that are suitable for various approaches. Results We constructed a platform with a flexible structure allowing the exchange of various elements, such as promoters, fusion tags, intergenic regions or resistance markers. This platform is based on Gateway® technology, to ensure a fast and efficient cloning system. We obtained plasmid vectors carrying genes for fluorescent proteins (green, cyan or yellow), and sequences for the c-myc epitope, and tandem affinity purification or polyhistidine tags. The vectors were verified by successful subcellular localization of two previously characterized proteins (TcRab7 and PAR 2) and a putative centrin. For the tandem affinity purification tag, the purification of two protein complexes (ribosome and proteasome) was performed. Conclusions We constructed plasmids with an efficient cloning system and suitable for use across various applications, such as protein localization and co-localization, protein partner identification and protein expression. This platform also allows vector customization, as the vectors were constructed to enable easy exchange of its elements. The development of this high-throughput platform is a step closer towards large-scale trypanosome applications and initiatives. PMID:20942965

2010-01-01

42

Systematic reverse genetics of transfer-DNA-tagged lines of Arabidopsis  

Microsoft Academic Search

The authors have developed an efficient reverse-genetics protocol that uses expedient pooling and hybridization strategies to identify individual transfer-DNA insertion lines from a collection of 6,000 independently transformed lines in as few as 36 polymerase chain reactions. The authors have used this protocol to systematically isolate Arabidopsis lines containing insertional mutations in individual cytochrome P450 genes. In higher plants P450

Rodney G. Winkler; Michael R. Frank; David W. Galbraith; R. Feyereisen; K. A. Feldmann

1998-01-01

43

Reverse genetics for peste-des-petits-ruminants virus (PPRV): Promoter and protein specificities  

Microsoft Academic Search

Peste-des-petits-ruminants virus (PPRV) (family Paramyxoviridae, genus Morbillivirus) causes an acute febrile illness in sheep and goats resulting in significant morbidity and mortality in infected herds. The paramyxoviruses all have negative sense, non-segmented RNA genomes and their host range and pathogenic determinants have been extensively studied using reverse genetics. This technology also enables a more rational approach to be taken with

Dalan Bailey; Louisa S. Chard; Pradyot Dash; Tom Barrett; Ashley C. Banyard

2007-01-01

44

An Assessment of Heavy Ion Irradiation Mutagenesis for Reverse Genetics in Wheat (Triticum aestivum L.)  

PubMed Central

Reverse genetic techniques harnessing mutational approaches are powerful tools that can provide substantial insight into gene function in plants. However, as compared to diploid species, reverse genetic analyses in polyploid plants such as bread wheat can present substantial challenges associated with high levels of sequence and functional similarity amongst homoeologous loci. We previously developed a high-throughput method to identify deletions of genes within a physically mutagenized wheat population. Here we describe our efforts to combine multiple homoeologous deletions of three candidate disease susceptibility genes (TaWRKY11, TaPFT1 and TaPLDß1). We were able to produce lines featuring homozygous deletions at two of the three homoeoloci for all genes, but this was dependent on the individual mutants used in crossing. Intriguingly, despite extensive efforts, viable lines possessing homozygous deletions at all three homoeoloci could not be produced for any of the candidate genes. To investigate deletion size as a possible reason for this phenomenon, we developed an amplicon sequencing approach based on synteny to Brachypodium distachyon to assess the size of the deletions removing one candidate gene (TaPFT1) in our mutants. These analyses revealed that genomic deletions removing the locus are relatively large, resulting in the loss of multiple additional genes. The implications of this work for the use of heavy ion mutagenesis for reverse genetic analyses in wheat are discussed. PMID:25719507

Fitzgerald, Timothy L.; Powell, Jonathan J.; Stiller, Jiri; Weese, Terri L.; Abe, Tomoko; Zhao, Guangyao; Jia, Jizeng; McIntyre, C. Lynne; Li, Zhongyi; Manners, John M.; Kazan, Kemal

2015-01-01

45

Mobile Timekeeping Application Built on Reverse-Engineered JPL Infrastructure  

NASA Technical Reports Server (NTRS)

Every year, non-exempt employees cumulatively waste over one man-year tracking their time and using the timekeeping Web page to save those times. This app eliminates this waste. The innovation is a native iPhone app. Libraries were built around a reverse- engineered JPL API. It represents a punch-in/punch-out paradigm for timekeeping. It is accessible natively via iPhones, and features ease of access. Any non-exempt employee can natively punch in and out, as well as save and view their JPL timecard. This app is built on custom libraries created by reverse-engineering the standard timekeeping application. Communication is through custom libraries that re-route traffic through BrowserRAS (remote access service). This has value at any center where employees track their time.

Witoff, Robert J.

2013-01-01

46

Fully-Reversible "Moving Fiber" Switch Permits Enhanced Applications  

NASA Astrophysics Data System (ADS)

Fiber optic switches which use the "moving fiber" principle to obtain low insertion loss and mode independence are discussed. Because the precisely-cleaved endfaces of the fibers are accurately aligned in close proximity, most of the modes can be transferred, and losses kept to a minimum (typically 0.6 dB). Due to the mature technology of electromechanical relays, and the low inertia associated with moving fibers instead of moving mirrors, prisms, or lenses, the switches are very reliable. Both bypass and fully-reversible versions will be discussed. The loopback capability of the fully-reversible switch makes possible an extended range of applications, including dual attachment station bypass and self-healing ring "wrap around".

Gurbaxani, Andrew

1988-02-01

47

[Applications of genetically modified animals].  

PubMed

The first transgenic animals, mice, were obtained in 1980. The techniques of gene transfer had to be adapted to obtain transgenic animals with an acceptable yield in about fifteen species. When the yield is low (low rate of random integration and targeted integration via homologous recombination), genetic modifications must be achieved in intermediate cells able to participate to the development of chimeric transgenic animals (ES cells, EG cells, iPS obtained by the dedifferentiation of somatic cells) or in somatic cells used as nuclear donor to generate transgenic clones. Various tools make possible a marked increase of homologous recombination efficiency (meganucleases and ZFN), or a gene inactivation at the genome level (direct or conditional knock out) or at the mRNA level (interfering RNAs). Vectors allow a more reliable transgene expression. Genetically modified animals are used mainly to obtain information on biological functions and human diseases. Transgenic animals produce recombinant pharmaceutical proteins in milk and soon in egg white. Pig organs adapted to be tolerated by patients might be tested in humans in five years. The projects based on the use of transgenesis to improve animal production are presently few. Transgenic salmon with accelerated growth might be on the market when their possible escape in oceans will be controlled. PMID:20122391

Houdebine, Louis-Marie

2009-01-01

48

Natural Genetic Variation of Xanthomonas campestris pv. campestris Pathogenicity on Arabidopsis Revealed by Association and Reverse Genetics  

PubMed Central

ABSTRACT The pathogenic bacterium Xanthomonas campestris pv. campestris, the causal agent of black rot of Brassicaceae, manipulates the physiology and the innate immunity of its hosts. Association genetic and reverse-genetic analyses of a world panel of 45 X. campestris pv. campestris strains were used to gain understanding of the genetic basis of the bacterium’s pathogenicity to Arabidopsis thaliana. We found that the compositions of the minimal predicted type III secretome varied extensively, with 18 to 28 proteins per strain. There were clear differences in aggressiveness of those X. campestris pv. campestris strains on two Arabidopsis natural accessions. We identified 3 effector genes (xopAC, xopJ5, and xopAL2) and 67 amplified fragment length polymorphism (AFLP) markers that were associated with variations in disease symptoms. The nature and distribution of the AFLP markers remain to be determined, but we observed a low linkage disequilibrium level between predicted effectors and other significant markers, suggesting that additional genetic factors make a meaningful contribution to pathogenicity. Mutagenesis of type III effectors in X. campestris pv. campestris confirmed that xopAC functions as both a virulence and an avirulence gene in Arabidopsis and that xopAM functions as a second avirulence gene on plants of the Col-0 ecotype. However, we did not detect the effect of any other effector in the X. campestris pv. campestris 8004 strain, likely due to other genetic background effects. These results highlight the complex genetic basis of pathogenicity at the pathovar level and encourage us to challenge the agronomical relevance of some virulence determinants identified solely in model strains. PMID:23736288

Guy, Endrick; Genissel, Anne; Hajri, Ahmed; Chabannes, Matthieu; David, Perrine; Carrere, Sébastien; Lautier, Martine; Roux, Brice; Boureau, Tristan; Arlat, Matthieu; Poussier, Stéphane; Noël, Laurent D.

2013-01-01

49

Rescue of Recent Virulent and Avirulent Field Strains of Bluetongue Virus by Reverse Genetics  

PubMed Central

Since 1998, Bluetongue virus (BTV)-serotypes 1, 2, 4, 9, and 16 have invaded European countries around the Mediterranean Basin. In 2006, a huge BT-outbreak started after incursion of BTV-serotype 8 (BTV8) in North-Western Europe. More recently, BTV6 and BTV11 were reported in North-Western Europe in 2008. These latter strains are closely related to live-attenuated vaccine, whereas BTV8 is virulent and can induce severe disease in ruminants, including cattle. In addition, Toggenburg orbivirus (TOV) was detected in 2008 in Swiss goats, which was recognized as a new serotype of BTV (BTV25). The (re-)emergency of known and unknown BTV-serotypes needs a rapid response to supply effective vaccines, and research to study this phenomenon. Recently, orbivirus research achieved an important breakthrough by the establishment of reverse genetics for BTV1. Here, reverse genetics for two recent BTV strains representing virulent BTV8 and avirulent BTV6 was developed. For this purpose, extensive sequencing of full-genomes was performed, resulting in the consensus sequences of BTV8/net07 and BTV6/net08. The recovery of ‘synthetic BTV’, respectively rgBTV8 and rgBTV6, completely from T7-derived RNA transcripts was confirmed by silent mutations by which these ‘synthetic BTVs’ could be genetically distinguished from wild type BTV, respectively wtBTV6 and wtBTV8. The in vitro and in vivo properties of rgBTV6 or rgBTV8 were comparable to the properties of their parent strains. The asymptomatic or avirulent properties of rgBTV6 and the virulence of rgBTV8 were confirmed by experimental infection of sheep. Reverse genetics of the vaccine-related BTV6 provides a perfect start to develop new generations of BT-vaccines. Reverse genetics of the virulent BTV8 will accelerate research on the special features of BTV8, like transmission by species of Culicoides in a moderate climate, transplacental transmission, and pathogenesis in cattle. PMID:22363444

van Gennip, René G. P.; van de Water, Sandra G. P.; Potgieter, Christiaan A.; Wright, Isabel M.; Veldman, Daniel; van Rijn, Piet A.

2012-01-01

50

Introduction to Genetic Engineering and Its Applications  

NSDL National Science Digital Library

Students learn how engineers apply their understanding of DNA to manipulate specific genes to produce desired traits, and how engineers have used this practice to address current problems facing humanity. They learn what genetic engineering means and examples of its applications, as well as moral and ethical problems related to its implementation. Students fill out a flow chart to list the methods to modify genes to create GMOs and example applications of bacteria, plant and animal GMOs.

2014-09-18

51

Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis.  

PubMed Central

Chemical mutagenesis has been the workhorse of traditional genetics, but it has not been possible to determine underlying rates or distributions of mutations from phenotypic screens. However, reverse-genetic screens can be used to provide an unbiased ascertainment of mutation statistics. Here we report a comprehensive analysis of approximately 1900 ethyl methanesulfonate (EMS)-induced mutations in 192 Arabidopsis thaliana target genes from a large-scale TILLING reverse-genetic project, about two orders of magnitude larger than previous such efforts. From this large data set, we are able to draw strong inferences about the occurrence and randomness of chemically induced mutations. We provide evidence that we have detected the large majority of mutations in the regions screened and confirm the robustness of the high-throughput TILLING method; therefore, any deviations from randomness can be attributed to selectional or mutational biases. Overall, we detect twice as many heterozygotes as homozygotes, as expected; however, for mutations that are predicted to truncate an encoded protein, we detect a ratio of 3.6:1, indicating selection against homozygous deleterious mutations. As expected for alkylation of guanine by EMS, >99% of mutations are G/C-to-A/T transitions. A nearest-neighbor bias around the mutated base pair suggests that mismatch repair counteracts alkylation damage. PMID:12807792

Greene, Elizabeth A; Codomo, Christine A; Taylor, Nicholas E; Henikoff, Jorja G; Till, Bradley J; Reynolds, Steven H; Enns, Linda C; Burtner, Chris; Johnson, Jessica E; Odden, Anthony R; Comai, Luca; Henikoff, Steven

2003-01-01

52

Application of Molecular Genetics and Transformation to Barley Improvement  

Technology Transfer Automated Retrieval System (TEKTRAN)

This chapter of the new barley monograph summarizes current applications of molecular genetics and transformation to barley improvement. The chapter describes recent applications of molecular markers including association genetics, QTL mapping and marker assisted selection in barley programs, and in...

53

Applications of Time-Reversal Processing for Planetary Surface Communications  

NASA Technical Reports Server (NTRS)

Due to the power constraints imposed on wireless sensor and communication networks deployed on a planetary surface during exploration, energy efficient transfer of data becomes a critical issue. In situations where groups of nodes within a network are located in relatively close proximity, cooperative communication techniques can be utilized to improve the range, data rate, power efficiency, and lifetime of the network. In particular, if the point-to-point communication channels on the network are well modeled as frequency non-selective, distributed or cooperative beamforming can employed. For frequency-selective channels, beamforming itself is not generally appropriate, but a natural generalization of it, time-reversal communication (TRC), can still be effective. Time-reversal processing has been proposed and studied previously for other applications, including acoustical imaging, electromagnetic imaging, underwater acoustic communication, and wireless communication channels. In this paper, we study both the theoretical advantages and the experimental performance of cooperative TRC for wireless communication on planetary surfaces. We give a brief introduction to TRC and present several scenarios where TRC could be profitably employed during planetary exploration. We also present simulation results illustrating the performance of cooperative TRC employed in a complex multipath environment and discuss the optimality of cooperative TRC for data aggregation in wireless sensor networks

Barton, Richard J.

2007-01-01

54

Homoclinic orbits in reversible systems and their applications in mechanics, fluids and optics  

Microsoft Academic Search

This survey article reviews the theory and application of homoclinic orbits to equilibria in reversible continuous-time dynamical systems, where the homoclinic orbit and the equilibrium are both reversible. The focus is on even-order reversible systems in four or more dimensions. Local theory, generic argument, and global existence theories are examined for each qualitatively distinct linearisation. Several recent results, such as

A. R. Champneys

1998-01-01

55

Transcription, reverse transcription, and analysis of RNA containing artificial genetic components.  

PubMed

Expanding the synthetic biology of artificially expanded genetic information systems (AEGIS) requires tools to make and analyze RNA molecules having added nucleotide "letters". We report here the development of T7 RNA polymerase and reverse transcriptase to catalyze transcription and reverse transcription of xNA (DNA or RNA) having two complementary AEGIS nucleobases, 6-amino-5-nitropyridin-2-one (trivially, Z) and 2-aminoimidazo[1,2a]-1,3,5-triazin-4(8H)-one (trivially, P). We also report MALDI mass spectrometry and HPLC-based analyses for oligomeric GACUZP six-letter RNA and the use of ribonuclease (RNase) A and T1 RNase as enzymatic tools for the sequence-specific degradation of GACUZP RNA. We then applied these tools to analyze the GACUZP and GACTZP products of polymerases and reverse transcriptases (respectively) made from DNA and RNA templates. In addition to advancing this 6-letter AEGIS toward the biosynthesis of proteins containing additional amino acids, these experiments provided new insights into the biophysics of DNA. PMID:25137127

Leal, Nicole A; Kim, Hyo-Joong; Hoshika, Shuichi; Kim, Myong-Jung; Carrigan, Matthew A; Benner, Steven A

2015-04-17

56

Divergent genetic mechanisms underlie reversals to radial floral symmetry from diverse zygomorphic flowered ancestors  

PubMed Central

Malpighiaceae possess flowers with a unique bilateral symmetry (zygomorphy), which is a hypothesized adaptation associated with specialization on neotropical oil bee pollinators. Gene expression of two representatives of the CYC2 lineage of floral symmetry TCP genes, CYC2A and CYC2B, demarcate the adaxial (dorsal) region of the flower in the characteristic zygomorphic flowers of most Malpighiaceae. Several clades within the family, however, have independently lost their specialized oil bee pollinators and reverted to radial flowers (actinomorphy) like their ancestors. Here, we investigate CYC2 expression associated with four independent reversals to actinomorphy. We demonstrate that these reversals are always associated with alteration of the highly conserved CYC2 expression pattern observed in most New World (NW) Malpighiaceae. In NW Lasiocarpus and Old World (OW) Microsteria, the expression of CYC2-like genes has expanded to include the ventral region of the corolla. Thus, the pattern of gene expression in these species has become radialized, which is comparable to what has been reported in the radial flowered legume clade Cadia. In striking contrast, in NW Psychopterys and OW Sphedamnocarpus, CYC2-like expression is entirely absent or at barely detectable levels. This is more similar to the pattern of CYC2 expression observed in radial flowered Arabidopsis. These results collectively indicate that, regardless of geographic distribution, reversals to similar floral phenotypes in this large tropical angiosperm clade have evolved via different genetic changes from an otherwise highly conserved developmental program. PMID:23970887

Zhang, Wenheng; Steinmann, Victor W.; Nikolov, Lachezar; Kramer, Elena M.; Davis, Charles C.

2013-01-01

57

Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics.  

PubMed

IR64, the most widely grown indica rice in South and Southeast Asia, possesses many positive agronomic characteristics (e.g., wide adaptability, high yield potential, tolerance to multiple diseases and pests, and good eating quality,) that make it an ideal genotype for identifying mutational changes in traits of agronomic importance. We have produced a large collection of chemical and irradiation-induced IR64 mutants with different genetic lesions that are amenable to both forward and reverse genetics. About 60,000 IR64 mutants have been generated by mutagenesis using chemicals (diepoxybutane and ethylmethanesulfonate) and irradiation (fast neutron and gamma ray). More than 38,000 independent lines have been advanced to M4 generation enabling evaluation of quantitative traits by replicated trials. Morphological variations at vegetative and reproductive stages, including plant architecture, growth habit, pigmentation and various physiological characters, are commonly observed in the four mutagenized populations. Conditional mutants such as gain or loss of resistance to blast, bacterial blight, and tungro disease have been identified at frequencies ranging from 0.01% to 0.1%. Results from pilot experiments indicate that the mutant collections are suitable for reverse genetics through PCR-detection of deletions and TILLING. Furthermore, deletions can be detected using oligomer chips suggesting a general technique to pinpoint deletions when genome-wide oligomer chips are broadly available. M4 mutant seeds are available for users for screening of altered response to multiple stresses. So far, more than 15,000 mutant lines have been distributed. To facilitate broad usage of the mutants, a mutant database has been constructed in the International Rice Information System (IRIS; http: //www.iris.irri.org) to document the phenotypes and gene function discovered by users. PMID:16217604

Wu, Jian-Li; Wu, Chanjian; Lei, Cailin; Baraoidan, Marietta; Bordeos, Alicia; Madamba, Ma Reina Suzette; Ramos-Pamplona, Marilou; Mauleon, Ramil; Portugal, Arlett; Ulat, Victor Jun; Bruskiewich, Richard; Wang, Guoliang; Leach, Jan; Khush, Gurdev; Leung, Hei

2005-09-01

58

DNA marker technologies and their applications in aquaculture genetics  

Microsoft Academic Search

The development of DNA-based genetic markers has had a revolutionary impact on animal genetics. With DNA markers, it is theoretically possible to observe and exploit genetic variation in the entire genome. Popular genetic markers in the aquaculture community include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite, SNP, and EST markers. The application of DNA markers has allowed rapid progress in

Z. J. Liu; J. F. Cordes

2004-01-01

59

Application of Genetic Algorithms in Seismic Tomography  

NASA Astrophysics Data System (ADS)

In the earth sciences several inverse problems that require data fitting and parameter estimation are nonlinear and can involve a large number of unknown parameters. Consequently, the application of analytical inversion or optimization techniques may be quite restrictive. In practice, most analytical methods are local in nature and rely on a linearized form of the problem in question, adopting an iterative procedure using partial derivatives to improve an initial model. This approach can lead to a dependence of the final model solution on the starting model and is prone to entrapment in local misfit minima. Moreover, the calculation of derivatives can be computationally inefficient and create instabilities when numerical approximations are used. In contrast to these local minimization methods, global techniques that do not rely on partial derivatives, are independent of the form of the data misfit criterion, and are computationally robust. Such methods often use random processes to sample a selected wider span of the model space. In this situation, randomly generated models are assessed in terms of their data-fitting quality and the process may be stopped after a certain number of acceptable models is identified or continued until a satisfactory data fit is achieved. A new class of methods known as genetic algorithms achieves the aforementioned approximation through novel model representation and manipulations. Genetic algorithms (GAs) were originally developed in the field of artificial intelligence by John Holland more than 20 years ago, but even in this field it is less than a decade that the methodology has been more generally applied and only recently did the methodology attract the attention of the earth sciences community. Applications have been generally concentrated in geophysics and in particular seismology. As awareness of genetic algorithms grows there surely will be many more and varied applications to earth science problems. In the present work, the application of hybrid genetic algorithms in seismic tomography is examined and the efficiency of least squares and genetic methods as representative of the local and global optimization, respectively, is presented and evaluated. The robustness of both optimization methods has been tested and compared for the same source-receiver geometry and characteristics of the model structure (anomalies, etc.). A set of seismic refraction synthetic (noise free) data was used for modeling. Specifically, cross-well, down-hole and typical refraction studies using 24 geophones and 5 shoots were used to confirm the applicability of the genetic algorithms in seismic tomography. To solve the forward modeling and estimate the traveltimes, the revisited ray bending method was used supplemented by an approximate computation of the first Fresnel volume. The root mean square (rms) error as the misfit function was used and calculated for the entire random velocity model for each generation. After the end of each generation and based on the misfit of the individuals (velocity models), the selection, crossover and mutation (typical process steps of genetic algorithms) were selected continuing the evolution theory and coding the new generation. To optimize the computation time, since the whole procedure is quite time consuming, the Matlab Distributed Computing Environment (MDCE) was used in a multicore engine. During the tests, we noticed that the fast convergence that the algorithm initially exhibits (first 5 generations) is followed by progressively slower improvements of the reconstructed velocity models. Thus, to improve the final tomographic models, a hybrid genetic algorithm (GA) approach was adopted by combining the GAs with a local optimization method after several generations, on the basis of the convergence of the resulting models. This approach is shown to be efficient, as it directs the solution search towards a model region close to the global minimum solution.

Soupios, Pantelis; Akca, Irfan; Mpogiatzis, Petros; Basokur, Ahmet; Papazachos, Constantinos

2010-05-01

60

Genetic Counseling Graduate Program Webinar: Preparing your GC Program Application  

E-print Network

Genetic Counseling Graduate Program Webinar: Preparing your GC Program Application Friday, October 31st, 2014 1:00-2:30 PM EDT Are you applying to genetic counseling programs for fall 2015 admission for an interactive webinar where we will: · Review the genetic counseling program application and admission process

Finley Jr., Russell L.

61

Genome-Wide Association Mapping Combined with Reverse Genetics Identifies New Effectors of Low Water Potential-Induced Proline Accumulation in Arabidopsis1[W][OPEN  

PubMed Central

Arabidopsis (Arabidopsis thaliana) exhibits natural genetic variation in drought response, including varying levels of proline (Pro) accumulation under low water potential. As Pro accumulation is potentially important for stress tolerance and cellular redox control, we conducted a genome-wide association (GWAS) study of low water potential-induced Pro accumulation using a panel of natural accessions and publicly available single-nucleotide polymorphism (SNP) data sets. Candidate genomic regions were prioritized for subsequent study using metrics considering both the strength and spatial clustering of the association signal. These analyses found many candidate regions likely containing gene(s) influencing Pro accumulation. Reverse genetic analysis of several candidates identified new Pro effector genes, including thioredoxins and several genes encoding Universal Stress Protein A domain proteins. These new Pro effector genes further link Pro accumulation to cellular redox and energy status. Additional new Pro effector genes found include the mitochondrial protease LON1, ribosomal protein RPL24A, protein phosphatase 2A subunit A3, a MADS box protein, and a nucleoside triphosphate hydrolase. Several of these new Pro effector genes were from regions with multiple SNPs, each having moderate association with Pro accumulation. This pattern supports the use of summary approaches that incorporate clusters of SNP associations in addition to consideration of individual SNP probability values. Further GWAS-guided reverse genetics promises to find additional effectors of Pro accumulation. The combination of GWAS and reverse genetics to efficiently identify new effector genes may be especially applicable for traits difficult to analyze by other genetic screening methods. PMID:24218491

Verslues, Paul E.; Lasky, Jesse R.; Juenger, Thomas E.; Liu, Tzu-Wen; Kumar, M. Nagaraj

2014-01-01

62

All-in-One Bacmids: an Efficient Reverse Genetics Strategy for Influenza A Virus Vaccines  

PubMed Central

ABSTRACT Vaccination is the first line of defense against influenza virus infection, yet influenza vaccine production methods are slow, antiquated, and expensive as a means to effectively reduce the virus burden during epidemic or pandemic periods. There is a great need for alternative influenza vaccines and vaccination methods with a global scale of impact. We demonstrate here a strategy to generate influenza A virus in vivo by using bacmid DNAs. Compared to the classical reverse genetics system, the “eight-in-one” bacmids (bcmd-RGFlu) showed higher efficiency of virus rescue in various cell types. Using a transfection-based inoculation (TBI) system, intranasal delivery to DBA/2J and BALB/c mice of bcmd-RGFlu plus 293T cells led to the generation of lethal PR8 virus in vivo. A prime-boost intranasal vaccination strategy using TBI in the context of a bcmd-RGFlu carrying a temperature-sensitive H1N1 virus resulted in protection of mice against lethal challenge with the PR8 strain. Taken together, these studies provide proof of principle to highlight the potential of vaccination against influenza virus by using in vivo reverse genetics. IMPORTANCE Vaccination is the first line of defense against influenza virus infections. A major drawback in the preparation of influenza vaccines is that production relies on a heavily time-consuming process of growing the viruses in eggs. We propose a radical change in the way influenza vaccination is approached, in which a recombinant bacmid, a shuttle vector that can be propagated in both Escherichia coli and insect cells, carries an influenza virus infectious clone (bcmd-RGFlu). Using a surrogate cell system, we found that intranasal delivery of bcmd-RGFlu resulted in generation of influenza virus in mice. Furthermore, mice vaccinated with this system were protected against lethal influenza virus challenge. The study serves as a proof of principle of a potentially universal vaccine platform against influenza virus and other pathogens. PMID:24942589

Chen, Hongjun; Angel, Matthew; Li, Weizhong; Finch, Courtney; Gonzalez, Ana Silvia; Sutton, Troy; Santos, Jefferson

2014-01-01

63

Applications for the 2014 Kenyon Award Each year, the Department of Genetics recognizes a graduating Genetics major with the  

E-print Network

of Genetics recognizes a graduating Genetics major with the Cynthia Kenyon Outstanding on a plaque that hangs in the Genetics office. This year students are invited. The applications will be reviewed by the Undergraduate Affairs Committee of the Genetics

Arnold, Jonathan

64

Genetic switchboard for synthetic biology applications  

PubMed Central

A key next step in synthetic biology is to combine simple circuits into higher-order systems. In this work, we expanded our synthetic riboregulation platform into a genetic switchboard that independently controls the expression of multiple genes in parallel. First, we designed and characterized riboregulator variants to complete the foundation of the genetic switchboard; then we constructed the switchboard sensor, a testing platform that reported on quorum-signaling molecules, DNA damage, iron starvation, and extracellular magnesium concentration in single cells. As a demonstration of the biotechnological potential of our synthetic device, we built a metabolism switchboard that regulated four metabolic genes, pgi, zwf, edd, and gnd, to control carbon flow through three Escherichia coli glucose-utilization pathways: the Embden–Meyerhof, Entner–Doudoroff, and pentose phosphate pathways. We provide direct evidence for switchboard-mediated shunting of metabolic flux by measuring mRNA levels of the riboregulated genes, shifts in the activities of the relevant enzymes and pathways, and targeted changes to the E. coli metabolome. The design, testing, and implementation of the genetic switchboard illustrate the successful construction of a higher-order system that can be used for a broad range of practical applications in synthetic biology and biotechnology. PMID:22454498

Callura, Jarred M.; Cantor, Charles R.; Collins, James J.

2012-01-01

65

Universal Influenza B Virus Genomic Amplification Facilitates Sequencing, Diagnostics, and Reverse Genetics  

PubMed Central

Although human influenza B virus (IBV) is a significant human pathogen, its great genetic diversity has limited our ability to universally amplify the entire genome for subsequent sequencing or vaccine production. The generation of sequence data via next-generation approaches and the rapid cloning of viral genes are critical for basic research, diagnostics, antiviral drugs, and vaccines to combat IBV. To overcome the difficulty of amplifying the diverse and ever-changing IBV genome, we developed and optimized techniques that amplify the complete segmented negative-sense RNA genome from any IBV strain in a single tube/well (IBV genomic amplification [IBV-GA]). Amplicons for >1,000 diverse IBV genomes from different sample types (e.g., clinical specimens) were generated and sequenced using this robust technology. These approaches are sensitive, robust, and sequence independent (i.e., universally amplify past, present, and future IBVs), which facilitates next-generation sequencing and advanced genomic diagnostics. Importantly, special terminal sequences engineered into the optimized IBV-GA2 products also enable ligation-free cloning to rapidly generate reverse-genetics plasmids, which can be used for the rescue of recombinant viruses and/or the creation of vaccine seed stock. PMID:24501036

Zhou, Bin; Lin, Xudong; Wang, Wei; Halpin, Rebecca A.; Bera, Jayati; Stockwell, Timothy B.; Barr, Ian G.

2014-01-01

66

Development of reverse genetics systems for bluetongue virus: recovery of infectious virus from synthetic RNA transcripts.  

PubMed

Bluetongue virus (BTV), an insect-vectored emerging pathogen of both wild ruminants and livestock, has had a severe economic impact in agriculture in many parts of the world. The investigation of BTV replication and pathogenesis has been hampered by the lack of a reverse genetics system. Recovery of infectious BTV is possible by the transfection of permissive cells with the complete set of 10 purified viral mRNAs derived in vitro from transcribing cores (M. Boyce and P. Roy, J. Virol. 81:2179-2186, 2007). Here, we report that in vitro synthesized T7 transcripts, derived from cDNA clones, can be introduced into the genome of BTV using a mixture of T7 transcripts and core-derived mRNAs. The replacement of genome segment 10 and the simultaneous replacement of segments 2 and 5 encoding the two immunologically important outer capsid proteins, VP2 and VP5, are described. Further, we demonstrate the recovery of infectious BTV entirely from T7 transcripts, proving that synthetic transcripts synthesized in the presence of cap analogue can functionally substitute for viral transcripts at all stages of the BTV replication cycle. The generation of BTV with a fully defined genome permits the recovery of mutations in a defined genetic background. The ability to generate specific mutants provides a new tool to investigate the BTV replication cycle as well as permitting the generation of designer vaccine strains, which are greatly needed in many countries. PMID:18562540

Boyce, Mark; Celma, Cristina C P; Roy, Polly

2008-09-01

67

Reverse Genetics in Eukaryotes1 Serge Hardy1,2, Vincent Legagneux1,2, Yann Audic 1,2, Luc Paillard1,26  

E-print Network

such mutations.53 "Reverse" genetics has emerged more recently in the beginning of the 1980s, with the541 Reverse Genetics in Eukaryotes1 2 3 4 5 Serge Hardy1,2, Vincent Legagneux1,2, Yann Audic 1,2, Luc 73. Fax +33 223 23 44 7817 18 19 20 21 Keywords Mutation; Gene targeting; phenotype; knock

Boyer, Edmond

68

The use of monoreassortants and reverse genetics to map reovirus lysis of a ras-transformed cell line  

Microsoft Academic Search

Reovirus has been shown to lyse most transformed cells while establishing a persistent or abortive infection in non-transformed cells. Developing methods to identify the reovirus genes associated with oncolysis is an important step toward understanding the mechanisms involved. This report is the first to develop and apply the use of monoreassortants and reverse genetics to identify an individual reovirus gene

Michael R. Roner; Christine Mutsoli

2007-01-01

69

Development of a Reverse Genetics System to Produce Live, Attenuated Infectious Salmon Anemia Virus (ISAV) Vaccine Candidates  

E-print Network

1 Development of a Reverse Genetics System to Produce Live, Attenuated Infectious Salmon Anemia Grant Number: NA03NMF4270132 March 29, 2006 Abstract Infectious salmon anemia (ISA), induced by the viral causative agent infectious salmon anemia virus (ISAV), has had a large, negative economic impact

70

Reverse Genetics Demonstrates that Proteolytic Processing of the Ebola Virus Glycoprotein Is Not Essential for Replication in Cell Culture  

Microsoft Academic Search

Ebola virus, a prime example of an emerging pathogen, causes fatal hemorrhagic fever in humans and in nonhuman primates. Identification of major determinants of Ebola virus pathogenicity has been hampered by the lack of effective strategies for experimental mutagenesis. Here we exploit a reverse genetics system that allows the generation of Ebola virus from cloned cDNA to engineer a mutant

Gabriele Neumann; Heinz Feldmann; Shinji Watanabe; Igor Lukashevich; Yoshihiro Kawaoka

2002-01-01

71

Genetically modified plants for law enforcement applications  

NASA Astrophysics Data System (ADS)

Plants are ubiquitous in the environment and have the unique ability to respond to their environment physiologically and through altered gene expression profiles (they cannot walk away). In addition, plant genetic transformation techniques and genomic information in plants are becoming increasingly advanced. We have been performing research to express the jellyfish green fluorescent protein (GFP) in plants. GFP emits green light when excited by blue or UV light. In addition, my group and collaborators have developed methods to detect GFP in plants by contact instruments and at a standoff. There are several law enforcement applications for this technology. One involves using tagging and perhaps modifying drug plants genetically. In one instance, we could tag them for destruction. In another, we could adulterate them directly. Another application is one that falls into the chemical terrorism and bioterrorism countermeasures category. We are developing plants to sense toxins and whole organisms covertly. Plants are well adapted to monitor large geographic areas; biosurveillance. Some examples of research being performed focus on plants with plant pathogen inducible promoters fused to GFP for disease sensing, and algae biosensors for chemicals.

Stewart, C. Neal, Jr.

2002-08-01

72

Application of real options to reverse logistics process  

E-print Network

In this thesis, real options are used to identify the optimal model for the reverse logistics process of a technology company in the circuit board business. Currently, customers return defective boards and the company ...

Kaga, Akihiro, 1975-

2004-01-01

73

Static Performance of Six Innovative Thrust Reverser Concepts for Subsonic Transport Applications: Summary of the NASA Langley Innovative Thrust Reverser Test Program  

NASA Technical Reports Server (NTRS)

The NASA Langley Configuration Aerodynamics Branch has conducted an experimental investigation to study the static performance of innovative thrust reverser concepts applicable to high-bypass-ratio turbofan engines. Testing was conducted on a conventional separate-flow exhaust system configuration, a conventional cascade thrust reverser configuration, and six innovative thrust reverser configurations. The innovative thrust reverser configurations consisted of a cascade thrust reverser with porous fan-duct blocker, a blockerless thrust reverser, two core-mounted target thrust reversers, a multi-door crocodile thrust reverser, and a wing-mounted thrust reverser. Each of the innovative thrust reverser concepts offer potential weight savings and/or design simplifications over a conventional cascade thrust reverser design. Testing was conducted in the Jet-Exit Test Facility at NASA Langley Research Center using a 7.9%-scale exhaust system model with a fan-to-core bypass ratio of approximately 9.0. All tests were conducted with no external flow and cold, high-pressure air was used to simulate core and fan exhaust flows. Results show that the innovative thrust reverser concepts achieved thrust reverser performance levels which, when taking into account the potential for system simplification and reduced weight, may make them competitive with, or potentially more cost effective than current state-of-the-art thrust reverser systems.

Asbury, Scott C.; Yetter, Jeffrey A.

2000-01-01

74

Static Performance of Six Innovative Thrust Reverser Concepts for Subsonic Transport Applications: Summary of the NASA Langley Innovative Thrust Reverser Test Program  

NASA Technical Reports Server (NTRS)

The NASA Langley Configuration Aerodynamics Branch has conducted an experimental investigation to study the static performance of innovative thrust reverser concepts applicable to high-bypass-ratio turbofan engines. Testing was conducted on a conventional separate-flow exhaust system configuration, a conventional cascade thrust reverser configuration, and six innovative thrust reverser configurations. The innovative thrust reverser configurations consisted of a cascade thrust reverser with porous fan-duct blocker, a blockerless thrust reverser, two core-mounted target thrust reversers, a multi-door crocodile thrust reverser, and a wing-mounted thrust reverser. Each of the innovative thrust reverser concepts offer potential weight savings and/or design simplifications over a conventional cascade thrust reverser design. Testing was conducted in the Jet-Exit Test Facility at NASA Langley Research Center using a 7.9%-scale exhaust system model with a fan-to-core bypass ratio of approximately 9.0. All tests were conducted with no external flow and cold, high-pressure air was used to simulate core and fan exhaust flows. Results show that the innovative thrust reverser concepts achieved thrust reverser performance levels which, when taking into account the potential for system simplification and reduced weight, may make them competitive with, or potentially more cost effective than current state-of-the-art thrust reverser systems. All data gathered in this investigation are contained in the CD-ROM.

Asbury, Scott C.; Yetter, Jeffrey A.

2000-01-01

75

INTERNAL/INTRACAMPUS TRANSFER APPLICATION NCSU Department of Genetics  

E-print Network

INTERNAL/INTRACAMPUS TRANSFER APPLICATION NCSU Department of Genetics If you are currently a student at NCSU and wish to transfer into the Department of Genetics, complete this form and submit deadlines are listed at http://genetics.ncsu.edu/undergrad. Students will be notified of the admission

Langerhans, Brian

76

Automated Reverse Engineering of UML Sequence Diagrams for Dynamic Web Applications  

E-print Network

Automated Reverse Engineering of UML Sequence Diagrams for Dynamic Web Applications Manar H. Alalfi based on reverse engineering of the structure and behav- ior of software to visual models such as UML of programs as UML class diagrams. However, the recovery of dynamic behavior, and particularly interaction

Cordy, James R.

77

Application of time reverse modeling on ultrasonic non-destructive testing of concrete  

E-print Network

Application of time reverse modeling on ultrasonic non-destructive testing of concrete Erik H-differences Wave propagation Source localization Non-destructive testing a b s t r a c t Time reverse modeling (TRM is to transform a method within exploration geo- physics to non-destructive testing. In contrast to previous time

78

Development of a Cucumis sativus TILLinG Platform for Forward and Reverse Genetics  

PubMed Central

Background Cucumber (Cucumis sativus) belongs to the Cucurbitaceae family that includes more than 800 species. The cucumber genome has been recently sequenced and annotated. Transcriptomics and genome sequencing of many plant genomes are providing information on candidate genes potentially related to agronomically important traits. To accelerate functional characterization of these genes in cucumber we have generated an EMS mutant population that can be used as a TILLinG platform for reverse genetics. Principal Findings A population of 3,331 M2 mutant seed families was generated using two EMS concentrations (0.5% and 0.75%). Genomic DNA was extracted from M2 families and eight-fold pooled for mutation detection by ENDO1 nuclease. To assess the quality of the mutant collection, we screened for induced mutations in five genes and identified 26 mutations. The average mutation rate was calculated as 1/1147?Kb giving rise to approximately 320 mutations per genome. We focused our characterization on three missense mutations, G33C, S238F and S249F identified in the CsACS2 sex determination gene. Protein modeling and crystallography studies predicted that mutation at G33 may affect the protein function, whereas mutations at S238 and S249 may not impair the protein function. As predicted, detailed phenotypic evaluation showed that the S238F and the S249F mutant lines had no sexual phenotype. In contrast, plants homozygous for the G33C mutation showed a complete sexual transition from monoecy to andromonoecy. This result demonstrates that TILLinG is a valuable tool for functional validation of gene function in crops recalcitrant to transgenic transformation. Conclusions We have developed a cucumber mutant population that can be used as an efficient reverse genetics tool. The cucumber TILLinG collection as well as the previously described melon TILLinG collection will prove to be a valuable resource for both fundamental research and the identification of agronomically-important genes for crop improvement in cucurbits in general. PMID:24835852

Troadec, Christelle; Audigier, Pascal; Kumar, Anish P. K.; Chatterjee, Manash; Alsadon, Abdullah A.; Sadder, Monther T.; Wahb-Allah, Mahmoud A.; Al-Doss, Abdullah A.; Bendahmane, Abdelhafid

2014-01-01

79

Reverse Genetics of SARS-Related Coronavirus Using Vaccinia Virus-Based Recombination  

PubMed Central

Severe acute respiratory syndrome (SARS) is a zoonotic disease caused by SARS-related coronavirus (SARS-CoV) that emerged in 2002 to become a global health concern. Although the original outbreak was controlled by classical public health measures, there is a real risk that another SARS-CoV could re-emerge from its natural reservoir, either in its original form or as a more virulent or pathogenic strain; in which case, the virus would be difficult to control in the absence of any effective antiviral drugs or vaccines. Using the well-studied SARS-CoV isolate HKU-39849, we developed a vaccinia virus-based SARS-CoV reverse genetic system that is both robust and biosafe. The SARS-CoV genome was cloned in separate vaccinia virus vectors, (vSARS-CoV-5prime and vSARS-CoV-3prime) as two cDNAs that were subsequently ligated to create a genome-length SARS-CoV cDNA template for in vitro transcription of SARS-CoV infectious RNA transcripts. Transfection of the RNA transcripts into permissive cells led to the recovery of infectious virus (recSARS-CoV). Characterization of the plaques produced by recSARS-CoV showed that they were similar in size to the parental SARS-CoV isolate HKU-39849 but smaller than the SARS-CoV isolate Frankfurt-1. Comparative analysis of replication kinetics showed that the kinetics of recSARS-CoV replication are similar to those of SARS-CoV Frankfurt-1, although the titers of virus released into the culture supernatant are approximately 10-fold less. The reverse genetic system was finally used to generate a recSARS-CoV reporter virus expressing Renilla luciferase in order to facilitate the analysis of SARS-CoV gene expression in human dendritic cells (hDCs). In parallel, a Renilla luciferase gene was also inserted into the genome of human coronavirus 229E (HCoV-229E). Using this approach, we demonstrate that, in contrast to HCoV-229E, SARS-CoV is not able to mediate efficient heterologous gene expression in hDCs. PMID:22412934

Zevenhoven, Jessika C.; Weber, Friedemann; Züst, Roland; Kuri, Thomas; Dijkman, Ronald; Chang, Guohui; Siddell, Stuart G.; Snijder, Eric J.; Thiel, Volker; Davidson, Andrew D.

2012-01-01

80

Reverse genetics of SARS-related coronavirus using vaccinia virus-based recombination.  

PubMed

Severe acute respiratory syndrome (SARS) is a zoonotic disease caused by SARS-related coronavirus (SARS-CoV) that emerged in 2002 to become a global health concern. Although the original outbreak was controlled by classical public health measures, there is a real risk that another SARS-CoV could re-emerge from its natural reservoir, either in its original form or as a more virulent or pathogenic strain; in which case, the virus would be difficult to control in the absence of any effective antiviral drugs or vaccines. Using the well-studied SARS-CoV isolate HKU-39849, we developed a vaccinia virus-based SARS-CoV reverse genetic system that is both robust and biosafe. The SARS-CoV genome was cloned in separate vaccinia virus vectors, (vSARS-CoV-5prime and vSARS-CoV-3prime) as two cDNAs that were subsequently ligated to create a genome-length SARS-CoV cDNA template for in vitro transcription of SARS-CoV infectious RNA transcripts. Transfection of the RNA transcripts into permissive cells led to the recovery of infectious virus (recSARS-CoV). Characterization of the plaques produced by recSARS-CoV showed that they were similar in size to the parental SARS-CoV isolate HKU-39849 but smaller than the SARS-CoV isolate Frankfurt-1. Comparative analysis of replication kinetics showed that the kinetics of recSARS-CoV replication are similar to those of SARS-CoV Frankfurt-1, although the titers of virus released into the culture supernatant are approximately 10-fold less. The reverse genetic system was finally used to generate a recSARS-CoV reporter virus expressing Renilla luciferase in order to facilitate the analysis of SARS-CoV gene expression in human dendritic cells (hDCs). In parallel, a Renilla luciferase gene was also inserted into the genome of human coronavirus 229E (HCoV-229E). Using this approach, we demonstrate that, in contrast to HCoV-229E, SARS-CoV is not able to mediate efficient heterologous gene expression in hDCs. PMID:22412934

van den Worm, Sjoerd H E; Eriksson, Klara Kristin; Zevenhoven, Jessika C; Weber, Friedemann; Züst, Roland; Kuri, Thomas; Dijkman, Ronald; Chang, Guohui; Siddell, Stuart G; Snijder, Eric J; Thiel, Volker; Davidson, Andrew D

2012-01-01

81

Reversal of autoimmune diabetes by restoration of antigen-specific tolerance using genetically modified Lactococcus lactis in mice  

PubMed Central

Current interventions for arresting autoimmune diabetes have yet to strike the balance between sufficient efficacy, minimal side effects, and lack of generalized immunosuppression. Introduction of antigen via the gut represents an appealing method for induction of antigen-specific tolerance. Here, we developed a strategy for tolerance restoration using mucosal delivery in mice of biologically contained Lactococcus lactis genetically modified to secrete the whole proinsulin autoantigen along with the immunomodulatory cytokine IL-10. We show that combination therapy with low-dose systemic anti-CD3 stably reverted diabetes in NOD mice and increased frequencies of local Tregs, which not only accumulated in the pancreatic islets, but also suppressed immune response in an autoantigen-specific way. Cured mice remained responsive to disease-unrelated antigens, which argues against excessive immunosuppression. Application of this therapeutic tool achieved gut mucosal delivery of a diabetes-relevant autoantigen and a biologically active immunomodulatory cytokine, IL-10, and, when combined with a low dose of systemic anti-CD3, was well tolerated and induced autoantigen-specific long-term tolerance, allowing reversal of established autoimmune diabetes. Therefore, we believe this method could be an effective treatment strategy for type 1 diabetes in humans. PMID:22484814

Takiishi, Tatiana; Korf, Hannelie; Van Belle, Tom L.; Robert, Sofie; Grieco, Fabio A.; Caluwaerts, Silvia; Galleri, Letizia; Spagnuolo, Isabella; Steidler, Lothar; Van Huynegem, Karolien; Demetter, Pieter; Wasserfall, Clive; Atkinson, Mark A.; Dotta, Francesco; Rottiers, Pieter; Gysemans, Conny; Mathieu, Chantal

2012-01-01

82

Applications of retrotransposons as genetic tools in plant biology  

Microsoft Academic Search

Retrotransposons are mobile genetic elements that accomplish transposition via an RNA intermediate that is reverse transcribed before integration into a new location within the host genome. They are ubiquitous in eukaryotic organisms and constitute a major portion of the nuclear genome (often more than half of the total DNA) in plants. Furthermore, they are dispersed as interspersed repetitive sequences throughout

Amar Kumar; Hirohiko Hirochika

2001-01-01

83

Association of genetic polymorphisms in the telomerase reverse transcriptase gene with prostate cancer aggressiveness.  

PubMed

Telomerase reverse transcriptase (TERT), encoded by the TERT gene, is an essential component of telomerase, essential for the maintenance of telomere DNA length, chromosomal stability and cellular immortality. The aim of the present study was to evaluate the association between common genetic variations across the TERT gene region and prostate cancer (PCa) aggressiveness in a Chinese population. A total of 12 TERT tagging single?nucleotide polymorphisms (SNPs) were genotyped on the Sequenom Mass?ARRAY iPLEX® platform in a case?case study with 1,210 Chinese patients with PCa. Unconditional logistic regression was used to investigate the association of genotypes with PCa aggressiveness, Gleason grade and risk of developing early?onset PCa. It was observed that the C allele of the TERT intron 2 SNP (rs2736100) was significantly associated with reduced risk of PCa aggressiveness [odds ratio (OR)=0.81; 95% confidence interval (CI): 0.66?0.99; P=0.037]. This allele was also significantly correlated with a reduced risk of developing a tumor with a high Gleason score (>7; OR=0.83; 95% CI: 0.70?0.99; P=0.039). The T allele of the intron 4 SNP (rs10069690) was found to be significantly associated with a decreased risk for an aggressive form of PCa (OR=0.76; 95% CI: 0.59?0.97; P=0.030). In addition, the A allele of rs10078761 located at the 3' end of the TERT gene exhibited a statistically significant association with the reduced risk of developing a higher grade disease (OR=0.48; 95% CI: 0.28?0.81; P=0.006). However, no association between TERT polymorphisms and age at diagnosis was observed in the present study. The present findings demonstrated for the first time, to the best of our knowledge, that genetic variations across the TERT gene are associated with PCa aggressiveness in a Chinese Han population. PMID:25738283

Wu, Dapeng; Yu, Hongjie; Sun, Jielin; Qi, Jun; Liu, Qiang; Li, Ruipeng; Zheng, Siqun Lily; Xu, Jianfeng; Kang, Jian

2015-07-01

84

Time Reversed Acoustics and applications to earthquake location and salt dome flank imaging  

E-print Network

The objective of this thesis is to investigate the applications of Time Reversed Acoustics (TRA) to locate seismic sources and image subsurface structures. The back-propagation process of the TRA experiment can be divided ...

Lu, Rongrong

2008-01-01

85

Genetic identification of potential RNA-binding regions in a group II intron-encoded reverse transcriptase  

PubMed Central

Mobile group II introns encode a reverse transcriptase that binds the intron RNA to promote RNA splicing and intron mobility, the latter via reverse splicing of the excised intron into DNA sites, followed by reverse transcription. Previous work showed that the Lactococcus lactis Ll.LtrB intron reverse transcriptase, denoted LtrA protein, binds with high affinity to DIVa, a stem–loop structure at the beginning of the LtrA open reading frame and makes additional contacts with intron core regions that stabilize the active RNA structure for forward and reverse splicing. LtrA's binding to DIVa down-regulates its translation and is critical for initiation of reverse transcription. Here, by using high-throughput unigenic evolution analysis with a genetic assay in which LtrA binding to DIVa down-regulates translation of GFP, we identified regions at LtrA's N terminus that are required for DIVa binding. Then, by similar analysis with a reciprocal genetic assay, we confirmed that residual splicing of a mutant intron lacking DIVa does not require these N-terminal regions, but does require other reverse transcriptase (RT) and X/thumb domain regions that bind the intron core. We also show that N-terminal fragments of LtrA by themselves bind specifically to DIVa in vivo and in vitro. Our results suggest a model in which the N terminus of nascent LtrA binds DIVa of the intron RNA that encoded it and nucleates further interactions with core regions that promote RNP assembly for RNA splicing and intron mobility. Features of this model may be relevant to evolutionarily related non-long-terminal-repeat (non-LTR)-retrotransposon RTs. PMID:20179150

Gu, Shan-Qing; Cui, Xiaoxia; Mou, Sijiong; Mohr, Sabine; Yao, Jun; Lambowitz, Alan M.

2010-01-01

86

Molecular modeling, organ culture and reverse genetics for a newly identified human rhinovirus C  

PubMed Central

A recently recognized human rhinovirus species C (HRV-C) is associated with up to half of HRV infections in young children. We for the first time propagated two HRV-C isolates ex vivo in organ culture of nasal epithelial cells, sequenced a new C15 isolate, and developed the first reverse genetics system for HRV-C. Using contact points for the known HRV receptors, intercellular adhesion molecule 1 (ICAM-1) and low density lipoprotein receptor (LDLR), inter- and intraspecies footprint analysis predicted a unique cell attachment site for HRV-Cs. Antibodies directed to binding sites for HRV-A and -B failed to inhibit HRV-C attachment, consistent with the alternative receptor footprint. HRV-A and -B infected HeLa and WisL cells, but HRV-C did not. However, HRV-C RNA synthesized in vitro and transfected into both cell types resulted in cytopathic effect and recovery of functional virus, indicating that the viral attachment mechanism is a primary distinguishing feature of HRV-C. PMID:21483405

Bochkov, Yury A; Palmenberg, Ann C; Lee, Wai-Ming; Rathe, Jennifer A; Amineva, Svetlana P; Sun, Xin; Pasic, Thomas R; Jarjour, Nizar N; Liggett, Stephen B; Gern, James E

2010-01-01

87

Reverse genetic studies of homologous DNA recombination using the chicken B-lymphocyte line, DT40.  

PubMed Central

DT40 is an avian leucosis virus-transformed chicken B-lymphocyte line which exhibits high ratios of targeted to random integration of transfected DNA constructs. This efficient targeted integration may be related to the ongoing diversification of the variable segment of the immunoglobulin gene through homologous DNA recombination-controlled gene conversion. DT40s are a convenient model system for making gene-targeted mutants. Another advantage is the relative tractability of these cells, which makes it possible to disrupt multiple genes in a single cell and to generate conditionally gene-targeted mutants including temperature-sensitive mutants. There are strong phenotypic similarities between murine and DT40 mutants of various genes involved in DNA recombination. These similarities confirm that the DT40 cell line is a reasonable model for the analysis of vertebrate DNA recombination, despite obvious concerns associated with the use of a transformed cell line, which may have certain cell-line-specific characteristics. Here we describe our studies of homologous DNA recombination in vertebrate somatic cells using reverse genetics in DT40 cells. PMID:11205323

Sonoda, E; Morrison, C; Yamashita, Y M; Takata, M; Takeda, S

2001-01-01

88

Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering  

NASA Technical Reports Server (NTRS)

Advances in molecular biological, analytical, and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-duster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e., who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting, and bioengineering.

Dhaeseleer, Patrik; Liang, Shoudan; Somogyi, Roland

2000-01-01

89

Genetic Algorithms: Basic principles and applications  

Microsoft Academic Search

Genetic Algorithms are a part of Soft Computing Techniques that deal with function optimization. The basic principles of Genetic Algorithms are stated. Its stochastic nature and various genetic operators are discussed. Some basic issues (e.g., convergence) related to these algorithms are also discussed.

C. A. Murthy

2012-01-01

90

An approach for reverse engineering of web-based applications  

Microsoft Academic Search

The new possibilities offered by WEB applications are pervasively and radically changing several areas. WEB applications, compared to WEB sites, offer substantially greater opportunities: a WEB application provides the WEB user with a means to modify the site status. WEB applications must cope with an extremely short development\\/evolution life cycle. Usually, they are implemented without producing any useful documentation for

G.A. Di Lucca; M. Di Penta; G. Antoniol; G. Casazza

2001-01-01

91

A genome-scale vector resource enables high-throughput reverse genetic screening in a malaria parasite.  

PubMed

The genome-wide identification of gene functions in malaria parasites is hampered by a lack of reverse genetic screening methods. We present a large-scale resource of barcoded vectors with long homology arms for effective modification of the Plasmodium berghei genome. Cotransfecting dozens of vectors into the haploid blood stages creates complex pools of barcoded mutants, whose competitive fitness can be measured during infection of a single mouse using barcode sequencing (barseq). To validate the utility of this resource, we rescreen the P. berghei kinome, using published kinome screens for comparison. We find that several protein kinases function redundantly in asexual blood stages and confirm the targetability of kinases cdpk1, gsk3, tkl3, and PBANKA_082960 by genotyping cloned mutants. Thus, parallel phenotyping of barcoded mutants unlocks the power of reverse genetic screening for a malaria parasite and will enable the systematic identification of genes essential for in vivo parasite growth and transmission. PMID:25732065

Gomes, Ana Rita; Bushell, Ellen; Schwach, Frank; Girling, Gareth; Anar, Burcu; Quail, Michael A; Herd, Colin; Pfander, Claudia; Modrzynska, Katarzyna; Rayner, Julian C; Billker, Oliver

2015-03-11

92

A Genome-Scale Vector Resource Enables High-Throughput Reverse Genetic Screening in a Malaria Parasite  

PubMed Central

Summary The genome-wide identification of gene functions in malaria parasites is hampered by a lack of reverse genetic screening methods. We present a large-scale resource of barcoded vectors with long homology arms for effective modification of the Plasmodium berghei genome. Cotransfecting dozens of vectors into the haploid blood stages creates complex pools of barcoded mutants, whose competitive fitness can be measured during infection of a single mouse using barcode sequencing (barseq). To validate the utility of this resource, we rescreen the P. berghei kinome, using published kinome screens for comparison. We find that several protein kinases function redundantly in asexual blood stages and confirm the targetability of kinases cdpk1, gsk3, tkl3, and PBANKA_082960 by genotyping cloned mutants. Thus, parallel phenotyping of barcoded mutants unlocks the power of reverse genetic screening for a malaria parasite and will enable the systematic identification of genes essential for in vivo parasite growth and transmission. PMID:25732065

Gomes, Ana Rita; Bushell, Ellen; Schwach, Frank; Girling, Gareth; Anar, Burcu; Quail, Michael A.; Herd, Colin; Pfander, Claudia; Modrzynska, Katarzyna; Rayner, Julian C.; Billker, Oliver

2015-01-01

93

Application of energy efficient reverse osmosis system for seawater desalination  

Microsoft Academic Search

A performance of an energy-efficient reverse osmosis (RO) system for seawater desalination was evaluated. The evaluation focused on energy saving performance of the RO system. The strategy adopted was to induce high recovery (50%) through the pressure increase. For this purpose, a pilot-scale RO plant (5 m3\\/h) was built and installed in a southern port of Korea. The study showed

Seung-Hyun Kim; Geon-Tae Kim; Seong-Keun Yim; Kwang-Ho Choi; Cho-Hee Yoon; Kwang-Ho Choo; Sang-June Choi

2002-01-01

94

Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants.  

PubMed

The study and eventual manipulation of leaf development in plants requires a thorough understanding of the genetic basis of leaf organogenesis. Forward genetic screens have identified hundreds of Arabidopsis mutants with altered leaf development, but the genome has not yet been saturated. To identify genes required for leaf development we are screening the Arabidopsis Salk Unimutant collection. We have identified 608 lines that exhibit a leaf phenotype with full penetrance and almost constant expressivity and 98 additional lines with segregating mutant phenotypes. To allow indexing and integration with other mutants, the mutant phenotypes were described using a custom leaf phenotype ontology. We found that the indexed mutation is present in the annotated locus for 78% of the 553 mutants genotyped, and that in half of these the annotated T-DNA is responsible for the phenotype. To quickly map non-annotated T-DNA insertions, we developed a reliable, cost-effective and easy method based on whole-genome sequencing. To enable comprehensive access to our data, we implemented a public web application named PhenoLeaf (http://genetics.umh.es/phenoleaf) that allows researchers to query the results of our screen, including text and visual phenotype information. We demonstrated how this new resource can facilitate gene function discovery by identifying and characterizing At1g77600, which we found to be required for proximal-distal cell cycle-driven leaf growth, and At3g62870, which encodes a ribosomal protein needed for cell proliferation and chloroplast function. This collection provides a valuable tool for the study of leaf development, characterization of biomass feedstocks and examination of other traits in this fundamental photosynthetic organ. PMID:24946828

Wilson-Sánchez, David; Rubio-Díaz, Silvia; Muñoz-Viana, Rafael; Pérez-Pérez, José Manuel; Jover-Gil, Sara; Ponce, María Rosa; Micol, José Luis

2014-09-01

95

Population genetic structure and direct observations reveal sex-reversed patterns of dispersal in a cooperative bird.  

PubMed

Sex-biased dispersal is pervasive and has diverse evolutionary implications, but the fundamental drivers of dispersal sex biases remain unresolved. This is due in part to limited diversity within taxonomic groups in the direction of dispersal sex biases, which leaves hypothesis testing critically dependent upon identifying rare reversals of taxonomic norms. Here, we use a combination of observational and genetic data to demonstrate a rare reversal of the avian sex bias in dispersal in the cooperatively breeding white-browed sparrow weaver (Plocepasser mahali). Direct observations revealed that (i) natal philopatry was rare, with both sexes typically dispersing locally to breed, and (ii), unusually for birds, males bred at significantly greater distances from their natal group than females. Population genetic analyses confirmed these patterns, as (i) corrected Assignment index (AIc), FST tests and isolation-by-distance metrics were all indicative of longer dispersal distances among males than females, and (ii) spatial autocorrelation analysis indicated stronger within-group genetic structure among females than males. Examining the spatial scale of extra-group mating highlighted that the resulting 'sperm dispersal' could have acted in concert with individual dispersal to generate these genetic patterns, but gamete dispersal alone cannot account entirely for the sex differences in genetic structure observed. That leading hypotheses for the evolution of dispersal sex biases cannot readily account for these sex-reversed patterns of dispersal in white-browed sparrow weavers highlights the continued need for attention to alternative explanations for this enigmatic phenomenon. We highlight the potential importance of sex differences in the distances over which dispersal opportunities can be detected. PMID:25346189

Harrison, Xavier A; York, Jennifer E; Young, Andrew J

2014-12-01

96

Population genetic structure and direct observations reveal sex-reversed patterns of dispersal in a cooperative bird  

PubMed Central

Sex-biased dispersal is pervasive and has diverse evolutionary implications, but the fundamental drivers of dispersal sex biases remain unresolved. This is due in part to limited diversity within taxonomic groups in the direction of dispersal sex biases, which leaves hypothesis testing critically dependent upon identifying rare reversals of taxonomic norms. Here, we use a combination of observational and genetic data to demonstrate a rare reversal of the avian sex bias in dispersal in the cooperatively breeding white-browed sparrow weaver (Plocepasser mahali). Direct observations revealed that (i) natal philopatry was rare, with both sexes typically dispersing locally to breed, and (ii), unusually for birds, males bred at significantly greater distances from their natal group than females. Population genetic analyses confirmed these patterns, as (i) corrected Assignment index (AIc), FST tests and isolation-by-distance metrics were all indicative of longer dispersal distances among males than females, and (ii) spatial autocorrelation analysis indicated stronger within-group genetic structure among females than males. Examining the spatial scale of extra-group mating highlighted that the resulting ‘sperm dispersal’ could have acted in concert with individual dispersal to generate these genetic patterns, but gamete dispersal alone cannot account entirely for the sex differences in genetic structure observed. That leading hypotheses for the evolution of dispersal sex biases cannot readily account for these sex-reversed patterns of dispersal in white-browed sparrow weavers highlights the continued need for attention to alternative explanations for this enigmatic phenomenon. We highlight the potential importance of sex differences in the distances over which dispersal opportunities can be detected. PMID:25346189

Harrison, Xavier A; York, Jennifer E; Young, Andrew J

2014-01-01

97

WARE: A Tool for the Reverse Engineering of Web Applications  

Microsoft Academic Search

The development of Web sites and applications is increasing dramatically to satisfy the market requests. The software industry is facing the new demand under the pressure of a very short time-to-market and an extremely high competition. As a result, Web sites and applications are usually developed without a disciplined process: Web applications are directly coded and no, or poor, documentation

Giuseppe A. Di Lucca; Anna Rita Fasolino; F. Pace; Porfirio Tramontana; Ugo De Carlini

2002-01-01

98

An Approach for Reverse Engineering of Web-Based Application  

Microsoft Academic Search

Abstract The new possibilities offered by WEB applications are pervasively and radically changing several areas WEB applications, compared to WEB sites, offer substantially greater opportunities: a WEB application provides the WEB user with a means to modify the site status WEB ap - plications represent a competitive advantage: they are criti - cal and strategically relevant resources, not only to

Giuseppe A. Di Lucca; Massimiliano Di Penta; Giuliano Antoniol; Gerardo Casazza

2001-01-01

99

Genetic loss of D-amino acid oxidase activity reverses schizophrenia-like phenotypes in mice  

PubMed Central

Reduced function of the N-methyl-D-aspartate receptor (NMDAR) has been implicated in the pathophysiology of schizophrenia. The NMDAR contains a glycine binding site in its NR1 subunit that may be a useful target for the treatment of schizophrenia. In this study, we assessed the therapeutic potential of long-term increases in the brain levels of the endogenous NMDAR glycine site agonist D-serine, through the genetic inactivation of its catabolic enzyme D-amino acid oxidase (DAO) in mice. The effects of eliminating DAO function were investigated in mice that display schizophrenia-related behavioral deficits due to a mutation (Grin1D481N) in the NR1 subunit that results in a reduction in NMDAR glycine affinity. Grin1D481N mice show deficits in sociability, prolonged latent inhibition, enhanced startle reactivity, and impaired spatial memory. The hypofunctional Dao1G181R mutation elevated brain levels of D-serine, but alone it did not affect performance in the behavioral measures. Compared to animals with only the Grin1D481N mutation, mice with both the Dao1G181R and Grin1D481N mutations displayed an improvement in social approach and spatial memory retention, as well as a reversal of abnormally persistent latent inhibition and a partial normalization of startle responses. Thus, an increased level of D-serine resulting from decreased catalysis corrected the performance of mice with deficient NMDAR glycine site activation in behavioral tasks relevant to the negative and cognitive symptoms of schizophrenia. Diminished DAO activity and elevations in D-serine may serve as an effective therapeutic intervention for the treatment of psychiatric symptoms. PMID:19751394

Labrie, V.; Wang, W.; Barger, S. W.; Baker, G. B.; Roder, J. C.

2009-01-01

100

Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications.  

PubMed Central

This review is a survey of bacterial dehalogenases that catalyze the cleavage of halogen substituents from haloaromatics, haloalkanes, haloalcohols, and haloalkanoic acids. Concerning the enzymatic cleavage of the carbon-halogen bond, seven mechanisms of dehalogenation are known, namely, reductive, oxygenolytic, hydrolytic, and thiolytic dehalogenation; intramolecular nucleophilic displacement; dehydrohalogenation; and hydration. Spontaneous dehalogenation reactions may occur as a result of chemical decomposition of unstable primary products of an unassociated enzyme reaction, and fortuitous dehalogenation can result from the action of broad-specificity enzymes converting halogenated analogs of their natural substrate. Reductive dehalogenation either is catalyzed by a specific dehalogenase or may be mediated by free or enzyme-bound transition metal cofactors (porphyrins, corrins). Desulfomonile tiedjei DCB-1 couples energy conservation to a reductive dechlorination reaction. The biochemistry and genetics of oxygenolytic and hydrolytic haloaromatic dehalogenases are discussed. Concerning the haloalkanes, oxygenases, glutathione S-transferases, halidohydrolases, and dehydrohalogenases are involved in the dehalogenation of different haloalkane compounds. The epoxide-forming halohydrin hydrogen halide lyases form a distinct class of dehalogenases. The dehalogenation of alpha-halosubstituted alkanoic acids is catalyzed by halidohydrolases, which, according to their substrate and inhibitor specificity and mode of product formation, are placed into distinct mechanistic groups. beta-Halosubstituted alkanoic acids are dehalogenated by halidohydrolases acting on the coenzyme A ester of the beta-haloalkanoic acid. Microbial systems offer a versatile potential for biotechnological applications. Because of their enantiomer selectivity, some dehalogenases are used as industrial biocatalysts for the synthesis of chiral compounds. The application of dehalogenases or bacterial strains in environmental protection technologies is discussed in detail. PMID:7854251

Fetzner, S; Lingens, F

1994-01-01

101

MINIGENOMES, TRANSCRIPTION AND REPLICATION COMPETENT VIRUS-LIKE PARTICLES AND BEYOND: REVERSE GENETICS SYSTEMS FOR FILOVIRUSES AND OTHER NEGATIVE STRANDED HEMORRHAGIC FEVER VIRUSES  

PubMed Central

Reverse-genetics systems are powerful tools enabling researchers to study the replication cycle of RNA viruses, including filoviruses and other hemorrhagic fever viruses, as well as to discover new antivirals. They include full-length clone systems as well as a number of life cycle modeling systems. Full-length clone systems allow for the generation of infectious, recombinant viruses, and thus are an important tool for studying the virus replication cycle in its entirety. In contrast, life cycle modeling systems such as minigenome and transcription and replication competent virus-like particle systems can be used to simulate and dissect parts of the virus life cycle outside of containment facilities. Minigenome systems are used to model viral genome replication and transcription, whereas transcription and replication competent virus-like particle systems also model morphogenesis and budding as well as infection of target cells. As such, these modeling systems have tremendous potential to further the discovery and screening of new antivirals targeting hemorrhagic fever viruses. This review provides an overview of currently established reverse genetics systems for hemorrhagic fever-causing negative-sense RNA viruses, with a particular emphasis on filoviruses, and the potential application of these systems for antiviral research. PMID:21699921

Hoenen, Thomas; Groseth, Allison; de Kok-Mercado, Fabian; Kuhn, Jens H.; Wahl-Jensen, Victoria

2012-01-01

102

Homoclinic Orbits in Reversible Systems and Their Applications in Mechanics, Fluids and Optics  

Microsoft Academic Search

This survey article reviews the theory and application of homoclinicorbits to equilibria in reversible continuous-time dynamical systems, where the homoclinicorbit and the equilibrium are both reversible. The focus is on even-orderreversible systems in four or more dimensions. Local theory, generic argument, andglobal existence theories are examined for each qualitatively distinct linearisation.Several recent results, such as coalescence caused by non-transversality and

A. r. Champneys

1997-01-01

103

Embryonic reversions and lineage infidelities in tumour cells: genome-based models and role of genetic instability  

PubMed Central

Reversions to ‘embryonic precursor’-type cells and infidelities of tumour cell lineage (including metaplasias) have been recognized as aspects of various tumour types since the 19th century. Since then, evidence of these phenomena has been obtained from numerous clinical, biochemical, immunological and molecular biological studies. In particular, microarray studies have suggested that ‘aberrant’ expressions of relevant genes are common. An unexplained aspect of the results of these studies is that, in many tumour types, the embryonic reversion or lineage infidelity only occurs in a proportion of cases. As a parallel development during the molecular biological investigation of tumours over the last several decades, genetic instability has been found much more marked, at least in some preparations of tumour cells, than that identified by means of previous karyotypic investigations of tumours. This study reviews examples of embryonic reversion and lineage infidelity phenomena, which have derived from the various lines of investigation of cancer over the last 150 or so years. Four categories of circumstances of the occurrence of embryonic reversions or lineage infidelities have been identified – (i) as part of the defining phenotype of the tumour, and hence being presumably integral to the tumour type, (ii) present ab initio in only some cases of the tumour type, and presumably being regularly associated with, but incidental to, the essential features of the tumour type, (iii) occurring later in the course of the disease and thus being possibly a manifestation of in vivo genetic instability and ‘tumour progression’ and (iv) arising probably by genetic instability, during the processes, especially cell culture, associated with ex vivo investigations. Genomic models are described which might account for the origin of these phenomena in each of these circumstances. PMID:15810978

Bignold, Leon P

2005-01-01

104

Nash Genetic Algorithms : examples and applications M. Sefrioui  

E-print Network

Nash Genetic Algorithms : examples and applications M. Sefrioui LIP6, University Paris 6 4, Place aspects and experimental results on Nash Genetic Algorithms. Nash GAs are an alternative for multiple. They are explained in details, along with the advantages conferred by their equilibrium state. This approach

Coello, Carlos A. Coello

105

Applications of terpene analysis in forest genetics  

Microsoft Academic Search

Terpenoid substances in forest trees are versatile biochemical systems for use as genetic markers and for studying genetic regulation at the biochemical level. Univariate, multivariate and correlative data analyses from numerous studies on different coniferous species are presented. These data indicate that fitness values for most terpenes examined are probably so low as to be unmeasurable except in long evolutionary

James W. Hanover

1992-01-01

106

Imaging-Genetics Applications in Child Psychiatry  

ERIC Educational Resources Information Center

Objective: To place imaging-genetics research in the context of child psychiatry. Method: A conceptual overview is provided, followed by discussion of specific research examples. Results: Imaging-genetics research is described linking brain function to two specific genes, for the serotonin-reuptake-transporter protein and a monoamine oxidase…

Pine, Daniel S.; Ernst, Monique; Leibenluft, Ellen

2010-01-01

107

Polyglot Programming in Applications Used for Genetic Data Analysis  

PubMed Central

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development. PMID:25197633

Nowak, Robert M.

2014-01-01

108

Polyglot programming in applications used for genetic data analysis.  

PubMed

Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development. PMID:25197633

Nowak, Robert M

2014-01-01

109

Reversibly switchable DNA nanocompartment on surfaces: experiments, applications, and theory  

NASA Astrophysics Data System (ADS)

This paper summarizes our studies of DNA nano-compartement in recent years. Biological macromolecules have been used to fabricate many nanostructures, bio-devices, and biomimetics because of their physical and chemical properties. But dynamic nanostructure and bio-machinery that depend on collective behavior of biomolecules have not been demonstrated. Here, we report the design of DNA nanocompartment on surfaces that exhibit reversible changes in molecular mechanical properties. Such molecular nanocompartment is served to encage molecules, switched by the collective effect of Watson-Crick base-pairing interactions. This effect is used to investigate the dynamic process of nanocompartment switching and molecular thermosensing, as well as perform molecular recognition. Further, we found that ‘fuel’ strands with single-base variation cannot afford an efficient closing of nanocompartment, which allows highly sensitive label-free DNA array detection. Theoretical analysis and computer simulations confirm our experimental observations, which are discussed in this review paper. Our results suggest that DNA nanocompartment can be used as building blocks for complex biomaterials, because its core functions are independent of substrates and mediators.

Mao, You-Dong; Luo, Chun-Xiong; Ou-Yang, Qi

2008-02-01

110

Reversibility of a quantum channel: General conditions and their applications to Bosonic linear channels  

SciTech Connect

The method of complementary channel for analysis of reversibility (sufficiency) of a quantum channel with respect to families of input states (pure states for the most part) are considered and applied to Bosonic linear (quasi-free) channels, in particular, to Bosonic Gaussian channels. The obtained reversibility conditions for Bosonic linear channels have clear physical interpretation and their sufficiency is also shown by explicit construction of reversing channels. The method of complementary channel gives possibility to prove necessity of these conditions and to describe all reversed families of pure states in the Schrodinger representation. Some applications in quantum information theory are considered. Conditions for existence of discrete classical-quantum subchannels and of completely depolarizing subchannels of a Bosonic linear channel are presented.

Shirokov, M. E. [Steklov Mathematical Institute, Moscow (Russian Federation)] [Steklov Mathematical Institute, Moscow (Russian Federation)

2013-11-15

111

Performance of a model cascade thrust reverser for short-haul applications  

NASA Technical Reports Server (NTRS)

Aerodynamic and acoustic characteristics are presented for a cowlmounted, model cascade thrust reverser suitable for short-haul aircraft. Thrust reverser efficiency and the influence on fan performance were determined from isolated fan-driven models under static and forward velocity conditions. Cascade reverser noise characteristics were determined statically in an isolated pipe-flow test, while aerodynamic installation effects were determined with a wind-tunnel, fan-powered airplane model. Application of test results to short-haul aircraft calculations demonstrated that such a cascade thrust reverser may be able to meet both the performance and noise requirements for short-haul aircraft operation. However, aircraft installation effects can be quite significant.

Dietrich, D. A.; Gutierrez, O. A.

1974-01-01

112

Stable transformation and reverse genetic analysis of Penium margaritaceum: a platform for studies of charophyte green algae, the immediate ancestors of land plants.  

PubMed

The charophyte green algae (CGA, Streptophyta, Viridiplantae) occupy a key phylogenetic position as the immediate ancestors of land plants but, paradoxically, are less well-studied than the other major plant lineages. This is particularly true in the context of functional genomic studies, where the lack of an efficient protocol for their stable genetic transformation has been a major obstacle. Observations of extant CGA species suggest the existence of some of the evolutionary adaptations that had to occur for land colonization; however, to date, there has been no robust experimental platform to address this genetically. We present a protocol for high-throughput Agrobacterium tumefaciens-mediated transformation of Penium margaritaceum, a unicellular CGA species. The versatility of Penium as a model for studying various aspects of plant cell biology and development was illustrated through non-invasive visualization of protein localization and dynamics in living cells. In addition, the utility of RNA interference (RNAi) for reverse genetic studies was demonstrated by targeting genes associated with cell wall modification (pectin methylesterase) and biosynthesis (cellulose synthase). This provided evidence supporting current models of cell wall assembly and inter-polymer interactions that were based on studies of land plants, but in this case using direct observation in vivo. This new functional genomics platform has broad potential applications, including studies of plant organismal biology and the evolutionary innovations required for transition from aquatic to terrestrial habitats. PMID:24308430

Sørensen, Iben; Fei, Zhangjun; Andreas, Amanda; Willats, William G T; Domozych, David S; Rose, Jocelyn K C

2014-02-01

113

Plastid, nuclear and reverse transcriptase sequences in the mitochondrial genome of Oenothera: is genetic information transferred between organelles via RNA?  

PubMed Central

We describe an open reading frame (ORF) with high homology to reverse transcriptase in the mitochondrial genome of Oenothera. This ORF displays all the characteristics of an active plant mitochondrial gene with a possible ribosome binding site and 39% T in the third codon position. It is located between a sequence fragment from the plastid genome and one of nuclear origin downstream from the gene encoding subunit 5 of the NADH dehydrogenase. The nuclear derived sequence consists of 528 nucleotides from the small ribosomal RNA and contains an expansion segment unique to nuclear rRNAs. The plastid sequence contains part of the ribosomal protein S4 and the complete tRNA(Ser). The observation that only transcribed sequences have been found i more than one subcellular compartment in higher plants suggests that interorganellar transfer of genetic information may occur via RNA and subsequent local reverse transcription and genomic integration. PMID:14650433

Schuster, W; Brennicke, A

1987-01-01

114

Plasmid-based human norovirus reverse genetics system produces reporter-tagged progeny virus containing infectious genomic RNA  

PubMed Central

Human norovirus (HuNoV) is the leading cause of gastroenteritis worldwide. HuNoV replication studies have been hampered by the inability to grow the virus in cultured cells. The HuNoV genome is a positive-sense single-stranded RNA (ssRNA) molecule with three open reading frames (ORFs). We established a reverse genetics system driven by a mammalian promoter that functions without helper virus. The complete genome of the HuNoV genogroup II.3 U201 strain was cloned downstream of an elongation factor-1? (EF-1?) mammalian promoter. Cells transfected with plasmid containing the full-length genome (pHuNoVU201F) expressed the ORF1 polyprotein, which was cleaved by the viral protease to produce the mature nonstructural viral proteins, and the capsid proteins. Progeny virus produced from the transfected cells contained the complete NoV genomic RNA (VP1, VP2, and VPg) and exhibited the same density in isopycnic cesium chloride gradients as native infectious NoV particles from a patient’s stool. This system also was applied to drive murine NoV RNA replication and produced infectious progeny virions. A GFP reporter construct containing the GFP gene in ORF1 produced complete virions that contain VPg-linked RNA. RNA from virions containing the encapsidated GFP-genomic RNA was successfully transfected back into cells producing fluorescent puncta, indicating that the encapsidated RNA is replication-competent. The EF-1? mammalian promoter expression system provides the first reverse genetics system, to our knowledge, generalizable for human and animal NoVs that does not require a helper virus. Establishing a complete reverse genetics system expressed from cDNA for HuNoVs now allows the manipulation of the viral genome and production of reporter virions. PMID:25192933

Katayama, Kazuhiko; Murakami, Kosuke; Sharp, Tyler M.; Guix, Susana; Oka, Tomoichiro; Takai-Todaka, Reiko; Nakanishi, Akira; Crawford, Sue E.; Atmar, Robert L.; Estes, Mary K.

2014-01-01

115

Progress in Studies on Hormonal Sex Reversal and Genetic Sex Control in Black Crappie  

Microsoft Academic Search

Sex control can solve the problem of stunted black crappie populations in small impoundments. The main objectives of the present study were (1) to identify sex-reversed males of black crappie from a previously obtained androgen-treated group using test crosses, and (2) to develop broodstock of sex-reversed males by masculinization of fish from those crosses. An additional objective of the study

Rafael Cuevas-Uribe; Boris Gomelsky; Steven D. Mims; Kirk W. Pomper

2009-01-01

116

Influence Zone and Its Applications in Reverse k Nearest Neighbors Processing  

E-print Network

Influence Zone and Its Applications in Reverse k Nearest Neighbors Processing Muhammad Aamir Cheema objects of p. In this paper, we introduce the concept of influence zone which is the area such that every to compute the influence zone. Then, based on the influence zone, we present efficient al- gorithms

New South Wales, University of

117

APPLICATION OF THE REVERSE ENGINEER IN THE MODELING OF A FRANCIS TURBINE IN A  

E-print Network

APPLICATION OF THE REVERSE ENGINEER IN THE MODELING OF A FRANCIS TURBINE IN A HYDROELECTRIC for the geometry reconstruction of a Francis turbine installed in a hydroelectric Minipower-station in Colombia directly from the machine and matched against the original incomplete drawings. The Francis Turbine

Alberta, University of

118

Stochastic Models of Energy Commodity Prices and Their Applications: Mean-reversion with  

E-print Network

for commodity spot prices and performed an empirical analysis based on copper, gold and crude oil price dataStochastic Models of Energy Commodity Prices and Their Applications: Mean-reversion with Jumps usion models to describe energy commodity spot prices. We incorporate multiple jumps, regime

119

Genetic Testing in the Employment Application Process  

Microsoft Academic Search

Genetic testing is a way in which mutations can be detected in DNA, proteins, and other parts of the human chromosome. By testing for these mutations, it may be possible to identify a predisposition for various forms of cancer, sickle cell anemia, and theoretically, any other hereditary disease. In the employment setting, the ability to forecast possible illnesses is accompanied

Kim Hill

2009-01-01

120

Statistical Applications in Genetics and Molecular Biology  

E-print Network

Chain Monte Carlo sampling is required for state-of-the-art statistical analysis of population genetics that the Griffiths-Tavar´e (GT) procedure is in essence importance sampling. Proceed- ing backward in time and its relation to the Stephens and Donnelly (SD) proposal distribution fo

Hobolth, Asger

121

Applications of graph theory to landscape genetics  

Microsoft Academic Search

We investigated the relationships among landscape quality, gene flow, and pop- ulation genetic structure of fishers (Martes pennanti) in ON, Canada. We used graph theory as an analytical framework considering each landscape as a net- work node. The 34 nodes were connected by 93 edges. Network structure was characterized by a higher level of clustering than expected by chance, a

Colin J. Garroway; Jeff Bowman; Denis Carr; Paul J. Wilson

2008-01-01

122

Development of a reverse genetics system based on RNA polymerase II for Newcastle disease virus genotype VII.  

PubMed

Newcastle disease virus (NDV) has only a single serotype but diversified genotypes. Genotype VII strains are the prevalent currently circulating genotype worldwide, and in particular, these strains cause outbreaks in waterfowl. In this study, a reverse genetics system for highly virulent NDV isolated from goose flocks was developed independent of conventional T7 RNA polymerase. Infectious virus was successfully generated by an RNA polymerase II promoter to drive transcription of the full-length virus antigenome. A green fluorescent protein (GFP)-expressing virus was generated by inserting an additional transcription cassette coding for the enhanced GFP between the P and M genes of the genome. The expression of GFP was confirmed by western blotting and fluorescence microscopy. The replication kinetics and pathogenicity of the recombinant viruses are indistinguishable from the parental wild-type virus. This reverse genetics system will provide a powerful tool for the analysis of goose-origin NDV dissemination and pathogenesis, as well as preparation for genotype-matched NDV attenuated vaccines. PMID:25384536

Wang, Jianzhong; Wang, Chunfeng; Feng, Na; Wang, Hualei; Zheng, Xuexing; Yang, Songtao; Gao, Yuwei; Xia, Xianzhu; Yin, Renfu; Liu, Xiufan; Hu, Shunlin; Ding, Chan; Yu, Shengqing; Cong, Yanlong; Ding, Zhuang

2015-02-01

123

Using the philosophy of mobile agent technology for e-service in the field of reverse engineering applications  

Microsoft Academic Search

Reverse engineering methodology paves an efficient way for simulating and manufacturing existing objects with complex shapes, and a range of applications also has shown this approach to be feasible and efficient. However, in many applications, a lot of sub-tasks in reverse engineering are usually not done in the same place, they need to be done cooperatively over the Internet or

Zhang Yingjie; Ge Liling

2004-01-01

124

Three-terminal intelligent power MOSFET with built-in reverse battery protection for automotive applications  

SciTech Connect

An intelligent power MOSFET with built-in reverse battery protection, which is important for automotive power switches, has been developed. The protection is accomplished by integrating an additional power MOSFET in series with a power MOSFET. The reverse battery protection is achieved without using external control signals. The positive drain breakdown voltage for the proposed MOSFET is 71 V and the negative drain current at a drain voltage of {minus}16 V is only {minus}750 {micro}A. The on-state resistance is 170 m{Omega}. This new intelligent power MOSFET can replace the conventional three-terminal power MOSFET's used in automotive applications.

Sakamoto, Kozo; Fuchigami, Nobutaka; Takagawa, Kyoichi; Ohtaka, Shigeo

1999-11-01

125

Population genetic tools: application to cancer.  

PubMed

The availability of a reference human genome sequence, an increasingly dense catalog, knowledge of common genetic variation, and new developments in technology present an unprecedented opportunity to systematically explore the genetic basis of complex human diseases such as cancer. An understanding of the common mutations that can cause distinct human cancers will be critical for identifying new targets for drug discovery, patient stratification for clinical trials, and analysis of drug response data to delineate classes of patients that respond to therapy. The genome structure of cancer can be examined in several ways: (1) large-scale case-control or family studies can investigate germline mutations; and (2) state-of-the-art genomic technologies (eg, high-density oligonucleotide arrays and targeted re-sequencing), can identify somatic alterations. Combined, these approaches will lead to a better understanding of the cancer genome. PMID:17449348

Gabriel, Stacey

2007-04-01

126

Applications of Genetic Programming in Cancer Research  

PubMed Central

The theory of Darwinian evolution is the fundamental keystones of modern biology. Late in the last century, computer scientists began adapting its principles, in particular natural selection, to complex computational challenges, leading to the emergence of evolutionary algorithms. The conceptual model of selective pressure and recombination in evolutionary algorithms allows scientists to efficiently search high dimensional space for solutions to complex problems. In the last decade, genetic programming has been developed and extensively applied for analysis of molecular data to classify cancer subtypes and characterize the mechanisms of cancer pathogenesis and development. This article reviews current successes using genetic programming and discusses its potential impact in cancer research and treatment in the near future. PMID:18929677

Worzel, William P.; Yu, Jianjun; Almal, Arpit A.; Chinnaiyan, Arul M.

2012-01-01

127

Methylcellulose Based Thermally Reversible Hydrogel System for Tissue Engineering Applications  

PubMed Central

The thermoresponsive behavior of a Methylcellulose (MC) polymer was systematically investigated to determine its usability in constructing MC based hydrogel systems in cell sheet engineering applications. Solution-gel analyses were made to study the effects of polymer concentration, molecular weight and dissolved salts on the gelation of three commercially available MCs using differential scanning calorimeter and rheology. For investigation of the hydrogel stability and fluid uptake capacity, swelling and degradation experiments were performed with the hydrogel system exposed to cell culture solutions at incubation temperature for several days. From these experiments, the optimal composition of MC-water-salt that was able to produce stable hydrogels at or above 32 °C, was found to be 12% to 16% of MC (Mol. wt. of 15,000) in water with 0.5× PBS (~150mOsm). This stable hydrogel system was then evaluated for a week for its efficacy to support the adhesion and growth of specific cells in culture; in our case the stromal/stem cells derived from human adipose tissue derived stem cells (ASCs). The results indicated that the addition (evenly spread) of ~200 µL of 2 mg/mL bovine collagen type -I (pH adjusted to 7.5) over the MC hydrogel surface at 37 °C is required to improve the ASC adhesion and proliferation. Upon con?uence, a continuous monolayer ASC sheet was formed on the surface of the hydrogel system and an intact cell sheet with preserved cell–cell and cell–extracellular matrix was spontaneously and gradually detached when the grown cell sheet was removed from the incubator and exposed to room temperature (~30 °C) within minutes. PMID:24709793

Thirumala, Sreedhar; Gimble, Jeffrey M.; Devireddy, Ram V.

2013-01-01

128

Design and optimization of desalination reverse osmosis plants driven by renewable energies using genetic algorithms  

Microsoft Academic Search

Renewable energy sources (RES) for powering desalination processes is a promising option especially in remote and arid regions where the use of conventional energy is costly or unavailable. Reverse Osmosis (RO) is one of the most suitable desalination processes to be coupled with different renewable energy sources such as solar and wind.If RES\\/RO systems are optimally designed, some combinations can

K. Bourouni; T. Ben M’Barek; A. Al Taee

2011-01-01

129

High volume molecular genetic identification of single nucleotide polymorphisms using Genetic Bit Analysis Application to human genetic diagnosis  

SciTech Connect

The most common type of genetic disease-associated mutation is the single nucleotide polymorphism (SNP). Because most genetic diseases can be caused by multiple SNPs in the same gene, effective routine diagnosis of complex genetic diseases is dependent on a simple and reliable method of interrogating SNP sites. Molecular Tool`s solid phase assay capable of direct genotyping (single base sequencing) of SNP sites, Genetic Bit Analysis (GBA), involves hybridization-capture of a single-stranded PCR product to a sequence-specific, microtiter plate-bound oligonucleotide primer. The captured PCR product then acts as template for single-base extension of the capture primer across the polymorphic site, enabling direct determination of the base composition of the polymorphism through a simple colormetric assay. Genotyping in a high volume, semi-automated, processing system with a current capacity of 100 SNP interrogations per technician per day enables the screening of candidate mutations rapidly and cost-effectively, critically important to comprehensive genetic diagnosis. Using this gel-free technology, we have developed prototype diagnostic tests for CFTR and ApoE polymorphisms which enable direct sequencing of the polymorphic base at each site of interest. Routine clinical diagnosis of genetically complex diseases such as cystic fibrosis is dependent on this combination of robust biochemistry and simple format. Additionally, the ability to transfer the format and biochemistry to any disease gene of interest enables the broad application of this technology to clinical diagnostics, especially for genetically complex diseases.

Boyce-Jacino, M.T.; Reynolds, J.; Nikiforov, T. [Molecular Tool, Inc., Baltimore, MD (United States)] [and others

1994-09-01

130

Applications of graph theory to landscape genetics  

PubMed Central

We investigated the relationships among landscape quality, gene flow, and population genetic structure of fishers (Martes pennanti) in ON, Canada. We used graph theory as an analytical framework considering each landscape as a network node. The 34 nodes were connected by 93 edges. Network structure was characterized by a higher level of clustering than expected by chance, a short mean path length connecting all pairs of nodes, and a resiliency to the loss of highly connected nodes. This suggests that alleles can be efficiently spread through the system and that extirpations and conservative harvest are not likely to affect their spread. Two measures of node centrality were negatively related to both the proportion of immigrants in a node and node snow depth. This suggests that central nodes are producers of emigrants, contain high-quality habitat (i.e., deep snow can make locomotion energetically costly) and that fishers were migrating from high to low quality habitat. A method of community detection on networks delineated five genetic clusters of nodes suggesting cryptic population structure. Our analyses showed that network models can provide system-level insight into the process of gene flow with implications for understanding how landscape alterations might affect population fitness and evolutionary potential. PMID:25567802

Garroway, Colin J; Bowman, Jeff; Carr, Denis; Wilson, Paul J

2008-01-01

131

Applications of graph theory to landscape genetics.  

PubMed

We investigated the relationships among landscape quality, gene flow, and population genetic structure of fishers (Martes pennanti) in ON, Canada. We used graph theory as an analytical framework considering each landscape as a network node. The 34 nodes were connected by 93 edges. Network structure was characterized by a higher level of clustering than expected by chance, a short mean path length connecting all pairs of nodes, and a resiliency to the loss of highly connected nodes. This suggests that alleles can be efficiently spread through the system and that extirpations and conservative harvest are not likely to affect their spread. Two measures of node centrality were negatively related to both the proportion of immigrants in a node and node snow depth. This suggests that central nodes are producers of emigrants, contain high-quality habitat (i.e., deep snow can make locomotion energetically costly) and that fishers were migrating from high to low quality habitat. A method of community detection on networks delineated five genetic clusters of nodes suggesting cryptic population structure. Our analyses showed that network models can provide system-level insight into the process of gene flow with implications for understanding how landscape alterations might affect population fitness and evolutionary potential. PMID:25567802

Garroway, Colin J; Bowman, Jeff; Carr, Denis; Wilson, Paul J

2008-11-01

132

Genetic Algorithm Application in Optimization of Wireless Sensor Networks  

PubMed Central

There are several applications known for wireless sensor networks (WSN), and such variety demands improvement of the currently available protocols and the specific parameters. Some notable parameters are lifetime of network and energy consumption for routing which play key role in every application. Genetic algorithm is one of the nonlinear optimization methods and relatively better option thanks to its efficiency for large scale applications and that the final formula can be modified by operators. The present survey tries to exert a comprehensive improvement in all operational stages of a WSN including node placement, network coverage, clustering, and data aggregation and achieve an ideal set of parameters of routing and application based WSN. Using genetic algorithm and based on the results of simulations in NS, a specific fitness function was achieved, optimized, and customized for all the operational stages of WSNs. PMID:24693235

Norouzi, Ali; Zaim, A. Halim

2014-01-01

133

The social and genetic mating system in flickers linked to partially reversed sex roles  

Microsoft Academic Search

The type of social and genetic mating system observed in birds is influenced by the need of both sexes to provide parental care. In woodpeckers, unlike most birds, females are partially emancipated as males provide most of the care including nocturnal incubation. We analyzed the mating system of northern flickers Colaptes auratus and used microsatellite markers to assess parentage of

Karen L. Wiebe; Bart Kempenaers

2009-01-01

134

Genetic Inactivation of D-Amino Acid Oxidase Enhances Extinction and Reversal Learning in Mice  

ERIC Educational Resources Information Center

Activation of the N-methyl-d-aspartate receptor (NMDAR) glycine site has been shown to accelerate adaptive forms of learning that may benefit psychopathologies involving cognitive and perseverative disturbances. In this study, the effects of increasing the brain levels of the endogenous NMDAR glycine site agonist D-serine, through the genetic

Labrie, Viviane; Duffy, Steven; Wang, Wei; Barger, Steven W.; Baker, Glen B.; Roder, John C.

2009-01-01

135

The Reverse Cholesterol Transport Pathway Improves Understanding of Genetic Networks for Fat Deposition and Muscle Growth in Beef Cattle  

PubMed Central

In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F1 bulls, 113 F1 dams, and 246 F2 progeny. A total of 37 amplicons were used to screen single nucleotide polymorphisms (SNPs) on 6 F1 bulls. Among 36 SNPs detected in 11 of these 13 genes, 19 were selected for genotyping by the Sequenom assay design on all F2 progeny. Single-marker analysis revealed seven SNPs in ATP binding cassette A1, apolipoproteins A1, B and E, phospholipid transfer protein and paraoxinase 1 genes significantly associated with nine phenotypes (P<0.05). Previously, we reported genetic networks associated with 19 complex phenotypes based on a total of 138 genetic polymorphisms derived from 71 known functional genes. Therefore, after Bonferroni correction, these significant (adjusted P<0.05) and suggestive (adjusted P<0.10) associations were then used to identify genetic networks related to the RCT pathway. Multiple-marker analysis suggested possible genetic networks involving the RCT pathway for kidney-pelvic-heart fat percentage, rib-eye area, and subcutaneous fat depth phenotypes with markers derived from paraoxinase 1, apolipoproteins A1 and E, respectively. The present study confirmed that genes involved in cholesterol homeostasis are useful targets for investigating obesity in humans as well as for improving meat quality phenotypes in a livestock production. PMID:21151936

Daniels, Tyler F.; Wu, Xiao-Lin; Pan, Zengxiang; Michal, Jennifer J.; Wright, Raymond W.; Killinger, Karen M.; MacNeil, Michael D.; Jiang, Zhihua

2010-01-01

136

Genetic algorithms and their applications in accelerator physics  

SciTech Connect

Multi-objective optimization techniques are widely used in an extremely broad range of fields. Genetic optimization for multi-objective optimization was introduced in the accelerator community in relatively recent times and quickly spread becoming a fundamental tool in multi-dimensional optimization problems. This discussion introduces the basics of the technique and reviews applications in accelerator problems.

Hofler, Alicia S. [JLAB

2013-12-01

137

Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation  

Microsoft Academic Search

Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and enable the association of heritable traits with underlying genomic variation. Molecular marker technology has developed rapidly over the last decade and two forms of sequence based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) now predominate applications in

Chris Duran; Nikki Appleby; David Edwards; Jacqueline Batley

2009-01-01

138

Genetic Susceptibility and Survival: Application to Breast Cancer  

E-print Network

Genetic Susceptibility and Survival: Application to Breast Cancer Edwin S. IVERSEN, JR., Giovanni are known to confer an elevated risk of both breast and ovarian cancers. The effect of carrying such a mutation on survival after developing breast or ovarian cancer is less well understood. We investigate

West, Mike

139

Reverse Genetics Demonstrates that Proteolytic Processing of the Ebola Virus Glycoprotein Is Not Essential for Replication in Cell Culture  

PubMed Central

Ebola virus, a prime example of an emerging pathogen, causes fatal hemorrhagic fever in humans and in nonhuman primates. Identification of major determinants of Ebola virus pathogenicity has been hampered by the lack of effective strategies for experimental mutagenesis. Here we exploit a reverse genetics system that allows the generation of Ebola virus from cloned cDNA to engineer a mutant Ebola virus with an altered furin recognition motif in the glycoprotein (GP). When expressed in cells, the GP of the wild type, but not of the mutant, virus was cleaved into GP1 and GP2. Although posttranslational furin-mediated cleavage of GP was thought to be an essential step in Ebola virus infection, generation of a viable mutant Ebola virus lacking a furin recognition motif in the GP cleavage site demonstrates that GP cleavage is not essential for replication of Ebola virus in cell culture. PMID:11739705

Neumann, Gabriele; Feldmann, Heinz; Watanabe, Shinji; Lukashevich, Igor; Kawaoka, Yoshihiro

2002-01-01

140

7 Quantum Computing Applications of Genetic Programming  

Microsoft Academic Search

Quantum computers are computational devices that use the dynamics of atomic-scale objects to store and manipulate information. Only a few, small-scale quantum computers have been built to date, but quantum computers can in principle outperform all possible classical computers in significant ways. Quantum computation is therefore a subject of considerable theoretical interest that may also have practical applications in the

Lee Spector; Howard Barnum; Herbert J. Bernstein; Nikhil Swamy

141

Reverse Engineering Financial Markets with Majority and Minority Games using Genetic Algorithms  

E-print Network

Using virtual stock markets with artificial interacting software investors, aka agent-based models (ABMs), we present a method to reverse engineer real-world financial time series. We model financial markets as made of a large number of interacting boundedly rational agents. By optimizing the similarity between the actual data and that generated by the reconstructed virtual stock market, we obtain parameters and strategies, which reveal some of the inner workings of the target stock market. We validate our approach by out-of-sample predictions of directional moves of the Nasdaq Composite Index.

Wiesinger, J; Satinover, J

2010-01-01

142

Quantitative genetic versions of Hamilton's rule with empirical applications  

PubMed Central

Hamilton's theory of inclusive fitness revolutionized our understanding of the evolution of social interactions. Surprisingly, an incorporation of Hamilton's perspective into the quantitative genetic theory of phenotypic evolution has been slow, despite the popularity of quantitative genetics in evolutionary studies. Here, we discuss several versions of Hamilton's rule for social evolution from a quantitative genetic perspective, emphasizing its utility in empirical applications. Although evolutionary quantitative genetics offers methods to measure each of the critical parameters of Hamilton's rule, empirical work has lagged behind theory. In particular, we lack studies of selection on altruistic traits in the wild. Fitness costs and benefits of altruism can be estimated using a simple extension of phenotypic selection analysis that incorporates the traits of social interactants. We also discuss the importance of considering the genetic influence of the social environment, or indirect genetic effects (IGEs), in the context of Hamilton's rule. Research in social evolution has generated an extensive body of empirical work focusing—with good reason—almost solely on relatedness. We argue that quantifying the roles of social and non-social components of selection and IGEs, in addition to relatedness, is now timely and should provide unique additional insights into social evolution. PMID:24686930

McGlothlin, Joel W.; Wolf, Jason B.; Brodie, Edmund D.; Moore, Allen J.

2014-01-01

143

Reverse sex-biased philopatry in a cooperative bird: genetic consequences and a social cause.  

PubMed

The genetic structure of a group or population of organisms can profoundly influence the potential for inbreeding and, through this, can affect both dispersal strategies and mating systems. We used estimates of genetic relatedness as well as likelihood-based methods to reconstruct social group composition and examine sex biases in dispersal in a Costa Rican population of white-throated magpie-jays (Calocitta formosa, Swainson 1827), one of the few birds suggested to have female-biased natal philopatry. We found that females within groups were more closely related than males, which is consistent with observational data indicating that males disperse upon maturity, whereas females tend to remain in their natal territories and act as helpers. In addition, males were generally unrelated to one another within groups, suggesting that males do not disperse with or towards relatives. Finally, within social groups, female helpers were less related to male than female breeders, suggesting greater male turnover within groups. This last result indicates that within the natal group, female offspring have more opportunities than males to mate with nonrelatives, which might help to explain the unusual pattern of female-biased philopatry and male-biased dispersal in this system. We suggest that the novel approach adopted here is likely to be particularly useful for short-term studies or those conducted on rare or difficult-to-observe species, as it allows one to establish general patterns of philopatry and genetic structure without the need for long-term monitoring of identifiable individuals. PMID:19627491

Berg, E C; Eadie, J M; Langen, T A; Russell, A F

2009-08-01

144

Ion beam application in genetic modification  

Microsoft Academic Search

People pay little attention to the interaction between low-energy ions and matter compared to that of high-energy ions. It is even more unusual to find studies of the interaction of low-energy ions and complicated organisms. The discovery of bioeffects induced by ion implantation has, however, opened a new branch in the field of ion beam applications in the life sciences.

Zengliang Yu

2000-01-01

145

Genetic algorithms and their applications to the design of neural networks. Antonia J. Jones  

E-print Network

Genetic algorithms and their applications to the design of neural networks. Antonia J. Jones 2002 1 Genetic algorithms and their applications to the design of neural networks. CONTENTS Review. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Figure 4 Stochastic equilibrium with stable niches using Goldberg sharing

Jones, Antonia J.

146

Adaptable Constrained Genetic Programming: Extensions and Applications  

NASA Technical Reports Server (NTRS)

An evolutionary algorithm applies evolution-based principles to problem solving. To solve a problem, the user defines the space of potential solutions, the representation space. Sample solutions are encoded in a chromosome-like structure. The algorithm maintains a population of such samples, which undergo simulated evolution by means of mutation, crossover, and survival of the fittest principles. Genetic Programming (GP) uses tree-like chromosomes, providing very rich representation suitable for many problems of interest. GP has been successfully applied to a number of practical problems such as learning Boolean functions and designing hardware circuits. To apply GP to a problem, the user needs to define the actual representation space, by defining the atomic functions and terminals labeling the actual trees. The sufficiency principle requires that the label set be sufficient to build the desired solution trees. The closure principle allows the labels to mix in any arity-consistent manner. To satisfy both principles, the user is often forced to provide a large label set, with ad hoc interpretations or penalties to deal with undesired local contexts. This unfortunately enlarges the actual representation space, and thus usually slows down the search. In the past few years, three different methodologies have been proposed to allow the user to alleviate the closure principle by providing means to define, and to process, constraints on mixing the labels in the trees. Last summer we proposed a new methodology to further alleviate the problem by discovering local heuristics for building quality solution trees. A pilot system was implemented last summer and tested throughout the year. This summer we have implemented a new revision, and produced a User's Manual so that the pilot system can be made available to other practitioners and researchers. We have also designed, and partly implemented, a larger system capable of dealing with much more powerful heuristics.

Janikow, Cezary Z.

2005-01-01

147

Identification of genes important for cutaneous function revealed by a large scale reverse genetic screen in the mouse.  

PubMed

The skin is a highly regenerative organ which plays critical roles in protecting the body and sensing its environment. Consequently, morbidity and mortality associated with skin defects represent a significant health issue. To identify genes important in skin development and homeostasis, we have applied a high throughput, multi-parameter phenotype screen to the conditional targeted mutant mice generated by the Wellcome Trust Sanger Institute's Mouse Genetics Project (Sanger-MGP). A total of 562 different mouse lines were subjected to a variety of tests assessing cutaneous expression, macroscopic clinical disease, histological change, hair follicle cycling, and aberrant marker expression. Cutaneous lesions were associated with mutations in 23 different genes. Many of these were not previously associated with skin disease in the organ (Mysm1, Vangl1, Trpc4ap, Nom1, Sparc, Farp2, and Prkab1), while others were ascribed new cutaneous functions on the basis of the screening approach (Krt76, Lrig1, Myo5a, Nsun2, and Nf1). The integration of these skin specific screening protocols into the Sanger-MGP primary phenotyping pipelines marks the largest reported reverse genetic screen undertaken in any organ and defines approaches to maximise the productivity of future projects of this nature, while flagging genes for further characterisation. PMID:25340873

DiTommaso, Tia; Jones, Lynelle K; Cottle, Denny L; Gerdin, Anna-Karin; Vancollie, Valerie E; Watt, Fiona M; Ramirez-Solis, Ramiro; Bradley, Allan; Steel, Karen P; Sundberg, John P; White, Jacqueline K; Smyth, Ian M

2014-10-01

148

Reverse Genetics Recovery of Lujo Virus and Role of Virus RNA Secondary Structures in Efficient Virus Growth  

PubMed Central

Arenaviruses are rodent-borne viruses with a bisegmented RNA genome. A genetically unique arenavirus, Lujo virus, was recently discovered as the causal agent of a nosocomial outbreak of acute febrile illness with hemorrhagic manifestations in Zambia and South Africa. The outbreak had a case fatality rate of 80%. A reverse genetics system to rescue infectious Lujo virus from cDNA was established to investigate the biological properties of this virus. Sequencing the genomic termini showed unique nucleotides at the 3? terminus of the S segment promoter element. While developing this system, we discovered that reconstructing infectious Lujo virus using the previously reported L segment intergenic region (IGR), comprising the arenaviral transcription termination signal, yielded an attenuated Lujo virus. Resequencing revealed that the correct L segment IGR was 36 nucleotides longer, and incorporating it into the reconstructed Lujo virus restored the growth rate to that of the authentic clinical virus isolate. These additional nucleotides were predicted to more than double the free energy of the IGR main stem-loop structure. In addition, incorporating the newly determined L-IGR into a replicon reporter system enhanced the expression of a luciferase reporter L segment. Overall, these results imply that an extremely stable secondary structure within the L-IGR is critical for Lujo virus propagation and viral protein production. The technology for producing recombinant Lujo virus now provides a method to precisely investigate the molecular determinants of virulence of this newly identified pathogen. PMID:22837210

Chakrabarti, Ayan K.; Bird, Brian H.; Dodd, Kim A.; McMullan, Laura K.; Spiropoulou, Christina F.; Nichol, Stuart T.; Albariño, César G.

2012-01-01

149

Identification of Genes Important for Cutaneous Function Revealed by a Large Scale Reverse Genetic Screen in the Mouse  

PubMed Central

The skin is a highly regenerative organ which plays critical roles in protecting the body and sensing its environment. Consequently, morbidity and mortality associated with skin defects represent a significant health issue. To identify genes important in skin development and homeostasis, we have applied a high throughput, multi-parameter phenotype screen to the conditional targeted mutant mice generated by the Wellcome Trust Sanger Institute's Mouse Genetics Project (Sanger-MGP). A total of 562 different mouse lines were subjected to a variety of tests assessing cutaneous expression, macroscopic clinical disease, histological change, hair follicle cycling, and aberrant marker expression. Cutaneous lesions were associated with mutations in 23 different genes. Many of these were not previously associated with skin disease in the organ (Mysm1, Vangl1, Trpc4ap, Nom1, Sparc, Farp2, and Prkab1), while others were ascribed new cutaneous functions on the basis of the screening approach (Krt76, Lrig1, Myo5a, Nsun2, and Nf1). The integration of these skin specific screening protocols into the Sanger-MGP primary phenotyping pipelines marks the largest reported reverse genetic screen undertaken in any organ and defines approaches to maximise the productivity of future projects of this nature, while flagging genes for further characterisation. PMID:25340873

DiTommaso, Tia; Jones, Lynelle K.; Cottle, Denny L.; Gerdin, Anna-Karin; Vancollie, Valerie E.; Watt, Fiona M.; Ramirez-Solis, Ramiro; Bradley, Allan; Steel, Karen P.; Sundberg, John P.; White, Jacqueline K.; Smyth, Ian M.

2014-01-01

150

Sex-Role Reversal and "Dominance Genes" in African Cichlid Fish The broad scope of my research aims to understand the genetic basis of behavior from an  

E-print Network

1 Sex-Role Reversal and "Dominance Genes" in African Cichlid Fish The broad scope of my research the genetic basis of species-specific "sex-role" behaviors, and how these behaviors relate to environmental specific aims designed to test the hypothesis that species- specific "sex-role" behaviors, imposed

Renn, Susan C.P.

151

Cross flow filtration for radwaste applications reverse osmosis demonstration case studies  

SciTech Connect

Today`s radwaste economic and regulatory scenarios signify the importance in the improvement of operational practices to reduce generator liabilities. This action is largely due to the rising cost dealing with burial sites and the imposed waste volume restriction. To control the economical burdens associated with waste burial and to comply with stricter environmental regulations, NPP`s are attempting to modify their radwaste system(s) design and operating philosophy by placing a major emphasis on waste volume reduction and processing techniques. The utilization of reverse osmosis technology as a means for treatment of process and wastewater streams in the nuclear power industry has been investigated for many years. This paper will outline reverse osmosis theory and highlight performance data for process and waste stream purification applications. Case studies performed at 5 nuclear plants have been outlined. The demonstrations were performed on a widely variety of process stream for both a PWR and BWR application. The data provided by the pilot systems, the equipment design, and the economical impact a reverse osmosis unit will have on producing treated (high purity) are as follows.

Malkmus, D. [VECTRA Technologies, Inc., Columbia, SC (United States)

1995-05-01

152

Reverse genetics of Escherichia coli glycerol kinase allosteric regulation and glucose control of glycerol utilization in vivo.  

PubMed

Reverse genetics is used to evaluate the roles in vivo of allosteric regulation of Escherichia coli glycerol kinase by the glucose-specific phosphocarrier of the phosphoenolpyruvate:glycose phosphotransferase system, IIA(Glc) (formerly known as III(glc)), and by fructose 1,6-bisphosphate. Roles have been postulated for these allosteric effectors in glucose control of both glycerol utilization and expression of the glpK gene. Genetics methods based on homologous recombination are used to place glpK alleles with known specific mutations into the chromosomal context of the glpK gene in three different genetic backgrounds. The alleles encode glycerol kinases with normal catalytic properties and specific alterations of allosteric regulatory properties, as determined by in vitro characterization of the purified enzymes. The E. coli strains with these alleles display the glycerol kinase regulatory phenotypes that are expected on the basis of the in vitro characterizations. Strains with different glpR alleles are used to assess the relationships between allosteric regulation of glycerol kinase and specific repression in glucose control of the expression of the glpK gene. Results of these studies show that glucose control of glycerol utilization and glycerol kinase expression is not affected by the loss of IIA(Glc) inhibition of glycerol kinase. In contrast, fructose 1,6-bisphosphate inhibition of glycerol kinase is the dominant allosteric control mechanism, and glucose is unable to control glycerol utilization in its absence. Specific repression is not required for glucose control of glycerol utilization, and the relative roles of various mechanisms for glucose control (catabolite repression, specific repression, and inducer exclusion) are different for glycerol utilization than for lactose utilization. PMID:11344141

Holtman, C K; Pawlyk, A C; Meadow, N D; Pettigrew, D W

2001-06-01

153

Pathogenicity study in sheep using reverse-genetics-based reassortant bluetongue viruses.  

PubMed

Bluetongue (BT) disease, caused by the non-enveloped bluetongue virus (BTV) belonging to the Reoviridae family, is an economically important disease that affects a wide range of wild and domestic ruminants. Currently, 26 different serotypes of BTV are recognized in the world, of which BTV-8 has been found to exhibit one of the most virulent manifestations of BT disease in livestock. In recent years incursions of BTV-8 in Europe have resulted in significant morbidity and mortality not only in sheep but also in cattle. The molecular and genetic basis of BTV-8 pathogenesis is not known. To understand the genetic basis of BTV-8 pathogenicity, we generated reassortant viruses by replacing the 3 most variable genes, S2, S6 and S10 of a recent isolate of BTV-8, in different combinations into the backbone of an attenuated strain of BTV-1. The growth profiles of these reassortant viruses were then analyzed in two different ovine cell lines derived from different organs, kidney and thymus. Distinct patterns for each reassortant virus in these two cell lines were observed. To determine the pathogenicity of these reassortant viruses, groups of BTV-susceptible sheep were infected with each of these viruses. The data suggested that the clinical manifestations of these two different serotypes, BTV-1 and BTV-8, were slightly distinct and BTV-1, when comprising all 3 genome segments of BTV-8, behaved differently to BTV-1. Our results also suggested that the molecular basis of BT disease is highly complex. PMID:25307940

Celma, Cristina C; Bhattacharya, Bishnupriya; Eschbaumer, Michael; Wernike, Kerstin; Beer, Martin; Roy, Polly

2014-11-01

154

Pathogenicity study in sheep using reverse-genetics-based reassortant bluetongue viruses  

PubMed Central

Bluetongue (BT) disease, caused by the non-enveloped bluetongue virus (BTV) belonging to the Reoviridae family, is an economically important disease that affects a wide range of wild and domestic ruminants. Currently, 26 different serotypes of BTV are recognized in the world, of which BTV-8 has been found to exhibit one of the most virulent manifestations of BT disease in livestock. In recent years incursions of BTV-8 in Europe have resulted in significant morbidity and mortality not only in sheep but also in cattle. The molecular and genetic basis of BTV-8 pathogenesis is not known. To understand the genetic basis of BTV-8 pathogenicity, we generated reassortant viruses by replacing the 3 most variable genes, S2, S6 and S10 of a recent isolate of BTV-8, in different combinations into the backbone of an attenuated strain of BTV-1. The growth profiles of these reassortant viruses were then analyzed in two different ovine cell lines derived from different organs, kidney and thymus. Distinct patterns for each reassortant virus in these two cell lines were observed. To determine the pathogenicity of these reassortant viruses, groups of BTV-susceptible sheep were infected with each of these viruses. The data suggested that the clinical manifestations of these two different serotypes, BTV-1 and BTV-8, were slightly distinct and BTV-1, when comprising all 3 genome segments of BTV-8, behaved differently to BTV-1. Our results also suggested that the molecular basis of BT disease is highly complex. PMID:25307940

Celma, Cristina C.; Bhattacharya, Bishnupriya; Eschbaumer, Michael; Wernike, Kerstin; Beer, Martin; Roy, Polly

2014-01-01

155

Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen  

PubMed Central

Permanent stop-and-shop large-scale mouse mutant resources provide an excellent platform to decipher tissue phenogenomics. Here we analyse skin from 538 knockout mouse mutants generated by the Sanger Institute Mouse Genetics Project. We optimize immunolabelling of tail epidermal wholemounts to allow systematic annotation of hair follicle, sebaceous gland and interfollicular epidermal abnormalities using ontology terms from the Mammalian Phenotype Ontology. Of the 50 mutants with an epidermal phenotype, 9 map to human genetic conditions with skin abnormalities. Some mutant genes are expressed in the skin, whereas others are not, indicating systemic effects. One phenotype is affected by diet and several are incompletely penetrant. In-depth analysis of three mutants, Krt76, Myo5a (a model of human Griscelli syndrome) and Mysm1, provides validation of the screen. Our study is the first large-scale genome-wide tissue phenotype screen from the International Knockout Mouse Consortium and provides an open access resource for the scientific community. PMID:24721909

Liakath-Ali, Kifayathullah; Vancollie, Valerie E.; Heath, Emma; Smedley, Damian P.; Estabel, Jeanne; Sunter, David; DiTommaso, Tia; White, Jacqueline K.; Ramirez-Solis, Ramiro; Smyth, Ian; Steel, Karen P.; Watt, Fiona M.

2014-01-01

156

[The genetic control of mouse coat color and its applications in genetics teaching].  

PubMed

Mice are the most commonly used mammalian model. The coat colors of mice are typical Mendelian traits, which have various colors such as white, black, yellow and agouti. The inheritance of mouse coat color is usually stated as an example only in teaching the knowledge of recessive lethal alleles. After searched the related literatures and summarized the molecular mechanisms of mouse coat color inheritance, we further expanded the application of this example into the introduction of the basic concepts of alleles and Mendelian laws, demonstration of the gene structure and function, regulation of gene expression, gene interaction, epigenetic modification, quantitative genetics, as well as evolutionary genetics. By running this example through the whole genetics-teaching lectures, we help the student to form a systemic and developmental view of genetic analysis. At the same time, this teaching approach not only highlights the advancement and integrity of genetics, but also results in a good teaching effect on inspiring the students' interest and attracting students' attention. PMID:25406255

Xing, Wanjin; Morigen, Morigen

2014-10-01

157

Genetic evidence for extreme polyandry and extraordinary sex-role reversal in a pipefish.  

PubMed Central

Due to the phenomenon of male pregnancy, the fish family Syngnathidae (seahorses and pipefishes) has historically been considered an archetypal example of a group in which sexual selection should act more strongly on females than on males. However, more recent work has called into question the idea that all species with male pregnancy are sex-role reversed with respect to the intensity of sexual selection. Furthermore, no studies have formally quantified the opportunity for sexual selection in any natural breeding assemblage of pipefishes or seahorses in order to demonstrate conclusively that sexual selection acts most strongly on females. Here, we use a DNA-based study of parentage in the Gulf pipefish Syngnathus scovelli in order to show that sexual selection indeed acts more strongly on females than on males in this species. Moreover, the Gulf pipefish exhibits classical polyandry with the greatest asymmetry in reproductive roles (as quantified by variances in mating success) between males and females yet documented in any system. Thus, the intensity of sexual selection on females in pipefish rivals that of any other taxon yet studied. PMID:11749706

Jones, A. G.; Walker, D.; Avise, J. C.

2001-01-01

158

The Genetic Basis of HIV-1 Resistance to Reverse Transcriptase and Protease Inhibitors  

PubMed Central

HIV-1 drug resistance is caused by mutations in the reverse transcriptase (RT) and protease enzymes, the molecular targets of antiretroviral therapy. At the beginning of the year 2000, two expert panels recommended that HIV-1 RT and protease susceptibility testing be used to help select antiretroviral drugs for HIV-1-infected patients. Genotypic assays have been developed to detect HIV-1 mutations known to confer antiretroviral drug resistance. Genotypic assays using dideoxynucleoside sequencing provide extensive insight into the presence of drug-resistant variants in the population of viruses within an individual. However, the interpretation of these assays in clinical settings is formidable because of the large numbers of drug resistance mutations and because these mutations interact with one another and emerge in complex patterns. In addition, cross-resistance between antiretroviral drugs is greater than that anticipated from initial in vitro studies. This review summarises the published data linking HIV-1 RT and protease mutations to in vitro and clinical resistance to the currently available nucleoside RT inhibitors, non-nucleoside RT inhibitors, and protease inhibitors. PMID:19096725

Shafer, Robert W.; Kantor, Rami; Gonzales, Matthew J.

2008-01-01

159

Application of Ionic Liquids in High Performance Reversed-Phase Chromatography  

PubMed Central

Ionic liquids, considered “green” chemicals, are widely used in many areas of analytical chemistry due to their unique properties. Recently, ionic liquids have been used as a kind of novel additive in separation and combined with silica to synthesize new stationary phase as separation media. This review will focus on the properties and mechanisms of ionic liquids and their potential applications as mobile phase modifier and surface-bonded stationary phase in reversed-phase high performance liquid chromatography (RP-HPLC). Ionic liquids demonstrate advantages and potential in chromatographic field. PMID:19582220

Wang, Ye; Tian, Minglei; Bi, Wentao; Row, Kyung Ho

2009-01-01

160

A Novel Application of Time Reversed Acoustics: Salt Dome Flank Imaging Using Walk Away VSP Surveys  

E-print Network

In the past few years, there has been considerable research and interest in a topic known by various names, such as Time Reverse Acoustics (TRA), Time Reverse Mirrors (TRM), and Time Reverse Cavities (TRC), which exploits ...

Hoop, Martijn de

2005-01-01

161

Application of genetic algorithms to tuning fuzzy control systems  

NASA Technical Reports Server (NTRS)

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

Espy, Todd; Vombrack, Endre; Aldridge, Jack

1993-01-01

162

Sub-population policies for a parallel multiobjective genetic algorithm with applications to wing design  

E-print Network

Sub-population policies for a parallel multiobjective genetic algorithm with applications to wing. 2. GENETIC ALGORITHM WITH SUB-POPULATIONS The algorithm here described, that will be called Virtual Sub- population Genetic Algorithm (VSGA), is an extension of the multi-objective genetic algorithm

Coello, Carlos A. Coello

163

A Hypomethylated population of Brassica rapa for forward and reverse Epi-genetics  

PubMed Central

Background Epigenetic marks superimposed on the DNA sequence of eukaryote chromosomes provide agility and plasticity in terms of modulating gene expression, ontology, and response to the environment. Modulating the methylation status of cytosine can generate epialleles, which have been detected and characterised at specific loci in several plant systems, and have the potential to generate novel and relatively stable phenotypes. There have been no systematic attempts to explore and utilise epiallelic variation, and so extend the range of phenotypes available for selection in crop improvement. We developed an approach for generating novel epialleles by perturbation of the DNA methylation status. 5- Azacytidine (5-AzaC) provides selective targeting of 5mCG, which in plants is associated with exonic DNA. Targeted chemical intervention using 5-AzaC has advantages over transgenic or mutant modulation of methyltransferases, allowing stochastic generation of epialleles across the genome. Results We demonstrate the potential of stochastic chemically-induced hypomethylation to generate novel and valuable variation for crop improvement. Systematic analysis of dose–response to 5-AzaC in B. rapa guided generation of a selfed stochastically hypomethylated population, used for forward screening of several agronomic traits. Dose–response was sigmoidal for several traits, similar to that observed for chemical mutagens such as EMS. We demonstrated transgenerational inheritance of some phenotypes. BraRoAZ is a unique hypomethylated population of 1000 E2 sib lines. When compared to untreated controls, 5-Aza C-treated lines exhibited reduced immuno-staining of 5mC on pachytene chromosomes, and Methylation Sensitive Amplified Polymorphism (MSAP) profiles that were both divergent and more variable. There was coincident phenotypic variation among these lines for a range of seed yield and composition traits, including increased seed protein content and decreased oil content, as well as decreased erucic acid and corresponding increases in linoleic and/or palmitic acid. Each 5-AzaC-treated line represents a unique combination of hypomethylated epialleles. Conclusions The approach and populations developed are available for forward and reverse screening of epiallelic variation and subsequent functional and inheritance studies. The generation of stochastically hypomethylated populations has utility in epiallele discovery for a wide range of crop plants, and has considerable potential as an intervention strategy for crop improvement. PMID:23082790

2012-01-01

164

Investigating CNS synaptogenesis at single-synapse resolution by combining reverse genetics with correlative light and electron microscopy.  

PubMed

Determining direct synaptic connections of specific neurons in the central nervous system (CNS) is a major technical challenge in neuroscience. As a corollary, molecular pathways controlling developmental synaptogenesis in vivo remain difficult to address. Here, we present genetic tools for efficient and versatile labeling of organelles, cytoskeletal components and proteins at single-neuron and single-synapse resolution in Drosophila mechanosensory (ms) neurons. We extended the imaging analysis to the ultrastructural level by developing a protocol for correlative light and 3D electron microscopy (3D CLEM). We show that in ms neurons, synaptic puncta revealed by genetically encoded markers serve as a reliable indicator of individual active zones. Block-face scanning electron microscopy analysis of ms axons revealed T-bar-shaped dense bodies and other characteristic ultrastructural features of CNS synapses. For a mechanistic analysis, we directly combined the single-neuron labeling approach with cell-specific gene disruption techniques. In proof-of-principle experiments we found evidence for a highly similar requirement for the scaffolding molecule Liprin-? and its interactors Lar and DSyd-1 (RhoGAP100F) in synaptic vesicle recruitment. This suggests that these important synapse regulators might serve a shared role at presynaptic sites within the CNS. In principle, our CLEM approach is broadly applicable to the developmental and ultrastructural analysis of any cell type that can be targeted with genetically encoded markers. PMID:25503410

Urwyler, Olivier; Izadifar, Azadeh; Dascenco, Dan; Petrovic, Milan; He, Haihuai; Ayaz, Derya; Kremer, Anna; Lippens, Saskia; Baatsen, Pieter; Guérin, Christopher J; Schmucker, Dietmar

2015-01-15

165

Isolation of Mutations in the Drosophila Homologues of the Human Neurofibromatosis 2 and Yeast Cdc42 Genes Using a Simple and Efficient Reverse-Genetic Method  

PubMed Central

Reverse genetic analysis in Drosophila has been greatly aided by a growing collection of lethal P transposable element insertions that provide molecular tags for the identification of essential genetic loci. However, because the screens performed to date primarily have generated autosomal P-element insertions, this collection has not been as useful for performing reverse genetic analysis of X-linked genes. We have designed a reverse genetic screen that takes advantage of the hemizygosity of the X chromosome in males together with a cosmid-based transgene that serves as an autosomally linked duplication of a small region of the X chromosome. The efficacy and efficiency of this method is demonstrated by the isolation of mutations in Drosophila homologues of two well-studied genes, the human Neurofibromatosis 2 tumor suppressor and the yeast CDC42 gene. The method we describe should be of general utility for the isolation of mutations in other X-linked genes, and should also provide an efficient method for the isolation of new alleles of existing X-linked or autosomal mutations in Drosophila. PMID:9136014

Fehon, R. G.; Oren, T.; LaJeunesse, D. R.; Melby, T. E.; McCartney, B. M.

1997-01-01

166

Protective efficacy of a high-growth reassortant swine H3N2 inactivated vaccine constructed by reverse genetic manipulation.  

PubMed

Novel reassortant H3N2 swine influenza viruses (SwIV) with the matrix gene from the 2009 H1N1 pandemic virus have been isolated in many countries as well as during outbreaks in multiple states in the United States, indicating that H3N2 SwIV might be a potential threat to public health. Since southern China is the world's largest producer of pigs, efficient vaccines should be developed to prevent pigs from acquiring H3N2 subtype SwIV infections, and thus limit the possibility of SwIV infection at agricultural fairs. In this study, a high-growth reassortant virus (GD/PR8) was generated by plasmid-based reverse genetics and tested as a candidate inactivated vaccine. The protective efficacy of this vaccine was evaluated in mice by challenging them with another H3N2 SwIV isolate [A/Swine/Heilongjiang/1/05 (H3N2) (HLJ/05)]. Prime and booster inoculation with GD/PR8 vaccine yielded high-titer serum hemagglutination inhibiting antibodies and IgG antibodies. Complete protection of mice against H3N2 SwIV was observed, with significantly reduced lung lesion and viral loads in vaccine-inoculated mice relative to mock-vaccinated controls. These results suggest that the GD/PR8 vaccine may serve as a promising candidate for rapid intervention of H3N2 SwIV outbreaks in China. PMID:24675833

Wen, Feng; Ma, Ji-Hong; Yu, Hai; Yang, Fu-Ru; Huang, Meng; Zhou, Yan-Jun; Li, Ze-Jun; Tong, Guang-Zhi

2014-01-01

167

Protective efficacy of a high-growth reassortant swine H3N2 inactivated vaccine constructed by reverse genetic manipulation  

PubMed Central

Novel reassortant H3N2 swine influenza viruses (SwIV) with the matrix gene from the 2009 H1N1 pandemic virus have been isolated in many countries as well as during outbreaks in multiple states in the United States, indicating that H3N2 SwIV might be a potential threat to public health. Since southern China is the world's largest producer of pigs, efficient vaccines should be developed to prevent pigs from acquiring H3N2 subtype SwIV infections, and thus limit the possibility of SwIV infection at agricultural fairs. In this study, a high-growth reassortant virus (GD/PR8) was generated by plasmid-based reverse genetics and tested as a candidate inactivated vaccine. The protective efficacy of this vaccine was evaluated in mice by challenging them with another H3N2 SwIV isolate [A/Swine/Heilongjiang/1/05 (H3N2) (HLJ/05)]. Prime and booster inoculation with GD/PR8 vaccine yielded high-titer serum hemagglutination inhibiting antibodies and IgG antibodies. Complete protection of mice against H3N2 SwIV was observed, with significantly reduced lung lesion and viral loads in vaccine-inoculated mice relative to mock-vaccinated controls. These results suggest that the GD/PR8 vaccine may serve as a promising candidate for rapid intervention of H3N2 SwIV outbreaks in China. PMID:24675833

Wen, Feng; Ma, Ji-Hong; Yang, Fu-Ru; Huang, Meng; Zhou, Yan-Jun; Li, Ze-Jun

2014-01-01

168

Reverse genetic morpholino approach using cardiac ventricular injection to transfect multiple difficult-to-target tissues in the zebrafish larva.  

PubMed

The zebrafish is an important model to understand the cell and molecular biology of organ and appendage regeneration. However, molecular strategies to employ reverse genetics have not yet been adequately developed to assess gene function in regeneration or tissue homeostasis during larval stages after zebrafish embryogenesis, and several tissues within the zebrafish larva are difficult to target. Intraventricular injections of gene-specific morpholinos offer an alternative method for the current inability to genomically target zebrafish genes in a temporally controlled manner at these stages. This method allows for complete dispersion and subsequent incorporation of the morpholino into various tissues throughout the body, including structures that were formerly impossible to reach such as those in the larval caudal fin, a structure often used to noninvasively research tissue regeneration. Several genes activated during larval finfold regeneration are also present in regenerating adult vertebrate tissues, so the larva is a useful model to understand regeneration in adults. This morpholino dispersion method allows for the quick and easy identification of genes required for the regeneration of larval tissues as well as other physiological phenomena regulating tissue homeostasis after embryogenesis. Therefore, this delivery method provides a currently needed strategy for temporal control to the evaluation of gene function after embryogenesis.  PMID:24961304

Konantz, Judith; Antos, Christopher L

2014-01-01

169

Ultrasonic beam focusing through tissue inhomogeneities with a time reversal mirror: application to transskull therapy  

Microsoft Academic Search

Time reversal of ultrasonic fields allows a very efficient approach to focus pulsed ultrasonic waves through lossless inhomogeneous media. Time reversal mirrors (TRMs) are made of large transducer arrays, allowing the incident field to be sampled, time reversed, and reemitted. Time reversal method corrects for phase, amplitude, and even shape aberration and thus, is more efficient than time shift compensation

Jean-Louis Thomas; Mathias A. Fink

1996-01-01

170

Molecular and reverse genetic characterization of NUCLEOSOME ASSEMBLY PROTEIN1 ( NAP1 ) genes unravels their function in transcription and nucleotide excision repair in Arabidopsis thaliana  

Microsoft Academic Search

SUMMARY Compared with the well-studied biochemical function of NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) as a histone chaperone in nucleosome assembly\\/disassembly, the physiological roles of NAP1 remain largely uncharacterized. Here, we define the NAP1 gene family members in Arabidopsis, examine their molecular properties, and use reverse genetics to characterize their biological roles. We show that the four AtNAP1-group proteins can form homodimers

Ziqiang Liu; Yan Zhu; Juan Gao; Fang Yu; Aiwu Dong; Wen-Hui Shen

2009-01-01

171

Two applications of time reversal mirrors: seismic radio and seismic radar.  

PubMed

Two seismic applications of time reversal mirrors (TRMs) are introduced and tested with field experiments. The first one is sending, receiving, and decoding coded messages similar to a radio except seismic waves are used. The second one is, similar to radar surveillance, detecting and tracking a moving object(s) in a remote area, including the determination of the objects speed of movement. Both applications require the prior recording of calibration Green's functions in the area of interest. This reference Green's function will be used as a codebook to decrypt the coded message in the first application and as a moving sensor for the second application. Field tests show that seismic radar can detect the moving coordinates (x(t), y(t), z(t)) of a person running through a calibration site. This information also allows for a calculation of his velocity as a function of location. Results with the seismic radio are successful in seismically detecting and decoding coded pulses produced by a hammer. Both seismic radio and radar are highly robust to signals in high noise environments due to the super-stacking property of TRMs. PMID:21973353

Hanafy, Sherif M; Schuster, Gerard T

2011-10-01

172

Reverse boundary layer capacitor model in glass/ceramic composites for energy storage applications  

NASA Astrophysics Data System (ADS)

Reverse boundary layer capacitor (RBLC) configuration model, where the grain boundary has a higher electrical conductivity than the grain, is proposed in glass/ceramic composites for dielectric energy storage applications. By introducing glass additives as grain boundaries with electrical conductivity higher than ceramic grains, the steady electric field across grains can be larger than grain boundaries as desired due to the conductivity difference. The breakdown field is thus expected to increase in the RBLC-type brick wall model because of the field distribution. The equivalent circuit, grain boundary conductivity dependence of energy density, low-loss frequency range of the RBLC model are discussed. The simulation results suggest that the RBLC approach has advantages in overall energy density, compared with normal insulating glass phase composites.

Wei, Xiaoyong; Yan, Haixue; Wang, Tong; Hu, Qingyuan; Viola, G.; Grasso, Salvatore; Jiang, Qinghui; Jin, Li; Xu, Zhuo; Reece, Michael J.

2013-01-01

173

Investigation on application of genetic algorithms to optimal reactive power dispatch of power systems  

NASA Astrophysics Data System (ADS)

A primary investigation into application of genetic algorithms in optimal reactive power dispatch and voltage control is presented. The application was achieved, based on (the United Kingdom) National Grid 48 bus network model, using a novel genetic search approach. Simulation results, compared with that obtained using nonlinear programming methods, are included to show the potential of applications of the genetic search methodology in power system economical and secure operations.

Wu, Q. H.; Ma, J. T.

1993-09-01

174

Nonlinear acoustics in underwater and biomedical applications: Array performance degradation and time reversal invariance  

NASA Astrophysics Data System (ADS)

This dissertation describes a model for acoustic propagation in inhomogeneous fluids, and explores the focusing by arrays onto targets under various conditions. The work explores the use of arrays, in particular the time reversal array, for underwater and biomedical applications. Aspects of propagation and phasing which can lead to reduced focusing effectiveness are described. An acoustic wave equation was derived for the propagation of finite-amplitude waves in lossy time-varying inhomogeneous fluid media. The equation was solved numerically in both Cartesian and cylindrical geometries using the finite-difference time-domain (FDTD) method. It was found that time reversal arrays are sensitive to several debilitating factors. Focusing ability was determined to be adequate in the presence of temporal jitter in the time reversed signal only up to about one- sixth of a period. Thermoviscous absorption also had a debilitating effect on focal pressure for both linear and nonlinear propagation. It was also found that nonlinearity leads to degradation of focal pressure through amplification of the received signal at the array, and enhanced absorption in the shocked waveforms. This dissertation also examined the heating effects of focused ultrasound in a tissue-like medium. The application considered is therapeutic heating for hyperthermia. The acoustic model and a thermal model for tissue were coupled to solve for transient and steady temperature profiles in tissue-like media. The Pennes bioheat equation was solved using the FDTD method to calculate the temperature fields in tissue-like media from focused acoustic sources. It was found that the temperature-dependence of the medium's background properties can play an important role in the temperature predictions. Finite-amplitude effects contributed excess heat when source conditions were provided for nonlinear effects to manifest themselves. The effect of medium heterogeneity was also found to be important in redistributing the acoustic and temperature fields, creating regions with hotter and colder temperatures than the mean by local scattering and lensing action. These temperature excursions from the mean were found to increase monotonically with increasing contrast in the medium's properties.

Hallaj, Ibrahim M.

175

Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis  

PubMed Central

Mobile group II introns are bacterial retrotransposons that combine the activities of an autocatalytic intron RNA (a ribozyme) and an intron-encoded reverse transcriptase to insert site-specifically into DNA. They recognize DNA target sites largely by base pairing of sequences within the intron RNA and achieve high DNA target specificity by using the ribozyme active site to couple correct base pairing to RNA-catalyzed intron integration. Algorithms have been developed to program the DNA target site specificity of several mobile group II introns, allowing them to be made into ‘targetrons.’ Targetrons function for gene targeting in a wide variety of bacteria and typically integrate at efficiencies high enough to be screened easily by colony PCR, without the need for selectable markers. Targetrons have found wide application in microbiological research, enabling gene targeting and genetic engineering of bacteria that had been intractable to other methods. Recently, a thermostable targetron has been developed for use in bacterial thermophiles, and new methods have been developed for using targetrons to position recombinase recognition sites, enabling large-scale genome-editing operations, such as deletions, inversions, insertions, and ‘cut-and-pastes’ (that is, translocation of large DNA segments), in a wide range of bacteria at high efficiency. Using targetrons in eukaryotes presents challenges due to the difficulties of nuclear localization and sub-optimal magnesium concentrations, although supplementation with magnesium can increase integration efficiency, and directed evolution is being employed to overcome these barriers. Finally, spurred by new methods for expressing group II intron reverse transcriptases that yield large amounts of highly active protein, thermostable group II intron reverse transcriptases from bacterial thermophiles are being used as research tools for a variety of applications, including qRT-PCR and next-generation RNA sequencing (RNA-seq). The high processivity and fidelity of group II intron reverse transcriptases along with their novel template-switching activity, which can directly link RNA-seq adaptor sequences to cDNAs during reverse transcription, open new approaches for RNA-seq and the identification and profiling of non-coding RNAs, with potentially wide applications in research and biotechnology. PMID:24410776

2014-01-01

176

Engineering Applications of Artificial Intelligence 13 (2000) 611623 Genetic adaptive state estimation$  

E-print Network

Engineering Applications of Artificial Intelligence 13 (2000) 611­623 Genetic adaptive state in a nonlinear jet engine. Our main conclusion is that the genetic adaptive state estimator has the potential Ltd. All rights reserved. Keywords: Estimation; Genetic algorithms; Jet engine surge=stall control 1

177

Recently Available Techniques Applicable to Genetic Problems in the Middle East  

Microsoft Academic Search

In this paper, we address the preventive health aspects of genetic problems in the Middle East and provide guidelines to prioritize preventive strategies. Applications of various novel genetic techniques such as comprehensive neonatal screening, high throughput heterozygote detection, preimplantation genetic diagnosis, Affymetrix systems, the NanoChip system and a new way of sensitive karyotyping for single-cell chromosome abnormalities are discussed. In

Pinar T. Ozand; Ali Al Odaib; Nadia Sakati; Ali M. Al-Hellani

2005-01-01

178

The Tricentennial People: Human Applications of the New Genetics.  

ERIC Educational Resources Information Center

This symposium focused on the social, political, and ethical implications of the current trends in genetic research. Four papers are presented here along with transcripts of the accompanying discussions. The topics include: (1) genetics and the biological basis of the human condition; (2) the pros and cons of genetic counseling; (3) genetics and…

Neumann, Marguerite, Ed.

179

The multi-niche crowding genetic algorithm: Analysis and applications  

SciTech Connect

The ability of organisms to evolve and adapt to the environment has provided mother nature with a rich and diverse set of species. Only organisms well adapted to their environment can survive from one generation to the next, transferring on the traits, that made them successful, to their offspring. Competition for resources and the ever changing environment drives some species to extinction and at the same time others evolve to maintain the delicate balance in nature. In this disertation we present the multi-niche crowding genetic algorithm, a computational metaphor to the survival of species in ecological niches in the face of competition. The multi-niche crowding genetic algorithm maintains stable subpopulations of solutions in multiple niches in multimodal landscapes. The algorithm introduces the concept of crowding selection to promote mating among members with qirnilar traits while allowing many members of the population to participate in mating. The algorithm uses worst among most similar replacement policy to promote competition among members with similar traits while allowing competition among members of different niches as well. We present empirical and theoretical results for the success of the multiniche crowding genetic algorithm for multimodal function optimization. The properties of the algorithm using different parameters are examined. We test the performance of the algorithm on problems of DNA Mapping, Aquifer Management, and the File Design Problem. Applications that combine the use of heuristics and special operators to solve problems in the areas of combinatorial optimization, grouping, and multi-objective optimization. We conclude by presenting the advantages and disadvantages of the algorithm and describing avenues for future investigation to answer other questions raised by this study.

Cedeno, W.

1995-09-01

180

Ormosil approach toward developing a completely reversible hydrogen sensor for aerospace applications  

NASA Astrophysics Data System (ADS)

Optical hydrogen sensors are intrinsically safe since they produce no arc or spark in an explosive environment caused by the leakage of hydrogen. Safety remains a top priority since leakage of hydrogen in air during production, storage, transfer and distribution creates an explosive atmosphere for concentrations between 4% (v/v) - the lower explosive limit (LEL) and 74.5% (v/v) - the upper explosive limit (UEL) at room temperature and pressure. Being a very small molecule, hydrogen is prone to leakage through seals and micro-cracks. Hydrogen detection in space application is very challenging; public acceptance of hydrogen fuel would require the integration of a reliable hydrogen safety sensor. For detecting leakage of cryogenic fluids in spaceport facilities, Launch vehicle industry and NASA are currently relying heavily on the bulky mass spectrometers, which fill one or more equipment racks, and weigh several hundred kilograms. An optical sensor system can decrease pay load while monitoring multiple leak locations in situ and in real time. In this paper design of ormsoil approach for developing a completely reversible optical hydrogen sensors for aerospace application is being discussed.

Kazemi, Alex A.; Goswami, Kisholoy; Sampathkumaran, Uma

2006-08-01

181

Innovative Applications of Genetic Algorithms to Problems in Accelerator Physics  

SciTech Connect

The genetic algorithm (GA) is a relatively new technique that implements the principles nature uses in biological evolution in order to optimize a multidimensional nonlinear problem. The GA works especially well for problems with a large number of local extrema, where traditional methods (such as conjugate gradient, steepest descent, and others) fail or, at best, underperform. The field of accelerator physics, among others, abounds with problems which lend themselves to optimization via GAs. In this paper, we report on the successful application of GAs in several problems related to the existing CEBAF facility, the proposed MEIC at Jefferson Lab, and a radio frequency (RF) gun based injector. These encouraging results are a step forward in optimizing accelerator design and provide an impetus for application of GAs to other problems in the field. To that end, we discuss the details of the GAs used, including a newly devised enhancement, which leads to improved convergence to the optimum and make recommendations for future GA developments and accelerator applications.

Hofler, Alicia [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Terzic, Balsa [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States) and Old Dominion University, Norfolk, VA (United States); Kramer, Matthew [University of California, Berkeley, CA (United States); Zvezdin, Anton [Stony Brook University, Stony Brook, NY (United States); Morozov, Vasiliy [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Roblin, Yves [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Lin, Fanglei [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Jarvis, Colin [Macalester College, Saint Paul, MN (United States)

2013-01-01

182

Programmable genetic algorithm IP core for sensing and surveillance applications  

NASA Astrophysics Data System (ADS)

Real-time evolvable systems are possible with a hardware implementation of Genetic Algorithms (GA). We report the design of an IP core that implements a general purpose GA engine which has been successfully synthesized and verified on a Xilinx Virtex II Pro FPGA Device (XC2VP30). The placed and routed IP core has an area utilization of only 13% and clock speed of 50MHz. The GA core can be customized in terms of the population size, number of generations, cross-over and mutation rates, and the random number generator seed. The GA engine can be tailored to a given application by interfacing with the application specific fitness evaluation module as well as the required storage memory (to store the current and new populations). The core is soft in nature i.e., a gate-level netlist is provided which can be readily integrated with the user's system. The GA IP core can be readily used in FPGA based platforms for space and military applications (for e.g., surveillance, target tracking). The main advantages of the IP core are its programmability, small footprint, and low power consumption. Examples of concept systems in sensing and surveillance domains will be presented.

Katkoori, Srinivas; Fernando, Pradeep; Sankaran, Hariharan; Stoica, Adrian; Keymeulen, Didier; Zebulum, Ricardo

2009-05-01

183

Innovative applications of genetic algorithms to problems in accelerator physics  

NASA Astrophysics Data System (ADS)

The genetic algorithm (GA) is a powerful technique that implements the principles nature uses in biological evolution to optimize a multidimensional nonlinear problem. The GA works especially well for problems with a large number of local extrema, where traditional methods (such as conjugate gradient, steepest descent, and others) fail or, at best, underperform. The field of accelerator physics, among others, abounds with problems which lend themselves to optimization via GAs. In this paper, we report on the successful application of GAs in several problems related to the existing Continuous Electron Beam Accelerator Facility nuclear physics machine, the proposed Medium-energy Electron-Ion Collider at Jefferson Lab, and a radio frequency gun-based injector. These encouraging results are a step forward in optimizing accelerator design and provide an impetus for application of GAs to other problems in the field. To that end, we discuss the details of the GAs used, include a newly devised enhancement which leads to improved convergence to the optimum, and make recommendations for future GA developments and accelerator applications.

Hofler, Alicia; Terzi?, Balša; Kramer, Matthew; Zvezdin, Anton; Morozov, Vasiliy; Roblin, Yves; Lin, Fanglei; Jarvis, Colin

2013-01-01

184

Gene-Assisted Selection Applications of Association Genetics for Forest Tree Breeding  

Microsoft Academic Search

SUMMARY This chapter describes application of association genetics in forest tree species for the purposes of selection. We use the term gene-assisted selection (GAS) to denote application of marker–trait associations determined via association genetics, which we anticipate will be based on polymorphisms associated with expressed genes. The salient features of forest trees are reviewed, including existing and somewhat limited knowledge

Phillip L. Wilcox; Craig E. Echt; Rowland D. Burdon

185

Polarization Reversal Over Flooded Regions and Applications to Large-Scale Flood Mapping with Spaceborne Scatterometers  

NASA Technical Reports Server (NTRS)

We present the polarization reversal in backscatter over flooded land regions, and demonstrate for the first time the utility of spaceborne Ku-band scatterometer for large-scale flood mapping. Scatterometer data were collected over the globe by the NASA Scatterometer (NSCAT) operated at 14 GHz on the Japanese ADEOS spacecraft from September 1996 to June 1997. During this time span, several severe floods occurred. Over most land surface, vertical polarization backscatter (Sigma(sub upsilon(upsilon)) is larger than horizontal polarization backscatter (sigma(sub hh)). Such polarization characteristics is reversed and sigma(sub upsilon(upsilon)) is smaller than sigma(sub hh) over flooded regions, except under a dense forest canopy. The total backscatter from the flooded landscape consists of direct backscatter and boundary-interaction backscatter. The direct term is contributed by direct backscattering from objects protruding above the water surface, and by backscattering from waves on the water surface. The boundary-interaction term is contributed by the forward scattering from the protruding objects and then reflected from the water surface, and also by the forward scattering from these objects after the water-surface reflection. Over flooded regions, the boundary-interaction term is dominant at large incidence angles and the strong water-surface reflection is much larger for horizontal polarization than the vertical one due to the Brewster effect in transverse-magnetic waves. These scattering mechanisms cause the polarization reversal over flooded regions. An example obtained with the Analytic Wave Theory is used to illustrate the scattering mechanisms leading to the polarization reversal. We then demonstrate the utility of spaceborne Ku-band scatterometer for large-scale flood mapping. We process NSCAT data to obtain the polarization ratio sigma(sub hh)/sigma(sub upsilon(upsilon)) with colocated data at incidence angles larger than 40 deg. The results over Asian summer monsoon regions in September-October 1996 indicate flooded areas in many countries such as Bangladesh, India, Lao, Vietnam, Cambodia, and China. Reports documented by the United Nation Department of Humanitarian Affairs (now called UN Office for the Coordination of Humanitarian Affairs) show loss of many lives and severe flood related damages which affected many million people in the corresponding flooded areas. We also map the NSCAT polarization ratio over the same regions in the "dry season" in January 1997 as a reference to confirm our results. Furthermore, we obtain concurrent ocean wind fields also derived from NSCAT data, and Asia topographic data (USGS GTOPO30) to investigate the flooded area. The results show that winds during summer monsoon season blowing inland, which perplex flood problems. Overlaying the topographic map over NSCAT results reveals an excellent correspondence between the confinement of flooded area within the relevant topographic features, which very well illustrates the value of topographic wetness index. Finally, we discuss the applications of future spaceborne scatterometers, including QuikSCAT and Seawinds, for flood mapping over the globe.

Nghiem, Son V.; Liu, W. Timothy; Xie, Xiao-Su

1999-01-01

186

Noise of model target type thrust reversers for engine-over-the-wing applications  

NASA Technical Reports Server (NTRS)

The present work reports on experiments concerning the noise generated by V-gutter and semicylindrical target reversers with circular and short-aspect-ratio slot nozzles having equivalent diameters of about 5 cm. At subsonic jet velocities of interest for engine-over-the-wing (OTW) powered-lift aircraft, the reversers were noisier than the nozzles alone and had a more uniform directional distribution and more high-frequency noise. Reverser shape was more important than nozzle shape in determining the reverser noise characteristics. An estimate is made of perceived noise level along the 152-m sideline for a hypothetical OTW powered-lift airplane.

Stone, J. R.; Gutierrez, O. A.

1974-01-01

187

Controlled reversal of Co/Pt Dots for nanomagnetic logic applications  

SciTech Connect

Domain reversal in perpendicular multilayer films is governed by an intrinsic distribution of anisotropy. However, control of the switching field distribution (SFD) of field-coupled, single domain Co/Pt dots is the key to building large integrated systems for nanomagnetic logic applications. In this work, partial Ga{sup +} focused ion beam (FIB) irradiation of single-domain Co/Pt dots is employed which locally reduces the anisotropy and renders the film-inherent SFD ineffective. Controlled reduction in the switching field compared to non-irradiated dots is achieved, depending on size and dose of irradiation. TEM images of an as-grown and irradiated Co/Pt stack show a change in morphology from distinct Co/Pt interfaces to intermixed and randomly oriented grains due to the Ga{sup +} ion impact. The presented method is highly suitable to control the switching behavior in field-coupled logic devices. Experimental results are used to demonstrate a nanomagnetic fanout operation.

Breitkreutz, Stephan; Kiermaier, Josef; Schmitt-Landsiedel, Doris; Becherer, Markus [Lehrstuhl fuer Technische Elektronik, Technische Universitaet Muenchen, Arcisstrasse 21, 80333 Munich (Germany); Vijay Karthik, Sankar; Csaba, Gyorgy [Center for Nano Science and Technology, University of Notre Dame, Notre Dame, Indiana 46556 (United States)

2012-04-01

188

Reversal of an acute parkinsonian syndrome associated with multiple sclerosis by application of weak electromagnetic fields.  

PubMed

The occurrence of movement disorders and particularly Parkinsonian symptoms is uncommon in patients with multiple sclerosis (MS) despite the rather frequent presence of demyelinating plaques in the basal ganglia. This disparity between the occurrence of clinical symptoms in MS and the distribution of demyelinating plaques suggests that impairment of neurotransmitter functions rather than demyelination may be critical to the clinical manifestations of the disease. A 48 year old woman with remitting-progressive MS developed a bilateral Parkinsonian syndrome in association with acute emotional stress which resolved after she received two brief successive extracerebral applications of low frequency picotesla flux density electromagnetic fields (EMFs). It is believed that in this patient Parkinsonism may have existed in a subclinical form and that acute stress, which previously has been shown to precipitate symptoms of Parkinson's disease, triggered the onset of Parkinsonism by further reducing dopaminergic and serotonergic neurotransmission in the basal ganglia. The rapid reversal of the Parkinsonian syndrome by EMFs was related to a presumed augmentation of dopaminergic and serotonergic neurotransmission which, on the basis of CSF studies, is reduced in chronic MS patients. The efficacy of EMFs in the treatment of Parkinson's disease had been documented previously but this report demonstrates that this treatment modality is beneficial also for the treatment of Parkinsonism developing in the setting of other neurodegenerative disorders. PMID:8828058

Sandyk, R

1996-07-01

189

Genetics  

MedlinePLUS

... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

190

Application of a hybrid model of neural networks and genetic algorithms to evaluate landslide susceptibility  

NASA Astrophysics Data System (ADS)

In the last few decades, the development of Geographical Information Systems (GIS) technology has provided a method for the evaluation of landslide susceptibility and hazard. Slope units were found to be appropriate for the fundamental morphological elements in landslide susceptibility evaluation. Following the DEM construction in a loess area susceptible to landslides, the direct-reverse DEM technology was employed to generate 216 slope units in the studied area. After a detailed investigation, the landslide inventory was mapped in which 39 landslides, including paleo-landslides, old landslides and recent landslides, were present. Of the 216 slope units, 123 involved landslides. To analyze the mechanism of these landslides, six environmental factors were selected to evaluate landslide occurrence: slope angle, aspect, the height and shape of the slope, distance to river and human activities. These factors were extracted in terms of the slope unit within the ArcGIS software. The spatial analysis demonstrates that most of the landslides are located on convex slopes at an elevation of 100-150 m with slope angles from 135°-225° and 40°-60°. Landslide occurrence was then checked according to these environmental factors using an artificial neural network with back propagation, optimized by genetic algorithms. A dataset of 120 slope units was chosen for training the neural network model, i.e., 80 units with landslide presence and 40 units without landslide presence. The parameters of genetic algorithms and neural networks were then set: population size of 100, crossover probability of 0.65, mutation probability of 0.01, momentum factor of 0.60, learning rate of 0.7, max learning number of 10 000, and target error of 0.000001. After training on the datasets, the susceptibility of landslides was mapped for the land-use plan and hazard mitigation. Comparing the susceptibility map with landslide inventory, it was noted that the prediction accuracy of landslide occurrence is 93.02%, whereas units without landslide occurrence are predicted with an accuracy of 81.13%. To sum up, the verification shows satisfactory agreement with an accuracy of 86.46% between the susceptibility map and the landslide locations. In the landslide susceptibility assessment, ten new slopes were predicted to show potential for failure, which can be confirmed by the engineering geological conditions of these slopes. It was also observed that some disadvantages could be overcome in the application of the neural networks with back propagation, for example, the low convergence rate and local minimum, after the network was optimized using genetic algorithms. To conclude, neural networks with back propagation that are optimized by genetic algorithms are an effective method to predict landslide susceptibility with high accuracy.

Wang, H. B.; Li, J. W.; Zhou, B.; Yuan, Z. Q.; Chen, Y. P.

2013-03-01

191

Genetic Applications of an Inverse Polymerase Chain Reaction  

Microsoft Academic Search

A method is presented for the rapid in vitro amplification of DNA sequences that flank a region of known sequence. The method uses the polymerase chain reaction (PCR), but it has the primers oriented in the reverse direction of the usual orientation. The template for the reverse primers is a restriction fragment that has been ligated upon itself to form

Howard Ochman; Anne S. Gerber; Daniel L. Hart

192

Genetics and psychiatry: a proposal for the application of the precautionary principle.  

PubMed

The paper suggests an application of the precautionary principle to the use of genetics in psychiatry focusing on scientific uncertainty. Different levels of uncertainty are taken into consideration--from the acknowledgement that the genetic paradigm is only one of the possible ways to explain psychiatric disorders, via the difficulties related to the diagnostic path and genetic methods, to the value of the results of studies carried out in this field. Considering those uncertainties, some measures for the use of genetics in psychiatry are suggested. Some of those measures are related to the conceptual limits of the genetic paradigm; others are related to present knowledge and should be re-evaluated. PMID:22460929

Porteri, Corinna

2013-08-01

193

Thermally responsive polymer systems for self-healing, reversible adhesion and shape memory applications  

NASA Astrophysics Data System (ADS)

Responsive polymers are "smart" materials that are capable of performing prescribed, dynamic functions under an applied stimulus. In this dissertation, we explore several novel design strategies to develop thermally responsive polymers and polymer composites for self-healing, reversible adhesion and shape memory applications. In the first case described in Chapters 2 and 3, a thermally triggered self-healing material was prepared by blending a high-temperature epoxy resin with a thermoplastic polymer, poly(epsilon-caprolactone) (PCL). The initially miscible system undergoes polymerization induced phase separation (PIPS) during the curing of epoxy and yields a variety of compositionally dependent morphologies. At a particular PCL loading, the cured blend displays a "bricks-and-mortar" morphology in which epoxy exists as interconnected spheres ("bricks") within a continuous PCL matrix ("mortar"). A heat induced "bleeding" phenomenon was observed in the form of spontaneous wetting of all free surfaces by the molten PCL, and is attributed to the volumetric thermal expansion of PCL above its melting point in excess of epoxy brick expansion, which we term differential expansive bleeding (DEB). This DEB is capable of healing damage such as cracks. In controlled self-healing experiments, heating of a cracked specimen led to PCL bleeding from the bulk that yields a liquid layer bridging the crack gap. Upon cooling, a "scar" composed of PCL crystals was formed at the site of the crack, restoring a significant portion of mechanical strength. We further utilized DEB to enable strong and thermally-reversible adhesion of the material to itself and to metallic substrates, without any requirement for macroscopic softening or flow. After that, Chapters 4--6 present a novel composite strategy for the design and fabrication of shape memory polymer composites. The basic approach involves physically combining two or more functional components into an interpenetrating fiber/matrix structure, allowing them to function in a synergistic fashion yet remain physically separated. This latter aspect is critical since it enables the control of overall composite properties and functions by separately tuning each component. Utilizing the intrinsic versatility of this approach, composites with novel properties and functions (in addition to "regular" shape memory) have been developed, including (1) shape memory elastomeric composites (SMECs; Chapter 4), (2) triple-shape polymeric composites (TSPCs; Chapter 5), and (3) electrically conductive nanocomposites (Chapter 6). Then in Chapter 7, by combining the success in both thermoplastic based self-healing and shape memory polymer composites, we demonstrate a thermally triggered self-healing coating. This coating features a unique "shape memory assisted self-healing" mechanism in which crack closure (via shape memory) and crack re-bonding (via melting and diffusion of the thermoplastic healing agent) are achieved simultaneously upon a single heating step, leading to both structural and functional (corrosion resistance) recovery. Finally, Chapter 8 presents for the first time the preparation of functionally graded shape memory polymers (SMPs) that, unlike conventional SMPs, have a range of glass transition temperatures that are spatially graded. This was achieved using a temperature gradient curing method that imposes different vitrification limits at different positions along the gradient. The resulting material is capable of responding to a wide range of thermal triggers and a good candidate for low-cost, material based temperature sensors. All the aforementioned materials and methods show great potential for practical applications due to their high performance, low cost and broad applicability. Some recommendations for future research and development are given in Chapter 9.

Luo, Xiaofan

194

Detection of genetically modified crops using multiplex asymmetric polymerase chain reaction and asymmetric hyperbranched rolling circle amplification coupled with reverse dot blot.  

PubMed

To meet the ever-increasing demand for detection of genetically modified crops (GMCs), low-cost, high-throughput and high-accuracy detection assays are needed. The new multiplex asymmetric polymerase chain reaction and asymmetric hyper-branched rolling circle amplification coupled with reverse dot blot (RDB) systems were developed to detect GMCs. Thirteen oligonucleotide probes were designed to identify endogenous targets (Lec1, Hmg and Sad1), event-specific targets (RRS-5C, RRS-3C, Bt176-3C and MON810-3C), screening targets (35S promoter and NOS terminator), and control targets (18S and PLX). Optimised conditions were as follows: tailed hybridization probes (1-2 pmol/l) were immobilized on a membrane by baking for 2h, and a 10:1 ratio of forward to reverse primers was used. The detection limits were 0.1 ?g/l of 2% RRS and 0.5 ng/l of DNA from genetically modified (GM) soybean. These results indicate that the RDB assay could be used to detect multiplex target genes of GMCs rapidly and inexpensively. PMID:25466120

Wang, Xiumin; Teng, Da; Guan, Qingfeng; Tian, Fang; Wang, Jianhua

2015-04-15

195

Designing a Multistage Supply Chain in Cross-Stage Reverse Logistics Environments: Application of Particle Swarm Optimization Algorithms  

PubMed Central

This study designed a cross-stage reverse logistics course for defective products so that damaged products generated in downstream partners can be directly returned to upstream partners throughout the stages of a supply chain for rework and maintenance. To solve this reverse supply chain design problem, an optimal cross-stage reverse logistics mathematical model was developed. In addition, we developed a genetic algorithm (GA) and three particle swarm optimization (PSO) algorithms: the inertia weight method (PSOA_IWM), VMax method (PSOA_VMM), and constriction factor method (PSOA_CFM), which we employed to find solutions to support this mathematical model. Finally, a real case and five simulative cases with different scopes were used to compare the execution times, convergence times, and objective function values of the four algorithms used to validate the model proposed in this study. Regarding system execution time, the GA consumed more time than the other three PSOs did. Regarding objective function value, the GA, PSOA_IWM, and PSOA_CFM could obtain a lower convergence value than PSOA_VMM could. Finally, PSOA_IWM demonstrated a faster convergence speed than PSOA_VMM, PSOA_CFM, and the GA did. PMID:24772026

Chiang, Tzu-An; Che, Z. H.

2014-01-01

196

Designing a multistage supply chain in cross-stage reverse logistics environments: application of particle swarm optimization algorithms.  

PubMed

This study designed a cross-stage reverse logistics course for defective products so that damaged products generated in downstream partners can be directly returned to upstream partners throughout the stages of a supply chain for rework and maintenance. To solve this reverse supply chain design problem, an optimal cross-stage reverse logistics mathematical model was developed. In addition, we developed a genetic algorithm (GA) and three particle swarm optimization (PSO) algorithms: the inertia weight method (PSOA_IWM), V(Max) method (PSOA_VMM), and constriction factor method (PSOA_CFM), which we employed to find solutions to support this mathematical model. Finally, a real case and five simulative cases with different scopes were used to compare the execution times, convergence times, and objective function values of the four algorithms used to validate the model proposed in this study. Regarding system execution time, the GA consumed more time than the other three PSOs did. Regarding objective function value, the GA, PSOA_IWM, and PSOA_CFM could obtain a lower convergence value than PSOA_VMM could. Finally, PSOA_IWM demonstrated a faster convergence speed than PSOA_VMM, PSOA_CFM, and the GA did. PMID:24772026

Chiang, Tzu-An; Che, Z H; Cui, Zhihua

2014-01-01

197

Genetic mapping of the autosomal region involved in XX sex-reversal and horn development in goats  

Microsoft Academic Search

Contrary to other genetic disorders, the genetic study of sex determination anomalies in humans stumbles over the difficulty\\u000a in observing large pedigrees. In goats, abnormalities in sex determination are intimately linked to a dominant Mendelian gene\\u000a coding for the “polled” (hornless) character, which could render this species an interesting animal model for the rare human\\u000a cases of SRY-negative XX males.

D. Vaiman; O. Koutita; A. Oustry; J.-M. Elsen; E. Manfredi; M. Fellous; E. P. Cribiu

1996-01-01

198

Reverse Genetics of Escherichia coli Glycerol Kinase Allosteric Regulation and Glucose Control of Glycerol Utilization In Vivo  

Microsoft Academic Search

effectors in glucose control of both glycerol utilization and expression of the glpK gene. Genetics methods based on homologous recombination are used to place glpK alleles with known specific mutations into the chromo- somal context of the glpK gene in three different genetic backgrounds. The alleles encode glycerol kinases with normal catalytic properties and specific alterations of allosteric regulatory properties,

C. KAY HOLTMAN; AARON C. PAWLYK; NORMAN D. MEADOW; DONALD W. PETTIGREW

2001-01-01

199

A Novel Application of Time Reversed Acoustics: Salt Dome Flank Imaging Using Walkaway VSP surveys  

E-print Network

In this paper we present initial results of applying Time-Reversed Acoustics (TRA) technology to saltdome flank, seismic imaging. We created a set of synthetic traces representing a multilevel, walkaway VSP for a model ...

deHoop, Maarten V.

2006-03-01

200

A reverse osmosis treatment process for produced water: optimization, process control, and renewable energy application  

E-print Network

consumption of various process design alternatives, and to test control strategies. By preserving the mechanical energy of the concentrate stream of the reverse osmosis membrane, process energy requirements can be reduced several fold from that of the current...

Mareth, Brett

2009-06-02

201

The application of reverse tubular medial upper arm flap in the reconstruction of ripped facial defects  

PubMed Central

Reverse medial upper arm flap is usually utilized in the reconstruction of defects in soft tissues of head and facial skin and is with good clinical efficacy. However, it has not been used in the reconstruction of ripped defects. In this study, we used the reverse tubular medial upper arm flap to repair the ripped facial defects. The reverse tubular skin flap from the medial upper arm was longitudinally cut into two parts. One part was used for the reconstruction of ripped facial defects. The other part was used as inner lining to repair the defects of mucosa. Using this method, 3 patients with ripped facial defects were successfully repaired. Thus the reverse tubular medial upper arm flap was successfully used in the reconstruction of ripped facial defects with little surgical trauma, simple manipulation of the operation, increased success rate of the operation and reduced incidence of complications. PMID:25550953

Dong, Xianglin; Ma, Juan; Ma, Shaolin; Wen, Hao

2014-01-01

202

From genes to public health: the applications of genetic technology in disease prevention. Genetics Working Group.  

PubMed Central

OBJECTIVES: With advances in the Human Genome Project, the implications of genetic technology in disease prevention should be assessed. METHODS: The paradigm suggested in The Future of Public Health--assessment, policy development, and assurance--was used to examine the continuum from genetic technology to public health practice. RESULTS: First, important public health functions are to (1) assess the impact of genes and their interactions with modifiable disease risk factors on the health status of the population and (2) assess the impact and safety of genetic testing on the population. Second, given the many implications of genetic testing, the public health community should participate in policy development related to the timing and use of genetic testing in disease prevention. Third, whenever appropriate, the public health community needs to ensure the development of public health genetics programs (e.g. newborn screening) and evaluate the quality and effectiveness of the use of genetic testing in disease prevention. CONCLUSIONS: Although most current genetic tests are not ready for disease prevention, there is an important role for the public health community in translating genetic technology into disease prevention. PMID:9003127

Khoury, M J

1996-01-01

203

Reverse time migration: A seismic processing application on the connection machine  

NASA Technical Reports Server (NTRS)

The implementation of a reverse time migration algorithm on the Connection Machine, a massively parallel computer is described. Essential architectural features of this machine as well as programming concepts are presented. The data structures and parallel operations for the implementation of the reverse time migration algorithm are described. The algorithm matches the Connection Machine architecture closely and executes almost at the peak performance of this machine.

Fiebrich, Rolf-Dieter

1987-01-01

204

General architecture of a genetic regulatory network. Applications to embryologic Jacques Demongeot1  

E-print Network

General architecture of a genetic regulatory network. Applications to embryologic control Jacques architecture of a genetic regulatory network consists of strong connected components of its interaction graph.e., translational inhibitors respectively of the messenger mRNAs and of the transfer tRNAs, or by gene repressors

Paris-Sud XI, Université de

205

Comparative application of artificial neural networks and genetic algorithms for multivariate time-series modelling  

E-print Network

Comparative application of artificial neural networks and genetic algorithms for multivariate time-series of artificial neural networks and genetic algorithms in terms of forecasting and understanding of algal blooms neural networks allow seven-days-ahead predictions of timing and magnitudes of algal blooms

Fernandez, Thomas

206

Impact localization combined with haptic feedback for touch panel applications based on the time-reversal approach.  

PubMed

In this paper, a combined impact localization and haptic feedback system based on time-reversal signal processing is presented for touch panel applications. Theoretical impulse responses are derived from a propagation model of bending waves in a thin elastic plate. On the basis of the impulse responses, the time-reversal technique is exploited to spot the impact location as well as to generate haptic feedback. The chief advantage of the time-reversal technique lies in its robustness of tackling broadband sources in a reverberant environment. Piezoelectric ceramic plates and voice-coil motors are used as sensors for localization, whereas only voice-coil motors are used as the actuator for haptic feedback. Experimental results demonstrated that the proposed system was effective in precise impact localization for a thin panel, while haptic feedback also implemented using time-reversal principle can generate an impulse at the previously touched position. The combined impact localization and haptic feedback system is capable of enhancing the sensation of man-machine interaction in real time fashion. PMID:21428493

Bai, Mingsian R; Tsai, Yao Kun

2011-03-01

207

Application of genetic algorithm in broadband microstrip antenna design  

Microsoft Academic Search

Genetic algorithm is utilized in the optimization of microstrip antenna with complicated structure. A broadband single-patch microstrip patch antenna is proposed. Capacitance compensated technique and E-shaped patch are combined together to expand the bandwidth of the antenna. Genetic algorithm combined with finite element software is applied to optimize the structure of the antenna. The optimization procedure is also discussed. The

Si-Yang Sun; Ying-Hua Lu; Dong-Sheng La

2009-01-01

208

Application of improved genetic algorithm in camera calibration  

NASA Astrophysics Data System (ADS)

With the camera internal parameters known, to calculate the external parameters is to solve a set of highly nonlinear over-determined equations. In this paper, an improved hybrid genetic algorithm is adopted to obtain external parameters. It combines the advantages of genetic algorithm and Newton method, making it possible to obtain results with high accuracy and a faster convergence.

Li, Weimin; Liu, Hui; Zhu, Lichun; Zhao, Yu

2014-09-01

209

A parallel electromagnetic genetic-algorithm optimization (EGO) application for patch antenna design  

Microsoft Academic Search

In this paper, we describe an electromagnetic genetic algorithm (GA) optimization (EGO) application developed for the cluster supercomputing platform. A representative patch antenna design example for commercial wireless applications is detailed, which illustrates the versatility and applicability of the method. We show that EGO allows us to combine the accuracy of full-wave EM analysis with the robustness of GA optimization

Frank J. Villegas; Tom Cwik; Yahya Rahmat-Samii; Majid Manteghi

2004-01-01

210

Reverse Correlation in Neurophysiology  

ERIC Educational Resources Information Center

This article presents a review of reverse correlation in neurophysiology. We discuss the basis of reverse correlation in linear transducers and in spiking neurons. The application of reverse correlation to measure the receptive fields of visual neurons using white noise and m-sequences, and classical findings about spatial and color processing in…

Ringach, Dario; Shapley, Robert

2004-01-01

211

The Reverse Cholesterol Transport Pathway Improves Understanding of Genetic Networks for Fat Deposition and Muscle Growth in Beef Cattle  

Microsoft Academic Search

In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F1 bulls, 113 F1 dams, and 246 F2 progeny. A total of 37 amplicons were used to screen single nucleotide

Tyler F. Daniels; Xiao-Lin Wu; Zengxiang Pan; Jennifer J. Michal; Raymond W. Wright; Karen M. Killinger; Michael D. MacNeil; Zhihua Jiang

2010-01-01

212

Genetic particle filter application to land surface temperature downscaling  

NASA Astrophysics Data System (ADS)

Thermal infrared data are widely used for surface flux estimation giving the possibility to assess water and energy budgets through land surface temperature (LST). Many applications require both high spatial resolution (HSR) and high temporal resolution (HTR), which are not presently available from space. It is therefore necessary to develop methodologies to use the coarse spatial/high temporal resolutions LST remote-sensing products for a better monitoring of fluxes at appropriate scales. For that purpose, a data assimilation method was developed to downscale LST based on particle filtering. The basic tenet of our approach is to constrain LST dynamics simulated at both HSR and HTR, through the optimization of aggregated temperatures at the coarse observation scale. Thus, a genetic particle filter (GPF) data assimilation scheme was implemented and applied to a land surface model which simulates prior subpixel temperatures. First, the GPF downscaling scheme was tested on pseudoobservations generated in the framework of the study area landscape (Crau-Camargue, France) and climate for the year 2006. The GPF performances were evaluated against observation errors and temporal sampling. Results show that GPF outperforms prior model estimations. Finally, the GPF method was applied on Spinning Enhanced Visible and InfraRed Imager time series and evaluated against HSR data provided by an Advanced Spaceborne Thermal Emission and Reflection Radiometer image acquired on 26 July 2006. The temperatures of seven land cover classes present in the study area were estimated with root-mean-square errors less than 2.4 K which is a very promising result for downscaling LST satellite products.

Mechri, Rihab; Ottlé, Catherine; Pannekoucke, Olivier; Kallel, Abdelaziz

2014-03-01

213

Noise of model target type thrust reversers for engine-over-the-wing applications  

NASA Technical Reports Server (NTRS)

The results of experiments on the noise generated by V-gutter and semicylindrical target reversers with circular and short-aspect-ratio slot nozzles having diameters of about 5 cm are presented. The experiments were conducted with cold-flow jets at velocities from 190-290 m/sec. The reversers at subsonic jet velocities had a more uniform noise distribution and higher frequency than the nozzles alone. The reverser shape was shown to be more important than the nozzle shape in determining the noise characteristics. The maximum sideline pressure level varied with the sixth power of the jet velocity, and the data were correlated for angles along the sideline. An estimate of the noise level along the 152 m sideline for an engine-over-the-wing powered-lift airplane was made.

Stone, J. R.; Gutierrez, O. A.

1974-01-01

214

Cystic fibrosis genetics: from molecular understanding to clinical application  

PubMed Central

The availability of the human genome sequence and tools for interrogating individual genomes provide an unprecedented opportunity to apply genetics to medicine. Mendelian conditions, which are caused by dysfunction of a single gene, offer powerful examples that illustrate how genetics can provide insights into disease. Cystic fibrosis, one of the more common lethalautosomal recessive Mendelian disorders, is presented here as an example. Recent progress in elucidating disease mechanism and causes of phenotypic variation, as well as in the development of treatments, demonstrates that genetics continues to play an important part in cystic fibrosis research 25 years after the d iscove1y of the disease-causing gene. PMID:25404111

Cutting, Garry R.

2015-01-01

215

Cystic fibrosis genetics: from molecular understanding to clinical application.  

PubMed

The availability of the human genome sequence and tools for interrogating individual genomes provide an unprecedented opportunity to apply genetics to medicine. Mendelian conditions, which are caused by dysfunction of a single gene, offer powerful examples that illustrate how genetics can provide insights into disease. Cystic fibrosis, one of the more common lethal autosomal recessive Mendelian disorders, is presented here as an example. Recent progress in elucidating disease mechanism and causes of phenotypic variation, as well as in the development of treatments, demonstrates that genetics continues to play an important part in cystic fibrosis research 25 years after the discovery of the disease-causing gene. PMID:25404111

Cutting, Garry R

2015-01-01

216

Genetically engineered phage fibers and coatings for antibacterial applications  

E-print Network

Multifunctionality can be imparted to protein-based fibers and coatings via either synthetic or biological approaches. Here, we demonstrate potent antimicrobial functionality of genetically engineered, phage-based fibers ...

Mao, Joan Y

2009-01-01

217

Production of Novel Ebola Virus-Like Particles from cDNAs: an Alternative to Ebola Virus Generation by Reverse Genetics  

PubMed Central

We established a plasmid-based system for generating infectious Ebola virus-like particles (VLPs), which contain an Ebola virus-like minigenome consisting of a negative-sense copy of the green fluorescent protein gene. This system produced nearly 103 infectious particles per ml of supernatant, equivalent to the titer of Ebola virus generated by a reverse genetics system. Interestingly, infectious Ebola VLPs were generated, even without expression of VP24. Transmission and scanning electron microscopic analyses showed that the morphology of the Ebola VLPs was indistinguishable from that of authentic Ebola virus. Thus, this system allows us to study Ebola virus entry, replication, and assembly without biosafety level 4 containment. Furthermore, it may be useful in vaccine production against this highly pathogenic agent. PMID:14694131

Watanabe, Shinji; Watanabe, Tokiko; Noda, Takeshi; Takada, Ayato; Feldmann, Heinz; Jasenosky, Luke D.; Kawaoka, Yoshihiro

2004-01-01

218

Soil-genetic zoning: Principles, goals, structure, and applications  

NASA Astrophysics Data System (ADS)

The soil-genetic zoning proposed, unlike the known scheme of soil-genetic zoning, is based on the analysis of soil properties and soil-forming processes. Its objective is to interpret the soil cover in the format of the substantive-genetic soil classification of Russia (2004). The units of the soil-genetic zoning are distinguished according to the manifestations of horizon-forming processes: the main processes determining the principal trend of pedogenesis and the soil profile composition at the first level and the additional processes (forming the associated soils) serving as criteria for distinguishing the units at the second level. The results obtained allow considering this investigation as an experience of a new interpretation of a small-scale soil map and its analysis from two positions: the geography of the soil-forming processes and the complexity of the soil cover. The soil-genetic zoning has been carried out on the basis of the State Soil Map sheets; it can be an instrument for the conversion of the map's contents into the substantive-genetic soil classification of Russia (2004).

Lebedeva, I. I.; Ovechkin, S. V.; Korolyuk, T. V.; Gerasimova, M. I.

2012-07-01

219

Central limit theorem for additive functionals of reversible Markov processes and applications to simple exclusions  

Microsoft Academic Search

We prove a functional central limit theorem for additive functionals of stationary reversible ergodic Markov chains under virtually no assumptions other than the necessary ones. We use these results to study the asymptotic behavior of a tagged particle in an infinite particle system performing simple excluded random walk.

C. Kipnis; S. R. S. Varadhan

1986-01-01

220

APPLICATION OF A SPRAY DEPOSITION METHOD FOR REVERSED PHASE LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY  

EPA Science Inventory

Four coal gasification wastewater samples were analyzed for nonvolatile and polar organics by liquid chromatography-mass spectrometry (LC/MS). Samples were separated on a reverse phase liquid chromatographic column using an aqueous solvent as the eluant. A special spray depositio...

221

Optical reversibility theorems for polarization: Application to remote control of polarization  

Microsoft Academic Search

The authors prove three optical reversibility theorems that relate the polarization ellipticity at the output of an optical system to the polarization of the retroreflected light at the input by using Jones's formalism. How these theorems can be used to measure the ellipticity of a polarization remotely and to control it remotely is described. To create a linear or a

N. Vansteenkiste; P. Vignolo; A. Aspect

1993-01-01

222

Application of reversed gas chromatography to the study of heavy petroleum products  

Microsoft Academic Search

Reversed chromatography has been used to study the heavy ends of the low-temperature oxidative cracking of petroleum. Oxidative cracking, although it gives high-quality light products, produces also a large amount of oxidized bitumen due to the presence of oxygen in the process, the properties of which are of great interest. Standard sorbates of different natures were used in the chromatographic

R. V. Tokareva; A. A. Martynov; M. S. Vigdergauz

1977-01-01

223

Implementing reverse genetics in Rosaceae: analysis of T-DNA flanking sequences of insertional mutant lines in the diploid strawberry, Fragaria vesca.  

PubMed

Reverse genetics is used for functional genomics research in model plants. To establish a model system for the systematic reverse genetics research in the Rosaceae family, we analyzed genomic DNA flanking the T-DNA insertions in 191 transgenic plants of the diploid strawberry, Fragaria vesca. One hundred and seventy-six T-DNA flanking sequences were amplified from the right border (RB) and 37 from the left border (LB) by thermal asymmetric interlaced PCR. Analysis of the T-DNA nick positions revealed that T-DNA was most frequently nicked at the cleavage sites. Analysis of 11 T-DNA integration sites indicated that T-DNA was integrated into the F. vesca genome by illegitimate recombination, as reported in other model plants: Arabidopsis, rice and tobacco. First, deletion of DNA was found at T-DNA integration target sites in all transgenic plants tested. Second, microsimilarities of a few base pairs between the left and/or right ends of the T-DNA and genomic sites were found in all transgenic plants tested. Finally, filler DNA was identified in four break-points. Out of 191 transgenic plants, T-DNA flanking sequences of 79 plants (41%) showed significant similarity to genes, elements or proteins of other plant species and 67 (35%) of the sequences are still unknown strawberry gene fragments. T-DNA flanking sequences of 126 plants (66%) showed homology to plant ESTs. This is the first report of T-DNA integration in a sizeable population of a rosaceous species. We have shown in this paper that T-DNA integration in strawberry is not random but directed by sequence microsimilarities in the host genome. PMID:20444194

Oosumi, Teruko; Ruiz-Rojas, Juan Jairo; Veilleux, Richard E; Dickerman, Allan; Shulaev, Vladimir

2010-09-01

224

On thermodynamic and microscopic reversibility  

SciTech Connect

The word 'reversible' has two (apparently) distinct applications in statistical thermodynamics. A thermodynamically reversible process indicates an experimental protocol for which the entropy change is zero, whereas the principle of microscopic reversibility asserts that the probability of any trajectory of a system through phase space equals that of the time reversed trajectory. However, these two terms are actually synonymous: a thermodynamically reversible process is microscopically reversible, and vice versa.

Crooks, Gavin E.

2011-07-12

225

Clinical application of genetics in management of colorectal cancer.  

PubMed

The extensive study of genetic alterations in colorectal cancer (CRC) has led to molecular diagnostics playing an increasingly important role in CRC diagnosis and treatment. Currently, it is believed that CRC is a consequence of the accumulation of both genetic and epigenetic genomic alterations. It is known that there are at least 3 major pathways that lead to colorectal carcinogenesis: (1) the chromosomal instability pathway, (2) the microsatellite instability pathway, and (3) the cytosine-phospho-guanine island methylator phenotype pathway. With recent advances in CRC genetics, the identification of specific molecular alterations responsible for CRC pathogenesis has directly influences clinical care. Patients at high risk for developing CRC can be identified by genetic testing for specific molecular alterations, and the use of molecular biomarkers for predictive and prognostic purposes is also increasing. This is clearly supported by the recent advances in genetic testing for CRC whereby specific molecular alterations are identified for the purpose of guiding treatment with targeting therapies such as anti-endothelial growth factor receptor monoclonal antibodies. PMID:25349592

Kim, Eun Ran; Kim, Young-Ho

2014-07-01

226

Genetic admixture and obesity: recent perspectives and future applications.  

PubMed

The process of the colonization of the New World that occurred centuries ago served as a natural experiment, creating unique combinations of genetic material in newly formed admixed populations. Through a genetic admixture approach, the identification and genotyping of ancestry informative markers have allowed for the estimation of proportions of ancestral parental populations among individuals in a sample. These admixture estimates have been used in different ways to understand the genetic contributions to individual variation in obesity and body composition parameters, particularly among diverse admixed groups known to differ in obesity prevalence within the United States. Although progress has been made through the use of genetic admixture approaches, further investigations are needed in order to explore the interaction of environmental factors with the degree of genetic ancestry in individuals. A challenge to confront at this time would be to further stratify and define environments in progressively more granular terms, including nutrients, muscle biology, stress responses at the cellular level, and the social and built environments. PMID:24081225

Fernández, José R; Pearson, Keith E; Kell, Kenneth P; Bohan Brown, Michelle M

2013-01-01

227

Genetic admixture and obesity: recent perspectives and future applications  

PubMed Central

The process of the colonization of the New World that occurred centuries ago served as a natural experiment, creating unique combinations of genetic material in newly formed admixed populations. The identification and genotyping of ancestry informative markers (AIMs) have allowed for the estimation of proportions of ancestral parental populations among individuals in a sample through the genetic admixture approach. These admixture estimates have been used in different ways to understand the genetic contributions to individual variation in obesity and body composition parameters, particularly among diverse admixed groups known to differ in obesity prevalence within the United States. Although progress has been made through the use of genetic admixture approaches, future investigations are needed in order to explore the interaction of environmental factors with the degree of genetic ancestry in individuals. A challenge to confront at this time would be to further stratify and define environments in progressively more granular terms, including nutrients, muscle biology, stress responses at the cellular level, and the social and built environments. PMID:24081225

Fernández, José R.; Pearson, Keith E.; Kell, Kenneth P.; Brown, Michelle M. Bohan

2013-01-01

228

Quantitative reverse sample genome probing of microbial communities and its application to oil field production waters  

SciTech Connect

This paper presents a protocol for quantitative analysis of microbial communities by reverse sample genome probing is presented in which (i) whole community DNA is isolated and labeled in the presence of a known amount of an added internal standard and (ii) the resulting spiked reverse genome probe is hybridized with a master filter on which denatured genomic DNAs from bacterial standards isolated from the target environment were spotted in large amounts (up to 1,500 ng) in order to improve detection sensitivity. This protocol allowed reproducible fingerprinting of the microbial community in oil field production waters at 19 sites from which water and biofilm samples were collected. It appeared that selected sulfate-reducing bacteria were significantly enhanced in biofilms covering the metal surfaces in contact with the production waters.

Voordouw, G.; Shen, Y.; Harrington, C.S.; Teland, A.J. (Univ. of Calgary, Alberta (Canada)); Jack, T.R. (Novacor Research and Technology Corporation, Calgary, Alberta (Canada)); Westlake, W.S. (Univ. of Alberta (Canada))

1993-12-01

229

Reverse line blot hybridization with species-specific oligonucleotide probes: application to piroplasm detection.  

PubMed

Reverse line blot (RLB) hybridization has become a well-established and widely used method for the multiplex identification of several Babesia and Theileria species in hosts and tick vectors. The procedure is based on the simultaneous PCR amplification of a polymorphic region of the 18S rRNA gene from different piroplasms followed by identification of the individual species by hybridization to species-specific oligonucleotide probes covalently linked to a nylon membrane in a macroarray format. PMID:25399097

Hurtado, Ana

2015-01-01

230

Noise in reverse-biased HgCdTe photodiodes for wideband applications  

NASA Astrophysics Data System (ADS)

The excess noise in photodiodes caused by the reverse-bias voltage has been measured and analyzed. It was found that the noise first increases slowly with the bias voltage up to a certain point, and then increases rapidly for higher voltages. The results indicate that the voltage, where the noise begins to increase is equal to the voltage where the junction capacitance saturates. Biasing the photodiode to that voltage, one can maximize the bandwidth without severely degrading the sensitivity.

Lundqvist, S.; Eklund, H.; Eng, S. T.

1980-07-01

231

Three-dimensional optical measurements and reverse engineering for automotive applications  

Microsoft Academic Search

The paper describes a very special and suggestive example of optical three-dimensional (3D) acquisition, reverse engineering and rapid prototyping of a historic automobile, a Ferrari 250 Mille Miglia, performed primarily using an optical 3D whole-field digitiser based on the projection of incoherent light (OPL-3D, developed in our laboratory). The entire process consists in the acquisition, the point cloud alignment, the

Giovanna Sansoni; Franco Docchio

2004-01-01

232

Reverse engineering biological networks :applications in immune responses to bio-toxins.  

SciTech Connect

Our aim is to determine the network of events, or the regulatory network, that defines an immune response to a bio-toxin. As a model system, we are studying T cell regulatory network triggered through tyrosine kinase receptor activation using a combination of pathway stimulation and time-series microarray experiments. Our approach is composed of five steps (1) microarray experiments and data error analysis, (2) data clustering, (3) data smoothing and discretization, (4) network reverse engineering, and (5) network dynamics analysis and fingerprint identification. The technological outcome of this study is a suite of experimental protocols and computational tools that reverse engineer regulatory networks provided gene expression data. The practical biological outcome of this work is an immune response fingerprint in terms of gene expression levels. Inferring regulatory networks from microarray data is a new field of investigation that is no more than five years old. To the best of our knowledge, this work is the first attempt that integrates experiments, error analyses, data clustering, inference, and network analysis to solve a practical problem. Our systematic approach of counting, enumeration, and sampling networks matching experimental data is new to the field of network reverse engineering. The resulting mathematical analyses and computational tools lead to new results on their own and should be useful to others who analyze and infer networks.

Martino, Anthony A.; Sinclair, Michael B.; Davidson, George S.; Haaland, David Michael; Timlin, Jerilyn Ann; Thomas, Edward Victor; Slepoy, Alexander; Zhang, Zhaoduo; May, Elebeoba Eni; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

2005-12-01

233

A reversal coarse-grained analysis with application to an altered functional circuit in depression  

PubMed Central

Introduction When studying brain function using functional magnetic resonance imaging (fMRI) data containing tens of thousands of voxels, a coarse-grained approach – dividing the whole brain into regions of interest – is applied frequently to investigate the organization of the functional network on a relatively coarse scale. However, a coarse-grained scheme may average out the fine details over small spatial scales, thus rendering it difficult to identify the exact locations of functional abnormalities. Methods A novel and general approach to reverse the coarse-grained approach by locating the exact sources of the functional abnormalities is proposed. Results Thirty-nine patients with major depressive disorder (MDD) and 37 matched healthy controls are studied. A circuit comprising the left superior frontal gyrus (SFGdor), right insula (INS), and right putamen (PUT) exhibit the greatest changes between the patients with MDD and controls. A reversal coarse-grained analysis is applied to this circuit to determine the exact location of functional abnormalities. Conclusions The voxel-wise time series extracted from the reversal coarse-grained analysis (source) had several advantages over the original coarse-grained approach: (1) presence of a larger and detectable amplitude of fluctuations, which indicates that neuronal activities in the source are more synchronized; (2) identification of more significant differences between patients and controls in terms of the functional connectivity associated with the sources; and (3) marked improvement in performing discrimination tasks. A software package for pattern classification between controls and patients is available in Supporting Information. PMID:24363967

Guo, Shuixia; Yu, Yun; Zhang, Jie; Feng, Jianfeng

2013-01-01

234

New genetic operators in the Fly algorithm: application to medical PET image reconstruction  

E-print Network

New genetic operators in the Fly algorithm: application to medical PET image reconstruction Franck through the human body using methods similar to those used in conventional X-ray computed tomography [7 Processing, EvoApplications 2010 6024 (2010)" #12;medicine, this method makes use of a gamma emitter as radio

Boyer, Edmond

235

Genetics  

Microsoft Academic Search

The author draws on modern research to introduce genetics in a molecular and cellular context. This work covers the structure of DNA and the gene and gene expression, replication, mutation, and recombination, looks at the gene in the context of the cell and organism, describes the elements of genetic analysis and the basic principles of inheritance, and examines classic experiments

1990-01-01

236

Genetic algorithms applications in the analysis of insolvency risk  

Microsoft Academic Search

This study analyses the comparison between a traditional statistical methodology for bankruptcy classification and prediction, i.e. linear discriminant analysis (LDA), and an artificial intelligence algorithm known as Genetic Algorithm (GA). The study was carried out at Centrale dei Bilanci, in Turin, Italy, analysing 1920 unsound and 1920 sound industrial Italian companies from 1982–1995. This paper follows our earlier examination of

Franco Varetto

1998-01-01

237

GENETIC MARKERS AND THEIR APPLICATION IN POULTRY BREEDING  

Technology Transfer Automated Retrieval System (TEKTRAN)

The current chicken genetic map contains at least 1,965 loci within 50 linkage groups and it covers about 4,000 cM. About 235 of these loci have homology with known human or mammalian genes. The remaining loci are anonymous molecular DNA markers, including microsatellites, AFLP, RAPD, CR1 and othe...

238

Genetic transformation of conifers and its application in forest biotechnology  

Microsoft Academic Search

Genetic modification of conifers through gene transfer technology is now an important field in forest biotechnology. Two basic methodologies, particle bombardment and Agrobacterium-mediated transformation, have been used on conifers. The use of particle bombardment has produced stable transgenic plants in Picea abies, P. glauca, P. mariana, and Pinus radiata. Transgenic plants have been produced from Larix decidua, Picea abies, P.

W. Tang; R. J. Newton

2003-01-01

239

QTL x Genetic Background Interaction: Application to Predicting Progeny Value  

Technology Transfer Automated Retrieval System (TEKTRAN)

Failures of the additive infinitesimal model continue to provide incentive to study other modes of gene action, in particular, epistasis. Epistasis can be modeled as a QTL by genetic background interaction. Association mapping models lend themselves to fitting such an interaction because they often ...

240

Clinical Application of Antenatal Genetic Diagnosis of Osteogenesis Imperfecta Type IV  

PubMed Central

Background Clinical analysis and genetic testing of a family with osteogenesis imperfecta type IV were conducted, aiming to discuss antenatal genetic diagnosis of osteogenesis imperfecta type IV. Material/Methods Preliminary genotyping was performed based on clinical characteristics of the family members and then high-throughput sequencing was applied to rapidly and accurately detect the changes in candidate genes. Results Genetic testing of the III5 fetus and other family members revealed missense mutation in c.2746G>A, pGly916Arg in COL1A2 gene coding region and missense and synonymous mutation in COL1A1 gene coding region. Conclusions Application of antenatal genetic diagnosis provides fast and accurate genetic counseling and eugenics suggestions for patients with osteogenesis imperfecta type IV and their families. PMID:25835785

Yuan, Jing; Li, Song; Xu, YeYe; Cong, Lin

2015-01-01

241

Clinical Application of Antenatal Genetic Diagnosis of Osteogenesis Imperfecta Type IV.  

PubMed

Background Clinical analysis and genetic testing of a family with osteogenesis imperfecta type IV were conducted, aiming to discuss antenatal genetic diagnosis of osteogenesis imperfecta type IV. Material and Methods Preliminary genotyping was performed based on clinical characteristics of the family members and then high-throughput sequencing was applied to rapidly and accurately detect the changes in candidate genes. Results Genetic testing of the III5 fetus and other family members revealed missense mutation in c.2746G>A, pGly916Arg in COL1A2 gene coding region and missense and synonymous mutation in COL1A1 gene coding region. Conclusions Application of antenatal genetic diagnosis provides fast and accurate genetic counseling and eugenics suggestions for patients with osteogenesis imperfecta type IV and their families. PMID:25835785

Yuan, Jing; Li, Song; Xu, YeYe; Cong, Lin

2015-01-01

242

Hybrid Application On Job-Shop Scheduling by Genetic Algorithm and MAS Spring-Net  

Microsoft Academic Search

To solve job-shop production scheduling problem, we presented a new hybrid optimum arithmetic of using genetic algorithm and MAS(multi-agent system) composite-spring-net. Introduced the structure and model of genetic algorithm, illuminated the basic principle of spring-net arithmetic. By the experiment proving, the hybrid application of GA and sping-net arithmetic can make favorable effect on solving the problems of job-shop schedule.

Dong Yumin; Xiao Shufen

2007-01-01

243

Next-generation sequencing technologies and applications for human genetic history and forensics  

PubMed Central

Rapid advances in the development of sequencing technologies in recent years have enabled an increasing number of applications in biology and medicine. Here, we review key technical aspects of the preparation of DNA templates for sequencing, the biochemical reaction principles and assay formats underlying next-generation sequencing systems, methods for imaging and base calling, quality control, and bioinformatic approaches for sequence alignment, variant calling and assembly. We also discuss some of the most important advances that the new sequencing technologies have brought to the fields of human population genetics, human genetic history and forensic genetics. PMID:22115430

2011-01-01

244

A General Reversible Hereditary Constitutive Model. Part 2; Application to a Titanium Alloy  

NASA Technical Reports Server (NTRS)

Given the mathematical framework and specific viscoelastic model in Part 1 our primary goal in this second part is focused on model characterization and assessment for the specific titanium alloy, TIMETAL 21S. The model is motivated by experimental evidence suggesting the presence of significant rate/time effects in the so-called quasilinear, reversible, material response range. An explanation of the various experiments performed and their corresponding results are also included. Finally, model correlations and predictions are presented for a wide temperature range.

Arnold, S. M.; Saleeb, A. F.; Castelli, M. G.

1997-01-01

245

Clinical application of genetically modified T cells in cancer therapy  

PubMed Central

Immunotherapies are emerging as highly promising approaches for the treatment of cancer. In these approaches, a variety of materials are used to boost immunity against malignant cells. A key component of many of these approaches is functional tumor-specific T cells, but the existence and activity of sufficient T cells in the immune repertoire is not always the case. Recent methods of generating tumor-specific T cells include the genetic modification of patient lymphocytes with receptors to endow them with tumor specificity. These T cells are then expanded in vitro followed by infusion of the patient in adoptive cell transfer protocols. Genes used to modify T cells include those encoding T-cell receptors and chimeric antigen receptors. In this review, we provide an introduction to the field of genetic engineering of T cells followed by details of their use against cancer in the clinic. PMID:25505964

Kershaw, Michael H; Westwood, Jennifer A; Slaney, Clare Y; Darcy, Phillip K

2014-01-01

246

Genetic Algorithms And Its Application To Economic Load Dispatch  

NASA Astrophysics Data System (ADS)

Genetic Algorithm (GA) is a search method that simulates the process of natural selection and it attempts to find a good solution to some problem by randomly generating a collection of potential solutions to the problem and then manipulating those solutions using genetic operators. Through selection, mutation and re-combination (crossover) operations, better solutions are hopefully generated out of the current set of potential solutions. This process continues until an acceptable solution is found. GA is becoming popular to solve the optimization problems mainly because of its robustness in finding optimal solution and ability to provide near optimal solution close to global optimum. The ELD approach is tested on sample 3-generator system with the load of 24 hours.

Borana, Kavita

2010-11-01

247

Genetics  

NSDL National Science Digital Library

This activity helps students to understand basic principles of genetics, including relationships of genotype to phenotype, concepts of recessive and dominant alleles, and how understanding meiosis and fertilization provides the basis for understanding inheritance, as summarized in Punnett squares. The Student Handout includes an analysis of the inheritance of albinism that teaches all of these concepts, a Coin Toss Genetics activity that helps students understand the probabilistic nature of Punnett square predictions, and an analysis of the inheritance of sickle cell anemia that reinforces the basic concepts and introduces some of the complexities of genetics. The Genetics Supplement includes two additional activities, an analysis of student data on the sex makeup of sibships and pedigree analyses of recessive and dominant alleles with challenge questions that introduce the role of mutations and an evaluation of Punnett squares and pedigrees as models of inheritance.

Jennifer Doherty

248

Clinical application of exome sequencing in undiagnosed genetic conditions  

PubMed Central

Background There is considerable interest in the use of next-generation sequencing to help diagnose unidentified genetic conditions, but it is difficult to predict the success rate in a clinical setting that includes patients with a broad range of phenotypic presentations. Methods The authors present a pilot programme of whole-exome sequencing on 12 patients with unexplained and apparent genetic conditions, along with their unaffected parents. Unlike many previous studies, the authors did not seek patients with similar phenotypes, but rather enrolled any undiagnosed proband with an apparent genetic condition when predetermined criteria were met. Results This undertaking resulted in a likely genetic diagnosis in 6 of the 12 probands, including the identification of apparently causal mutations in four genes known to cause Mendelian disease (TCF4, EFTUD2, SCN2A and SMAD4) and one gene related to known Mendelian disease genes (NGLY1). Of particular interest is that at the time of this study, EFTUD2 was not yet known as a Mendelian disease gene but was nominated as a likely cause based on the observation of de novo mutations in two unrelated probands. In a seventh case with multiple disparate clinical features, the authors were able to identify homozygous mutations in EFEMP1 as a likely cause for macular degeneration (though likely not for other features). Conclusions This study provides evidence that next-generation sequencing can have high success rates in a clinical setting, but also highlights key challenges. It further suggests that the presentation of known Mendelian conditions may be considerably broader than currently recognised. PMID:22581936

Need, Anna C; Shashi, Vandana; Hitomi, Yuki; Schoch, Kelly; Shianna, Kevin V; McDonald, Marie T; Meisler, Miriam H

2012-01-01

249

Genetic Algorithms applications to optimization and system identification  

E-print Network

. Optimal Results of the Second Model; Abs. Viscosity vs. Rot. Speed. . . . . . . . 20 5. The Frequency Spectrum of the Real System. . . . 25 6 The Frequency Spectrum of the Estimated System by GA. . . . . . . 25 vlu LIST OF TABLES TABLE Page 1... the strings of first generation. Start Produce 10 strings Fitness- evaluation Ranking Reproduction Selecting Reproducing Crossover Mutation Fig. 1 Flow Chart of Genetic Algorithms Program The second step is for the 10 binary strings to go through...

Lin, Yun-Jeng

1998-01-01

250

The Concentration Dependence of the (Delta)s Term in the Gibbs Free Energy Function: Application to Reversible Reactions in Biochemistry  

ERIC Educational Resources Information Center

The concentration dependence of (delta)S term in the Gibbs free energy function is described in relation to its application to reversible reactions in biochemistry. An intuitive and non-mathematical argument for the concentration dependence of the (delta)S term in the Gibbs free energy equation is derived and the applicability of the equation to…

Gary, Ronald K.

2004-01-01

251

A reverse genetics system for the Great Lakes strain of viral hemorrhagic septicemia virus: the NV gene is required for pathogenicity.  

PubMed

Viral hemorrhagic septicemia virus (VHSV), belonging to the genus Novirhabdovirus in the family of Rhabdoviridae, causes a highly contagious disease of fresh and saltwater fish worldwide. Recently, a novel genotype of VHSV, designated IVb, has invaded the Great Lakes in North America, causing large-scale epidemics in wild fish. An efficient reverse genetics system was developed to generate a recombinant VHSV of genotype IVb from cloned cDNA. The recombinant VHSV (rVHSV) was comparable to the parental wild-type strain both in vitro and in vivo, causing high mortality in yellow perch (Perca flavescens). A modified recombinant VHSV was generated in which the NV gene was substituted with an enhanced green fluorescent protein gene (rVHSV-?NV-EGFP), and another recombinant was made by inserting the EGFP gene into the full-length viral clone between the P and M genes (rVHSV-EGFP). The in vitro replication kinetics of rVHSV-EGFP was similar to rVHSV; however, the rVHSV-?NV-EGFP grew 2 logs lower. In yellow perch challenges, wtVHSV and rVHSV induced 82-100% cumulative per cent mortality (CPM), respectively, whereas rVHSV-EGFP produced 62% CPM and rVHSV-?NV-EGFP caused only 15% CPM. No reversion of mutation was detected in the recovered viruses and the recombinant viruses stably maintained the foreign gene after several passages. These results indicate that the NV gene of VHSV is not essential for viral replication in vitro and in vivo, but it plays an important role in viral replication efficiency and pathogenicity. This system will facilitate studies of VHSV replication, virulence, and production of viral vectored vaccines. PMID:20936318

Ammayappan, Arun; Kurath, Gael; Thompson, Tarin M; Vakharia, Vikram N

2011-08-01

252

A reverse genetics system for the Great Lakes strain of viral hemorrhagic septicemia virus: the NV gene is required for pathogenicity  

USGS Publications Warehouse

Viral hemorrhagic septicemia virus (VHSV), belonging to the genus Novirhabdovirus in the family of Rhabdoviridae, causes a highly contagious disease of fresh and saltwater fish worldwide. Recently, a novel genotype of VHSV, designated IVb, has invaded the Great Lakes in North America, causing large-scale epidemics in wild fish. An efficient reverse genetics system was developed to generate a recombinant VHSV of genotype IVb from cloned cDNA. The recombinant VHSV (rVHSV) was comparable to the parental wild-type strain both in vitro and in vivo, causing high mortality in yellow perch (Perca flavescens). A modified recombinant VHSV was generated in which the NV gene was substituted with an enhanced green fluorescent protein gene (rVHSV-?NV-EGFP), and another recombinant was made by inserting the EGFP gene into the full-length viral clone between the P and M genes (rVHSV-EGFP). The in vitro replication kinetics of rVHSV-EGFP was similar to rVHSV; however, the rVHSV-?NV-EGFP grew 2 logs lower. In yellow perch challenges, wtVHSV and rVHSV induced 82-100% cumulative per cent mortality (CPM), respectively, whereas rVHSV-EGFP produced 62% CPM and rVHSV-?NV-EGFP caused only 15% CPM. No reversion of mutation was detected in the recovered viruses and the recombinant viruses stably maintained the foreign gene after several passages. These results indicate that the NV gene of VHSV is not essential for viral replication in vitro and in vivo, but it plays an important role in viral replication efficiency and pathogenicity. This system will facilitate studies of VHSV replication, virulence, and production of viral vectored vaccines.

Ammayappan, Arun; Kurath, Gael; Thompson, Tarin M.; Vakharia, Vikram N.

2011-01-01

253

Prospects for applications of genetic engineering in pig breeding P. MULSANT, M. DALENS, Genevive ECHARD, J. GELLIN,  

E-print Network

Prospects for applications of genetic engineering in pig breeding P. MULSANT, M. DALENS, Geneviève, 31326 Castanet-Tolosan Cedex Genetic engineering provides an extremely high number of cloned mammalian DNA sequences. These sequences should be powerful tools for genetic analysis or improvement of the pig

Paris-Sud XI, Université de

254

Application of Adjoint Methodology to Supersonic Aircraft Design Using Reversed Equivalent Areas  

NASA Technical Reports Server (NTRS)

This paper presents an approach to shape an aircraft to equivalent area based objectives using the discrete adjoint approach. Equivalent areas can be obtained either using reversed augmented Burgers equation or direct conversion of off-body pressures into equivalent area. Formal coupling with CFD allows computation of sensitivities of equivalent area objectives with respect to aircraft shape parameters. The exactness of the adjoint sensitivities is verified against derivatives obtained using the complex step approach. This methodology has the benefit of using designer-friendly equivalent areas in the shape design of low-boom aircraft. Shape optimization results with equivalent area cost functionals are discussed and further refined using ground loudness based objectives.

Rallabhandi, Sriram K.

2013-01-01

255

Genetic algorithms and their application to in silico evolution of genetic regulatory networks.  

PubMed

A genetic algorithm (GA) is a procedure that mimics processes occurring in Darwinian evolution to solve computational problems. A GA introduces variation through "mutation" and "recombination" in a "population" of possible solutions to a problem, encoded as strings of characters in "genomes," and allows this population to evolve, using selection procedures that favor the gradual enrichment of the gene pool with the genomes of the "fitter" individuals. GAs are particularly suitable for optimization problems in which an effective system design or set of parameter values is sought.In nature, genetic regulatory networks (GRNs) form the basic control layer in the regulation of gene expression levels. GRNs are composed of regulatory interactions between genes and their gene products, and are, inter alia, at the basis of the development of single fertilized cells into fully grown organisms. This paper describes how GAs may be applied to find functional regulatory schemes and parameter values for models that capture the fundamental GRN characteristics. The central ideas behind evolutionary computation and GRN modeling, and the considerations in GA design and use are discussed, and illustrated with an extended example. In this example, a GRN-like controller is sought for a developmental system based on Lewis Wolpert's French flag model for positional specification, in which cells in a growing embryo secrete and detect morphogens to attain a specific spatial pattern of cellular differentiation. PMID:20835807

Knabe, Johannes F; Wegner, Katja; Nehaniv, Chrystopher L; Schilstra, Maria J

2010-01-01

256

Genetic testing for pharmacogenetics and its clinical application in drug therapy.  

PubMed

There is wide individual variation in drug responses and adverse effects. As the main causes of the variation in drug responses, attention has focused on the genetic polymorphisms that encode metabolic enzymes regulating pharmacodynamics and receptors modulating the affinity with the responsive sites. Tailor-made drug therapy analyzes genetic polymorphisms involved in drug responses before drug administration and selects drugs and doses suitable for the individual genetic background. Establishment of tailor-made drug therapy is expected to contribute to medical economy by avoiding wasteful drug administration. To promote such medical practice, it is necessary to use simple genetic testing that is clinically convenient. Currently, genetic testing using real-time PCR has been frequently employed at laboratories with its clinical application anticipated. As to the many genes involved in drug responses, to date, the application of patient genetic information to tailor-made drug therapy has been achieved at the practical level. Information on pharmacogenetics will be a critical factor in medical practice in the near future. PMID:16126184

Hiratsuka, Masahiro; Sasaki, Takamitsu; Mizugaki, Michinao

2006-01-01

257

Genetics  

NSDL National Science Digital Library

What affects how physical characteristics are transmitted from parent to offspring? This is a question that can be answered at many levels. Molecular biologists examine the pattern of nucleotides in deoxyribonucleic acid (DNA) and the effect of mutations on the proteins produced. Classical geneticists explore the patterns by which traits are transmitted through families. Medical geneticists attempt to describe and develop treatments for diseases that have a genetic component. Genetic engineers analyze how traits can be altered in organisms through modern technology. These are only a few of the strategies that scientists employ to explain the nature of heredity. Explore historical perspectives on the study of genetics and investigate how cutting-edge technology is being used to expand our understanding of heredity.

National Science Teachers Association (NSTA)

2005-04-01

258

Successful application of preimplantation genetic diagnosis for hypokalaemic periodic paralysis.  

PubMed

Hypokalaemic periodic paralysis is a rare dominant inherited disease where a person suffers sudden falls of circulating potassium concentrations, producing muscle weakness and sometimes severe paralysis. Attacks can occur as frequently as several times a day or once in a year. The age of onset is usually adolescence but symptoms can appear as early as 10 years of age. Muscle weakness can compromise vital functions such as breathing or swallowing and heart arrhythmias are also frequent during attacks. Preimplantation genetic diagnosis, an early form of prenatal diagnosis for couples at risk of transmitting inherited diseases, was used to prevent the transmission of this disease. Six polymorphic short tandem repeat or microsatellite markers (STR) closely linked to the CACNA1S gene were tested. Three fully informative markers were chosen to establish the disease-bearing haplotype in the family and to determine the genetic status of five embryos by multiplex fluorescent heminested PCR. Four of the five embryos tested were diagnosed as non-affected and one as affected. Two embryos were transferred resulting in a singleton pregnancy and the birth of a healthy girl. PMID:20541469

Alberola, Trinitat M; Vendrell, Xavier; Bautista-Llácer, Rosa; Vila, Maria; Calatayud, Carmen; Pérez-Alonso, Manuel

2010-08-01

259

Application of Genetic Algorithm to Hexagon-Based Motion Estimation  

PubMed Central

With the improvement of science and technology, the development of the network, and the exploitation of the HDTV, the demands of audio and video become more and more important. Depending on the video coding technology would be the solution for achieving these requirements. Motion estimation, which removes the redundancy in video frames, plays an important role in the video coding. Therefore, many experts devote themselves to the issues. The existing fast algorithms rely on the assumption that the matching error decreases monotonically as the searched point moves closer to the global optimum. However, genetic algorithm is not fundamentally limited to this restriction. The character would help the proposed scheme to search the mean square error closer to the algorithm of full search than those fast algorithms. The aim of this paper is to propose a new technique which focuses on combing the hexagon-based search algorithm, which is faster than diamond search, and genetic algorithm. Experiments are performed to demonstrate the encoding speed and accuracy of hexagon-based search pattern method and proposed method. PMID:24592178

Cheng, Wan-Shu

2014-01-01

260

The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera  

PubMed Central

Microsatellite markers are difficult to apply within lepidopteran studies due to the lack of locus-specific PCR amplification and the high proportion of “null” alleles, such that erroneous estimations of population genetic parameters often result. Herein single nucleotide polymorphism (SNP) markers are developed from Ostrinia nubilalis (Lepidoptera: Crambidae) using next generation expressed sequence tag (EST) data. A total of 2742 SNPs were predicted within a reference assembly of 7414 EST contigs, and a subset of 763 were incorporated into 24 multiplex PCR reactions. To validate this pipeline, 5 European and North American sample sites were genotyped at 178 SNP loci, which indicated 84 (47.2%) were in Hardy–Weinberg equilibrium. Locus-by-locus FST, analysis of molecular variance, and STRUCTURE analyses indicate significant genetic differentiation may exist between European and North American O. nubilalis. The observed genetic diversity was significantly lower among European sites, which may result from genetic drift, natural selection, a genetic bottleneck, or ascertainment bias due to North American origin of EST sequence data. SNPs are an abundant source of mutation data for molecular genetic marker development in non-model species, with shared ancestral SNPs showing application within closely related species. These markers offer advantages over microsatellite markers for genetic and genomic analyses of Lepidoptera, but the source of mutation data may affect the estimation of population parameters and likely need to be considered in the interpretation of empirical data. PMID:22303334

Coates, Brad Steven; Bayles, Darrell O.; Wanner, Kevin W.; Robertson, Hugh M.; Hellmich, Richard L.; Sappington, Thomas W.

2011-01-01

261

Reversible loss of gravitropic sensitivity in maize roots after tip application of calcium chelators  

NASA Technical Reports Server (NTRS)

The application of calcium chelating agents (EDTA or EGTA) to the tips of maize roots caused a loss of gravitropic sensitivity. When the chelator was replaced with calcium chloride, gravitropic sensitivity was restored. Asymmetric application of calcium chloride near the tip of a vertical root caused curvature toward the calcium source. When the calcium was applied to the upper surface of the tip of a root oriented horizontally, the root curved upward even though control roots exhibited strong downward curvature. Application of calcium chloride to the tips of decapped roots, which are known to be gravitropically insensitive, did not restore gravitropic sensitivity. However, asymmetric application of calcium chloride near the tips of decapped roots caused curvature toward the calcium source. Calcium may play a key role in linking gravity detection to gravitropic curvature in roots.

Lee, J. S.; Mulkey, T. J.; Evans, M. L.

1983-01-01

262

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

NASA Astrophysics Data System (ADS)

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.

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

263

Generation by Reverse Genetics of an Effective, Stable, Live-Attenuated Newcastle Disease Virus Vaccine Based on a Currently Circulating, Highly Virulent Indonesian Strain  

PubMed Central

Newcastle disease virus (NDV) can cause severe disease in chickens. Although NDV vaccines exist, there are frequent reports of outbreaks in vaccinated chickens. During 2009–2010, despite intense vaccination, NDV caused major outbreaks among commercial poultry farms in Indonesia. These outbreaks raised concern regarding the protective immunity of current vaccines against circulating virulent strains in Indonesia. In this study, we investigated whether a recombinant attenuated Indonesian NDV strain could provide better protection against prevalent Indonesian viruses. A reverse genetics system for the highly virulent NDV strain Banjarmasin/010/10 (Ban/010) isolated in Indonesia in 2010 was constructed. The Ban/010 virus is classified in genotype VII of class II NDV, which is genetically distinct from the commercial vaccine strains B1 and LaSota, which belong to genotype II, and shares only 89 and 87% amino acid identity for the protective antigens F and HN, respectively. A mutant virus, named Ban/AF, was developed in which the virulent F protein cleavage site motif “RRQKR?F” was modified to an avirulent motif “GRQGR?L” by three amino acid substitutions (underlined). The Ban/AF vaccine virus did not produce syncytia or plaques in cell culture, even in the presence of added protease. Pathogenicity tests showed that Ban/AF was completely avirulent. Ban/AF replicated efficiently during 10 consecutive passages in chickens and remained genetically stable. Serological analysis showed that Ban/AF induced higher neutralization and hemagglutination inhibition antibody titers against the prevalent viruses than the commercial vaccines B1 or LaSota. Both Ban/AF and commercial vaccines provided protection against clinical disease and mortality after challenge with virulent NDV strain Ban/010 (genotype VII) or GB Texas (genotype II). However, Ban/AF significantly reduced challenge virus shedding from the vaccinated birds compared to B1 vaccine. These results suggest that Ban/AF can provide better protection than commercial vaccines and is a promising vaccine candidate against NDV strains circulating in Indonesia. PMID:23285174

Xiao, Sa; Nayak, Baibaswata; Samuel, Arthur; Paldurai, Anandan; Kanabagattebasavarajappa, Mallikarjuna; Prajitno, Teguh Y.; Bharoto, Eny E.; Collins, Peter L.; Samal, Siba K.

2012-01-01

264

The effect of ultrafiltration as pretreatment to reverse osmosis in wastewater reuse and seawater desalination applications  

Microsoft Academic Search

With an ever-growing world-wide demand for water and decreasing availability, emerging technologies such as ultrafiltration (UF) hold the key to future water treatment. Two applications to use unconventional sources for water production are described. The reuse of effluent of wastewater treatment plants (WWTP) for high-quality water production will certainly be an interesting application of UF in the years to come.

S. C. J. M. van Hoof; A. Hashim; A. J. Kordes

1999-01-01

265

Development and application of a broadly reactive real-time reverse transcription-PCR assay for detection of murine noroviruses.  

PubMed

Murine norovirus (MNV) is a viral agent newly identified in laboratory mice and a large number of genetically diverse MNV strains have been reported to date. A broadly reactive TaqMan-based real-time reverse transcription (RT)-polymerase chain reaction (PCR) assay was developed for MNVs. Novel primers and a TaqMan MGB probe were designed targeting highly conserved sequences among MNV strains, which are located in the open reading frames 1 (ORF1)-ORF2 junction region. The quantitative range of this assay was determined as 1.0 × 10(2)-1.0 × 10(8)copies/PCR tube based on a 10-fold serial dilution of plasmid DNA containing the target sequences. Viral RNA in eight murine stool specimens positive by nested RT-PCR assay was measured, and the highest viral RNA load was calculated at 4.7 × 10(6)copies/g-stool. MNV was inoculated into RAW 264.7 cells, and the viral RNA was monitored to validate assay sensitivity. MNV-RNA in the supernatant was detected during in vitro replication, which increased substantially from 5 to 30 h post-infection (hpi) and reached more than 1.0 × 10(10)copies/mL at 96 hpi. This real-time RT-PCR assay is a useful tool to detect and quantify MNV-RNA in in vivo and in vitro studies. PMID:20670657

Kitajima, Masaaki; Oka, Tomoichiro; Takagi, Hirotaka; Tohya, Yukinobu; Katayama, Hiroyuki; Takeda, Naokazu; Katayama, Kazuhiko

2010-11-01

266

Genetics  

Technology Transfer Automated Retrieval System (TEKTRAN)

The genus Capsicum represents one of several well characterized Solanaceous genera. A wealth of classical and molecular genetics research is available for the genus. Information gleaned from its cultivated relatives, tomato and potato, provide further insight for basic and applied studies. Early ...

267

Genetics  

Technology Transfer Automated Retrieval System (TEKTRAN)

Maintaining genetic variation in wild populations of Arctic organisms is fundamental to the long-term persistence of high latitude biodiversity. Variability is important because it provides options for species to respond to changing environmental conditions and novel challenges such as emerging path...

268

Application of genetic algorithm in atmospheric carbon dioxide concentration retrieval  

NASA Astrophysics Data System (ADS)

This paper introduces the basic theory and method of carbon dioxide (CO2) retrieval. The key step is to search for the optimal solution and the random search algorithm Genetic Algorithm (GA) which can effectively avoid the local optimization. We first investigate the basic principles of GA in CO2 retrieval and then design the corresponding encoding and decoding methods as well as the fitness function. This newly-developed GA is further applied to retrieve the atmospheric CO2 concentration using Atmospheric Infrared Sounder (AIRS) observations from January 2006 to December 2008 centered at 20°N, 144°E. Compared to the aircraft measurements, the GA retrieval yields the small root mean square error of 1.13 ppmv and reproduces good results with the observed seasonal cycle.

Li, Jingyao; Shi, Runhe; Gao, Wei

2013-09-01

269

The orthoenstatite to clinoenstatite transformation by shearing and reversion by annealing: Mechanism and potential applications  

USGS Publications Warehouse

Clinoenstatite (CE) was produced by deforming single-crystal specimens of ortho-enstatite (OE) in several different sorta of experiments. Examination with light and trans-mission electron microscopes shows that the transformation is coherent and involves a macroscopic shear on (100) [001] through an angle of 12.8??1.3 ??, in good agreement with the theoretically expected value of 13.3 ??, and that the transformation is accomplished by glide on (100) of partial dislocations with b= 0.83[001]. Structural analysis provides further insight into the transformation mechanism. Reversion occurs in specimens annealed under a variety of conditions, and thin lamellae of CE in unconstrained, low-strain specimens recover their original shape during transformation back to OE. Our experiments and thermodynamic estimates both suggest that the equilibrium transition temperature is raised roughly 300 ?? C per kilobar of shear stress on (100) [001]. This provides the basis of a method by which it may be possible to determine the magnitude as well as the orientation of the principal stresses that produce CE in nature during deformation of enstatite-bearing rocks. ?? 1975 Springer-Verlag.

Coe, R.S.; Kirby, S.H.

1975-01-01

270

The reversibility of ionic transport in PEDOT with application to a complementary electrochromic device  

NASA Astrophysics Data System (ADS)

The electrochemistry and ion transport properties of PEDOT in different solvents have been investigated. Conductivity enhancement has been observed in dimethyl sulfoxide (DMSO) and ethylene glycol (EG). This is attributed to the transformation of polymer chains from compact to linear structure induced by such high dipole moment solvent treatment (DMSO or EG). The results of electrochemical quartz crystal microbalance (EQCM) indicate that the solvent plays an important role in redox process. The poly(3,4-ethylenedioxythiophene) (PEDOT) reveals a better reversibility of ionic transfer in DMSO compared with that measured in acetonitrile (ACN). A solution and thin film system electrochromic device (ECD) based on 4-phenothiazin-10-yl-anisole (APS) solution and a PEDOT thin film was assembled and studied. The device demonstrates the color change from colorless (0 V) to deep blue violet (1.6 V). A maximum transmittance window 65% was obtained at 520 nm with the operating potentials between 0 and 1.6 V in DMSO electrolytes. Coloration efficiency of the ECD has been found to be 410 cm2/C. No pre-darkening or pre-bleaching of the electrodes is required for assembly of such ECD.

Chiang, Tun-Yuan; Huang, Ming-Chao; Tsai, Chien-Huang

2014-07-01

271

Control of nonlinear systems using periodic parametric perturbations with application to a reversed field pinch  

SciTech Connect

In this thesis, the possibility of controlling low- and high-dimensional chaotic systems by periodically driving an accessible system parameter is examined. This method has been carried out on several numerical systems and the MST Reversed Field Pinch. The numerical systems investigated include the logistic equation, the Lorenz equations, the Roessler equations, a coupled lattice of logistic equations, a coupled lattice of Lorenz equations, the Yoshida equations, which model tearing mode fluctuations in a plasma, and a neural net model for magnetic fluctuations on MST. This method was tested on the MST by sinusoidally driving a magnetic flux through the toroidal gap of the device. Numerically, periodic drives were found to be most effective at producing limit cycle behavior or significantly reducing the dimension of the system when the perturbation frequency was near natural frequencies of unstable periodic orbits embedded in the attractor of the unperturbed system. Several different unstable periodic orbits have been stabilized in this way for the low-dimensional numerical systems, sometimes with perturbation amplitudes that were less than 5% of the nominal value of the parameter being perturbed. In high-dimensional systems, limit cycle behavior and significant decreases in the system dimension were also achieved using perturbations with frequencies near the natural unstable periodic orbit frequencies. Results for the MST were not this encouraging, most likely because of an insufficient drive amplitude, the extremely high dimension of the plasma behavior, large amounts of noise, and a lack of stationarity in the transient plasma pulses.

Mirus, K.A.

1998-06-01

272

Application of Fluorescence In Situ Hybridization (FISH) to Fish Genetics and Genome Mapping  

Microsoft Academic Search

The various applications of the technique of fluorescence in situ hybridization (FISH) to fish genetics will be reviewed for fishes being used as model organisms to study human disease, including those species for which major genome projects have been initiated. ``FISH on fish'' has been used to map highly repetitive sequences including centromere-specific sequences and sex-specific sequences, moderately repetitive sequences

Ruth B. Phillips

2001-01-01

273

A low sidelobe level nonequispaced microstrip array antenna design for BTS application using genetic algorithm  

Microsoft Academic Search

Achieving low side lobe level array antennas without implementation of phase shifters or amplitude tapering is a valuable solution in cases, which the simplicity of the structure is of high importance. In this paper a low sidelobe level microstrip array antenna is designed for GSM base-station antenna application using genetic algorithm by variation of the distances between elements around their

S. Ebadi; N. Amiri; K. Forooraghi

2005-01-01

274

Credit card fraud detection: An application of the gene expression messy genetic algorithm  

Microsoft Academic Search

This paper describes an application of the recently introduced gene expression messy genetic algorithm (GEMGA) (Kargupta, 1996) for detecting fraudulent transactions of credit cards. It also explains the fundamental concepts underlying the GEMGA in the light of the SEARCH (Search Envisioned As Relation and Class Hierarchizing) (Kargupta, 1995) framework.

H. Kargupta; J. R. Gattiker; K. Buescher

1996-01-01

275

Credit card fraud detection: An application of the gene expression messy genetic algorithm  

SciTech Connect

This paper describes an application of the recently introduced gene expression messy genetic algorithm (GEMGA) (Kargupta, 1996) for detecting fraudulent transactions of credit cards. It also explains the fundamental concepts underlying the GEMGA in the light of the SEARCH (Search Envisioned As Relation and Class Hierarchizing) (Kargupta, 1995) framework.

Kargupta, H.; Gattiker, J.R.; Buescher, K.

1996-05-01

276

Application of genetic algorithm for optimization of control strategy in parallel hybrid electric vehicles  

Microsoft Academic Search

This paper describes the application of the genetic algorithm for the optimization of the control parameters in parallel hybrid electric vehicles (HEV). The HEV control strategy is the algorithm according to which energy is produced, used, and saved. Therefore, optimal management of the energy components is a key element for the success of a HEV. In this study, based on

Morteza Montazeri-Gh; Amir Poursamad; Babak Ghalichi

2006-01-01

277

Application of approximate variances of variance components and their ratios in genetic tests  

Microsoft Academic Search

The application and underlying assumptions of formulae used to estimate the variance of variance components and ratios of variance components are fully described for (1) variance components estimated using Henderson's Method 3 (HM3) and Restricted Maximum Likelihood (REML) and (2) ratios of variance components commonly used in genetic tests — biased and unbiased heritabilities. A first-order Taylor series approximation is

M. J. Dieters; T. L. White; R. C. Littell; G. R. Hodge

1995-01-01

278

Genetics and Alcoholism: How Close Are We to Potential Clinical Applications?  

Microsoft Academic Search

Rapid advancement of genetic knowledge has provided a wealth of data demonstrating a significant contribution of genes to the development of alcoholism but has suggested little in the way of clinical applicability. Twin and adoption studies suggest that 50% to 60% of the development of alcoholism is due to heritable factors, and linkage and association studies have identified chromosomal regions

Jeremy Quickfall

2006-01-01

279

Application of the polymerase chain reaction to the diagnosis of human genetic disease  

Microsoft Academic Search

In vitro DNA amplification by means of the polymerase chain reaction is currently revolutionizing human molecular genetics. Since its inception in 1985, a wide variety of different methods and their applications in the diagnosis of disease have been described. This review is intended to serve as a brief guide to current and emerging possibilities in this rapidly expanding field.

Jochen Reiss; David N. Cooper

1990-01-01

280

Applicability of bovine microsatellite markers for population genetic studies on African buffalo (Syncerus caffer)  

Microsoft Academic Search

The applicability of bovine autosomal micro- satellite markers for population genetic studies on African buffalo was investigated. A total of 168 microsatellite markers were tested for PCR amplification on a test panel of seven African buffalo. Amplification was observed for 139 markers (83%), and 101 markers were studied further with 91 (90%) being polymorphic. The mean number of alleles per

Hooft van W. F; O. Hanotte; P. W. Wenink; A. F. Groen; Y. Sugimoto; H. H. T. Prins; A. Teale

1999-01-01

281

THE HUMAN GENOME & GENETIC DISEASES MED263: Bioinformatic Applications to Human Disease  

E-print Network

you will learn. History of the human genome project Structure and content of the human genome HapTHE HUMAN GENOME & GENETIC DISEASES MED263: Bioinformatic Applications to Human Disease #12;WhatMap project Categories of Human Disease: Monogenic (Single gene disorders) Multigenic (Complex disorders

Gleeson, Joseph G.

282

Catalan agriculture and genetically modified organisms (GMOs) — An application of DPSIR model  

Microsoft Academic Search

Although there is a strong controversy regarding the introduction and commercialisation of genetically modified organisms (GMOs) in Europe, GM maize has been sown in Spain since 1998. Stakeholders' positions on the role that GMOs play in trends of the state of agriculture and environment in Catalonia are analysed. The application of the Driving forces –Pressures – State – Impact –

Rosa Binimelis; Iliana Monterroso; Beatriz Rodríguez-Labajos

2009-01-01

283

Genetic algorithm optimization and its application to antenna design  

Microsoft Academic Search

Synthesis of antenna patterns employing iterative optimization techniques has been studied by many authors. However, successful application of these approaches to pattern synthesis has usually been limited to relatively simple arrays or has required careful, intelligent selection of the optimization starting points dictated by the nature of the optimization techniques used and the functions being optimized. This is because conventional

J. Michael Johnson; Yahya Rahmat-samii

1994-01-01

284

Genetic transformation and biotechnological application of the yeast Arxula adeninivorans.  

PubMed

The relatively unknown, non-pathogenic, dimorphic, haploid, ascomycetous yeast Arxula adeninivorans exhibits some unusual properties which are of biotechnological interest. The yeast is able to assimilate and ferment many compounds as sole source of carbon and/or nitrogen, it utilises n-alkanes and degrades starch efficiently. A. adeninivorans features such as thermo- and haloresistance as well as the yeast's uncommon growth and secretion behaviour should be especially emphasised. In media containing up to 20% NaCl, A. adeninivorans is able to grow at cultivation temperatures up to 48 degrees C. Additionally, the dimorphism of the yeast is unusual. Arxula grows at up temperatures of up to 42 degrees C as budding cells, which turn into mycelia at higher temperatures. This environmentally conditioned dimorphism is reversible and budding is reestablished when the cultivation temperature is decreased below 42 degrees C. Alteration of morphology correlates with changes in secretion behaviour. Mycelium cultures accumulate two-fold higher protein concentrations and contain two- to five-fold higher glucoamylase and invertase activities in the medium than budding cells. Based on these unusual properties, Arxula adeninivorans is used for heterologous gene expression and as a gene donor to construct more suitable yeasts for biotechnology. For example the Arxula glucoamylase gene was successfully expressed in Saccharomyces cerevisiae and Kluyveromyces lactis. Both transformed yeasts are able to assimilate and ferment starch as carbon source. A transformation system is used for heterologous gene expression which is based on integration of linearised DNA fragments in two to ten copies, e.g. into the 25S rDNA of A. adeninivorans by homologous recombination. The obtained transformants are mitotically stable. The expression of the lacZ gene from E. coli as well as the XylE gene from Pseudomonas putida indicates the suitability of A. adeninivorans as host for heterologous gene expression. PMID:11131385

Wartmann, T; Kunze, G

2000-11-01

285

Spatial and temporal evolution of organic foulant layers on reverse osmosis membranes in wastewater reuse applications.  

PubMed

Advanced treatment to remove trace constituents and emerging contaminants is an important consideration for wastewater treatment for potable reuse, and reverse osmosis (RO) can be a suitable technology to provide the necessary level of treatment. However, membrane fouling by biological and organic matter is a concern. This research examined the development of the RO membrane fouling layer using a bench-scale membrane bioreactor operating at different solids retention times (SRTs), followed by a custom-designed RO test cell. The RO test cell contained stacked plates that sandwich five sheets of RO membrane material, which can be extracted for autopsy at separate times over the course of an experiment without disturbing the remaining membranes. The MBR-RO system was run continuously for 2 weeks at each SRT. The RO membranes were stained for live and dead cells, protein, and carbohydrate-like materials, and visualized using confocal laser scanning microscopy. Images of the stained foulant layers were obtained at different depths within the foulant layer at each time point for all SRT conditions. As the RO foulant layer developed, changes occurred in the distribution and morphology of the live cells and carbohydrates, but not the proteins. These trends were similar for all three SRT conditions tested. RO membrane fouling increased with increased MBR SRT, and the highest SRT had the highest ratios of live to dead cells and carbohydrate-like material to dead cells. The autopsied membranes were also analyzed for protein and carbohydrate content, and it was found that the carbohydrate concentration on the membranes after 14 days increased as the SRT increased. PMID:24747141

Farias, Elizabeth L; Howe, Kerry J; Thomson, Bruce M

2014-07-01

286

Olfactory bulb recovery following reversible deafferentation with repeated detergent application in the adult zebrafish.  

PubMed

The neuroplasticity and regenerative properties of the olfactory system make it a useful model for studying the ability of the nervous system to recover from damage. We have developed a novel method for examining the effects of long-term deafferentation and regeneration of the olfactory organ and resulting influence on the olfactory bulb in adult zebrafish. To test the hypothesis that repeated damage to the olfactory epithelium causes reduced olfactory bulb afferent input and cessation of treatment allows recovery, we chronically ablated the olfactory organ every 2-3 days for 3 weeks with the detergent Triton X-100 while another group was allowed 3 weeks of recovery following treatment. Animals receiving chronic treatment showed severe morphological disruption of the olfactory organ, although small pockets of epithelium remained. These pockets were labeled by anti-calretinin, indicating the presence of mature olfactory sensory neurons (OSNs). Following a recovery period, the epithelium was more extensive and neuronal labeling increased, with three different morphologies of sensory neurons observed. Repeated peripheral exposure to Triton X-100 also affected the olfactory bulb. Bulb volumes and anti-tyrosine hydroxylase-like immunoreactivity, which is an indicator of afferent activity, were diminished in the olfactory bulb of the chronically treated group compared to the control side. In the recovery group, there was little difference in bulb volume or antibody staining. These results suggest that repeated, long-term nasal irrigation with Triton X-100 eliminates a substantial number of mature OSNs and reduces afferent input to the olfactory bulb. It also appears that these effects are reversible and regeneration will occur in both the peripheral olfactory organ and the olfactory bulb when given time to recover following cessation of treatment. We report here a new method that allows observation not only of the effects of deafferentation on the olfactory bulb but also the effects of reinnervation. PMID:21933699

Paskin, T R; Iqbal, T R; Byrd-Jacobs, C A

2011-11-24

287

Rejection of emerging organic micropollutants in nanofiltration-reverse osmosis membrane applications.  

PubMed

The rejection of emerging trace organics by a variety of commercial reverse osmosis (RO), nanofiltration (NF), and ultra-low-pressure RO (ULPRO) membranes was investigated using TFC-HR, NF-90, NF-200, TFC-SR2, and XLE spiral membrane elements (Koch Membrane Systems, Wilmington, Massachusetts) to simulate operational conditions for drinking-water treatment and wastewater reclamation. In general, the presence of effluent organic matter (EfOM) improved the rejection of ionic organics by tight NF and RO membranes, as compared to a type-II water matrix (adjusted by ionic strength and hardness), likely as a result of a decreased negatively charged membrane surface. Rejection of ionic pharmaceutical residues and pesticides exceeded 95% by NF-90, XLE, and TFC-HR membranes and was above 89% for the NF-200 membrane. Hydrophobic nonionic compounds, such as bromoform and chloroform, exhibited a high initial rejection, as a result of both hydrophobic-hydrophobic solute-membrane interactions and steric exclusion, but rejection decreased significantly after 10 hours of operation because of partitioning of solutes through the membranes. This resulted in a partial removal of disinfection byproducts by the RO membrane TFC-HR. In a type-II water matrix, the effect of increasing feed water recoveries on rejection of hydrophilic ionic and nonionic compounds was compound-dependent and not consistent for different membranes. The presence of EfOM, however, could neutralize the effect of hydrodynamic operating condition on rejection performance. The ULPRO and tight NF membranes were operated at lower feed pressure, as compared to the TFC-HR, and provided a product water quality similar to a conventional RO membrane, regarding trace organics of interest. PMID:15765934

Xu, Pei; Drewes, Jörg E; Bellona, Christopher; Amy, Gary; Kim, Tae-Uk; Adam, Marc; Heberer, Thomas

2005-01-01

288

An Advanced Reverse Osmosis Technology For Application in Nuclear Desalination Facilities  

SciTech Connect

The lack of adequate supplies of clean, safe water is a growing global problem that has reached crisis proportions in many parts of the world. It is estimated that 1.5 billion people do not have access to adequate supplies of safe water, and that as a result nearly 10,000 people die every day and thousands more suffer from a range of debilitating illnesses due to water related diseases. Included in this total is an estimated 2.2 million child deaths annually. As the world's need for additional sources of fresh water continues to grow, seawater and brackish water desalination are providing an increasingly important contribution to the solution of this problem. Because desalination is an energy intensive process, nuclear desalination provides an economically attractive and environmentally sound alternative to the burning of fossil fuels for desalination. Nevertheless, the enormity of the problem dictates that additional steps must be taken to improve the efficiency of energy utilization and reduce the cost of water production in order to reduce the financial and environmental burden to communities in need. An advanced reverse osmosis (RO) desalination technology has been developed that emphasizes a nontraditional approach to system design and operation, and makes use of a sophisticated design optimization process that can lead to highly optimized design configurations and operating regimes. The technology can be coupled with a nuclear generating station (NGS) to provide an integrated facility for the co-generation of both water and electricity. Waste heat from the NGS allows the use of 'preheated' feedwater into the RO system, improving the efficiency of the RO process and reducing the cost of water production. Because waste heat, rather than process heat, is used the desalination system can be readily coupled to any existing or advanced reactor technology with little or no impact on reactor design and operation and without introducing additional reactor safety considerations. Analyses of nuclear desalination systems employing this advanced RO technology under a variety of seawater feed conditions have consistently shown that the cost of potable water production can be reduced by as much as 15-20% relative to systems designed in a more traditional manner. Demonstration testing has been carried out using a trailer mounted system producing up to 150 m{sup 3}/d of potable water. Experimental results from the demonstration testing are behaving as expected based on the analytical performance models, validating the advanced design concept and confirming that the performance improvements indicated by the analyses can be achieved in operating systems. Further demonstration testing is planned using a 1000 m{sup 3}/d containerized system, currently under design, coupled to an existing nuclear power reactor. (authors)

Humphries, J.R.; Davies, K.; Ackert, J.A. [CANDESAL Technologies Limited, Ottawa (Canada)

2002-07-01

289

Modelling liquid crystal elastomers and potential application as a reversibly switchable adhesive  

NASA Astrophysics Data System (ADS)

Liquid crystal elastomers (LCEs) are rubbery materials that composed of liquid crystalline polymers (LCPs) crosslinked into a network. The rod-like mesogens incorporated into the LCPs are have random orientations in the high temperature isotropic phase, but can adopt the canonical liquid crystalline phases as the temperature is lowered. Smectic liquid crystal elastomers have highly anisotropic mechanical behaviour. This arises in side chain smectic-A systems because the smectic layers behave as if they are embedded in the rubber matrix [1]. The macroscopic mechanical behaviour of these solids is sensitive to the buckling of the layers, so is a multiscale problem. A coarse grained free energy that includes the fine-scale buckling of the layers has been developed [2], which enables continuum modelling of these systems. In the first part of this talk I present a model of the mechanical behaviour of side chain smectic elastomers. The properties of nematic LCEs, such as their high loss tangent, and mechanical strain hardening, might enable them to be used as reversibly switchable pressure sensitive adhesive (PSA). PSAs are typically made from viscoelastic polymers. The quality of their adhesion can be measured by the tack energy, which is the work required to separate two bodies. To obtain a high tack energy a PSA should be capable of a large strain. It should strain soften at low strain to produce crack blunting, and then strain harden at high strain to stiffen the fibrils formed late in the debonding process. I will present a model of the tack energy of weakly crosslinked nematic polymers. To describe the constitutive properties of this system the nematic dumbbell model of Maffettone et al. was used [3]. This constutitive model was then combined with the block model of Yamaguchi et al. describing PSAs [4]. It was found that the parallel orientation of the nematic has a higher tack energy than both the isotropic and the perpendicular director orientation [5].[4pt] [1] C. M. Spillmann et al, Phys. Rev. E 82, 031705, (2010).[0pt] [2] J. Adams, S. Conti and A. DeSimone, Mathematical Models and methods in Applied Sciences, 18, 1 (2008).[0pt] [3] P. L. Maffettone and G. Marrucci, Journal of Rheology 36 (8) 1547 (1992).[0pt] [4] T. Yamaguchi, H. Morita, and M. Doi, Eur. Phys. J. E 20, 7 (2006).[0pt] [5] D. R. Corbett and J. M. Adams, Soft Matter, DOI:10.1039/C2SM26868J (2012).

Adams, James

2013-03-01

290

The Design and Application of Genetically Encodable Biosensors Based on Fluorescent Proteins  

PubMed Central

To track the activity of cellular signaling molecules within the endogenous cellular environment, researchers have developed a diverse set of genetically encodable fluorescent biosensors. These sensors, which can be targeted to specific subcellular regions to monitor specific pools of a given signaling molecule in real time, rely upon conformational changes in a sensor domain to alter the photophysical properties of green fluorescent protein (GFP) family members. In this introductory chapter, we first discuss the properties of GFP family members before turning our attention to the design and application of genetically encodable fluorescent biosensors to live cell imaging. PMID:24052376

Newman, Robert H.; Zhang, Jin

2014-01-01

291

Detection of Colorado tick fever virus by using reverse transcriptase PCR and application of the technique in laboratory diagnosis.  

PubMed Central

Colorado tick fever (CTF) virus elicits an acute illness in humans, producing nonspecific flu-like symptoms and a biphasic fever in approximately 50% of patients. The disease is transmitted by the adult Rocky Mountain wood tick (Dermacentor andersoni), and therefore incidence is limited by the habitat and life cycle of that vector. The early symptoms of infection are difficult to distinguish from those of several other agents, especially Rickettsia rickettsii. Serologic testing is usually unable to provide evidence of CTF viral infection during the acute phase because of the late appearance of the various antibodies. Here we report the development and clinical application of a test to diagnose this disease during the acute stages. Oligonucleotide primers to the S2 segment of CTF (Florio) virus were made, and these were used in the amplification of a 528-bp fragment of DNA, transcribed from the double-stranded CTF virus RNA template by reverse transcriptase PCR. RNAs processed from 16 CTF virus isolates yielded similar results when analyzed on agarose gels. These were distinguishable from their antigenic relatives Eyach, S6-14-03, and T5-2092 and from other coltiviruses and an orbivirus but not from the antigenically distinct CTF virus-related isolate 720896. A mouse model demonstrated the utility of this method with whole-blood specimens, and CTF virus was successfully detected in human sera from the initial day of the onset of symptoms to 8 days later. The reverse transcriptase PCR method is a promising tool for the early diagnosis of CTF viral infection, or for ruling out CTF virus as the etiologic agent, in order to facilitate appropriate medical support. PMID:9114408

Johnson, A J; Karabatsos, N; Lanciotti, R S

1997-01-01

292

Large volume injection of 1-octanol as sample diluent in reversed phase liquid chromatography: Application in bioanalysis for assaying of indapamide in whole blood  

Microsoft Academic Search

Large volume injection of samples in strong diluents immiscible with the mobile phases used in reversed phase liquid chromatography (RPLC) has been recently introduced in practice. In the present work, the potential of the technique has been evaluated for bioanalytical applications. The process consists of the liquid–liquid extraction of indapamide from whole blood into 1-octanol, followed by the direct injection

Stefan Udrescu; Iulia Daniela Sora; Florin Albu; Victor David; Andrei Medvedovici

2011-01-01

293

Advances in Time Reversal Nonlinear Elastic Wave Spectroscopy (TR NEWS) for Application to Nonlinear NonDestructive Evaluation, Imaging and Source Complexity  

E-print Network

in a solid. If a crack is present, nonlinear mixing results at the crack, and manifestations of waveAdvances in Time Reversal Nonlinear Elastic Wave Spectroscopy (TR NEWS) for Application Nonlinear Elastic Wave Spectroscopy (TR NEWS). The basis of the method is to excite one or more waves

294

Clinical, genetic, and pharmacogenetic applications of the Invader assay.  

PubMed

The Invader technology has been developed for the detection of nucleic acids. It is a signal amplification system able to accurately quantify DNA and RNA targets with high sensitivity. Exquisite specificity is achieved by combining hybridization with enzyme recognition, which provides the ability to discriminate mutant from wild-type at ratios greater than 1/1000 (mutant/wt). The technology is isothermal and flexible and incorporates a homogeneous fluorescence readout. It is therefore readily adaptable for use in clinical reference laboratories, as well as high-throughput applications using 96-, 384-, and 1,536-well microtiter plate formats. The molecular mechanism of the system and specific applications for use in clinical and research laboratories are described. These include direct analysis of unamplified human genomic DNA to detect mutations and single-nucleotide polymorphisms associated with factor V Leiden, factor II, cystic fibrosis, and apolipoprotein E, and gene expression assays that quantify messenger RNA levels in cells using direct lysates. PMID:10671646

Kwiatkowski, R W; Lyamichev, V; de Arruda, M; Neri, B

1999-12-01

295

Genetics  

NSDL National Science Digital Library

Genetics is the branch of biology that studies the ways in which hereditary information is passed on from the parents to their offspring. As we study this unit, I will be asking you to visit the following websites to emphasize concepts brought up during class. DNA Structure and Replication Build a DNA molecule Use this website to practice matching up complementary nucleotides in the DNA molecule. How DNA Replicates Take a look at this short video clip that demonstrates how the DNA molecule replicates. A Science Odyssey :You Try It: DNA Workshop When you get to this website, click on \\"Go directly to the DNA Workshop\\". Click on DNA replication on the left ...

Miss Goodfellow

2007-10-23

296

Genetics  

NSDL National Science Digital Library

This online tutorial from the TheTech Museum of Innovation focuses on genetics. The interactive topics will initially introduce the user to the DNA, chromosomes, and the make up of human genes. Further topics will examine forensic science, the history of forensics, fingerprinting, and cloning background research and community response to cloning. Finally, the resource provides connections to gallery exhibits, science labs, and a design challenge that engages the learner to write a persuasive letter to a group or organization responsible for cloning or DNA decision making. Copyright 2005 International Technology Education Association

The Tech Museum of Innovation

2004-01-01

297

Reverse Osmosis  

NSDL National Science Digital Library

Reverse Osmosis: In reverse osmosis, the idea is to use the membrane to act like an extremely fine filter to create drinkable water from salty (or otherwise contaminated) water. A complete explanation is here along with helpful diagrams.

298

Application of a reversible chemical reaction system to solar thermal power plants  

NASA Technical Reports Server (NTRS)

Three distributed dish solar thermal power systems using various applications of SO2/SO3 chemical energy storage and transport technology were comparatively assessed. Each system features various roles for the chemical system: (1) energy storage only, (2) energy transport, or (3) energy transport and storage. These three systems were also compared with the dish-Stirling, using electrical transport and battery storage, and the central receiver Rankine system, with thermal storage, to determine the relative merit of plants employing a thermochemical system. As an assessment criterion, the busbar energy costs were compared. Separate but comparable solar energy cost computer codes were used for distributed receiver and central receiver systems. Calculations were performed for capacity factors ranging from 0.4 to 0.8. The results indicate that SO2/SO3 technology has the potential to be more cost effective in transporting the collected energy than in storing the energy for the storage capacity range studied (2-15 hours)

Hanseth, E. J.; Won, Y. S.; Seibowitz, L. P.

1980-01-01

299

Chloroplast Transformation and Reverse Genetics  

Microsoft Academic Search

For chloroplast transformation, the most efficient method to introduce DNA is particle bombardment. To then select the cells which harbor a transformed plastid, two classes of markers are available. With one class, selection is based on the rescue of a non-photosynthetic mutant with the wild-type chloroplast gene. With the other class, selection is based on a mutation or a foreign

Michel Goldschmidt-Clermont

300

BB Seminar: Methods application to genetic variants for smoking & lung cancer  

Cancer.gov

Methods developed for causal mediation analysis with a dichotomous outcome, applicable to case-control studies via prevalence weighting will be presented. These methods generalize traditional approaches to mediation in the social sciences by allowing for interactions and non-linear models. Methods for sensitivity analysis for unmeasured confounding and measurement error in the context of mediated effects will be described. The methodology is used to resolve a question concerning direct and indirect effects in genetic epidemiology.

301

Conifer genetic engineering: Particle bombardment and Agrobacterium -mediated gene transfer and its application in future forests  

Microsoft Academic Search

Many important advances in forest biotechnology have been made. The use of genetic transformation and the applications of\\u000a transgenic trees in modern forestry is now an important field. Two basic methodologies particle bombardment andAgrobacterium-mediated transformation have been used on conifers. However, routine procedures exist for only a limited number of conifers.\\u000a As a result only a few species have been

Tang Wei

2001-01-01

302

Evaluating the performance of a block updating MCMC sampler in a simple genetic application  

Microsoft Academic Search

Markov chain Monte Carlo (MCMC) methods have provided an enormous break-through in the analysis of large complex problems\\u000a such as those which frequently arise in genetic applications. The richness of the inference and the flexibility of an MCMC\\u000a Bayesian approach in terms of design, data structure that can be analyzed, and models that can be posed, is indisputable.\\u000a However, despite

N. A. Sheehan; B. Guldbrandtsen; D. A. Sorensen

2007-01-01

303

Reversal of Acute Complex Regional Pain Syndrome Using the Practical Application of Neurodiagnostic Evaluation Process: A Case Study  

PubMed Central

In 2005, a patient in my practice developed complex regional pain syndrome type 1 (CRPS 1) after bunion surgery. The condition was properly diagnosed within 4 weeks with a diagnostic technique that I routinely use to diagnose chronic musculoskeletal pain, and it was successfully treated. The tests, which are based on primitive and postural reflexes in infants, were adapted to reflect normal and abnormal motor behaviors in adults after provocation of reflexes of the autonomic nervous system (afferent C fibers in peripheral nerves). Approximately 60 days after my patient’s operation, the tests indicated a positive reflex at the posterior tibial nerve in the operated foot. Surgery to remove an accessory ossicle from the talus adjacent to this nerve resolved the CRPS 1 within 2 weeks. Since CRPS 1 is a dysfunctional state of the autonomic regulatory control of pain, it was postulated that a test based on autonomic nerve function could isolate the source of CRPS 1. The Practical Application of Neurodiagnostic Evaluation process was shown to be diagnostic for the cause of acute CRPS 1 and to allow its reversal. Further evaluation of the test for diagnosis and treatment of CRPS is needed. PMID:24355904

Anderson, Karen E

2013-01-01

304

Preparation and application of reversed phase Chromatorotor for the isolation of natural products by centrifugal preparative chromatography.  

PubMed

A method of preparation of rotors with a reversed phase (RP) solid silica gel sorbent layer has been developed for centrifugal preparative chromatography (CPC), also known as rotational planar chromatography (RPC). The rotors consist of binder free RP solid SiO2 layers of different thicknesses packed between two supported circular glass discs and can be used in any appropriate device for centrifugal chromatography, like Chromatotron and CycloGraph. Polar and /or semi-polar compounds with close R(f) values, as well as extracts and column fractions were separated and/or purified in a preparative and/or semi-preparative scale using the RP rotors, eluted with mixtures of aqueous-based solvents. We herein report three examples of its application, using RP Chromatorotors, for the isolation of the diastereoisomeric alkaloids banistenosides I and II from Banisteriopsis caapi, saponins III and IV from Fagonia cretica, and the sesquiterpenes artemisinin (V) and artemisinic acid (VI) from Artemisia annua. PMID:23678798

Muhammad, Ilias; Samoylenko, Volodymyr; Machumi, Francis; Zakia, Mohamed Ahmed; Mohammed, Rabab; Hetta, Mona H; Gillum, Van

2013-03-01

305

Engineering Applications of Artificial Intelligence 14 (2001) 114 Genetic adaptive control for an inverted wedge: experiments and  

E-print Network

Engineering Applications of Artificial Intelligence 14 (2001) 1­14 Genetic adaptive control. Passino* Department of Electrical Engineering, The Ohio State University, 2015 Neil Avenue, Columbus, OH and real-time implementation issues will be discussed and the genetic adaptive strategy will be compared

306

Multi-Atlas Tensor-Based Morphometry and its Application to a Genetic Study of 92 Twins  

E-print Network

Multi-Atlas Tensor-Based Morphometry and its Application to a Genetic Study of 92 Twins Natasha of Queensland, Brisbane, Australia 3 Genetic Epidemiology Lab, Queensland Institute of Medical Research the transformations. Using an MRI dataset from 23 monozygotic and 23 dizygotic twin pairs, we instead registered each

Paris-Sud XI, Université de

307

Extracting directed information flow networks: an application to genetics and semantics.  

PubMed

We introduce a general method to infer the directional information flow between populations whose elements are described by n-dimensional vectors of symbolic attributes. The method is based on the Jensen-Shannon divergence and on the Shannon entropy and has a wide range of application. We show here the results of two applications: first we extract the network of genetic flow between meadows of the seagrass Poseidonia oceanica, where the meadow elements are specified by sets of microsatellite markers, and then we extract the semantic flow network from a set of Wikipedia pages, showing the semantic channels between different areas of knowledge. PMID:21405885

Masucci, A P; Kalampokis, A; Eguíluz, V M; Hernández-García, E

2011-02-01

308

Extracting directed information flow networks: An application to genetics and semantics  

NASA Astrophysics Data System (ADS)

We introduce a general method to infer the directional information flow between populations whose elements are described by n-dimensional vectors of symbolic attributes. The method is based on the Jensen-Shannon divergence and on the Shannon entropy and has a wide range of application. We show here the results of two applications: first we extract the network of genetic flow between meadows of the seagrass Poseidonia oceanica, where the meadow elements are specified by sets of microsatellite markers, and then we extract the semantic flow network from a set of Wikipedia pages, showing the semantic channels between different areas of knowledge.

Masucci, A. P.; Kalampokis, A.; Eguíluz, V. M.; Hernández-García, E.

2011-02-01

309

Single Real-Time Reverse Transcription-PCR Assay for Detection and Quantification of Genetically Diverse HIV-1, SIVcpz, and SIVgor Strains  

PubMed Central

Although antiretroviral treatment availability has improved, the virological monitoring of patients remains largely uneven across regions. In addition, viral quantification tests are suffering from human immunodeficiency virus type 1 (HIV-1) genetic diversity, fueled by the emergence of new recombinants and of lentiviruses from nonhuman primates. We developed a real-time reverse transcription-PCR (RT-PCR) assay that is relatively inexpensive and able to detect and quantify all circulating forms of HIV-1 and its simian immunodeficiency virus (SIV) precursors, SIVcpz and SIVgor. Primers and a probe were designed to detect all variants of the HIV-1/SIVcpz/SIVgor lineage. HIV-1 M plasma (n = 190; 1.68 to 7.78 log10 copies/ml) representing eight subtypes, nine circulating recombinant forms, and 21 unique recombinant forms were tested. The mean PCR efficiency was 99%, with low coefficients of intra- and interassay variation (<5%) and a limit of quantification of <2.50 log10 copies/ml, with a 200-?l plasma volume. On the studied range, the specificity and the analytical sensitivity were 100 and 97.4%, respectively. The viral loads were highly correlated (r = 0.95, P < 0.0001) with the reference method (generic HIV assay; Biocentric) and had no systematic difference, irrespective of genotype. Furthermore, 22 HIV-1 O plasmas were screened and were better quantified compared to the gold-standard RealTime HIV-1 assay (Abbott), including four samples that were only quantified by our assay. Finally, we could quantify SIVcpzPtt and SIVcpzPts from chimpanzee plasma (n = 5) and amplify SIVcpz and SIVgor from feces. Thus, the newly developed real-time RT-PCR assay detects and quantifies strains from the HIV-1/SIVcpz/SIVgor lineage, including a wide diversity of group M strains and HIV-1 O. It can therefore be useful in geographical areas of high HIV diversity and at risk for the emergence of new HIV variants. PMID:23254130

Etienne, Lucie; Eymard-Duvernay, Sabrina; Aghokeng, Avelin; Butel, Christelle; Monleau, Marjorie

2013-01-01

310

Simulating Population Genetics of Pathogen Vectors in Changing Landscapes: Guidelines and Application with Triatoma brasiliensis  

PubMed Central

Background Understanding the mechanisms that influence the population dynamics and spatial genetic structure of the vectors of pathogens infecting humans is a central issue in tropical epidemiology. In view of the rapid changes in the features of landscape pathogen vectors live in, this issue requires new methods that consider both natural and human systems and their interactions. In this context, individual-based model (IBM) simulations represent powerful yet poorly developed approaches to explore the response of pathogen vectors in heterogeneous social-ecological systems, especially when field experiments cannot be performed. Methodology/Principal Findings We first present guidelines for the use of a spatially explicit IBM, to simulate population genetics of pathogen vectors in changing landscapes. We then applied our model with Triatoma brasiliensis, originally restricted to sylvatic habitats and now found in peridomestic and domestic habitats, posing as the most important Trypanosoma cruzi vector in Northeastern Brazil. We focused on the effects of vector migration rate, maximum dispersal distance and attraction by domestic habitat on T. brasiliensis population dynamics and spatial genetic structure. Optimized for T. brasiliensis using field data pairwise fixation index (FST) from microsatellite loci, our simulations confirmed the importance of these three variables to understand vector genetic structure at the landscape level. We then ran prospective scenarios accounting for land-use change (deforestation and urbanization), which revealed that human-induced land-use change favored higher genetic diversity among sampling points. Conclusions/Significance Our work shows that mechanistic models may be useful tools to link observed patterns with processes involved in the population genetics of tropical pathogen vectors in heterogeneous social-ecological landscapes. Our hope is that our study may provide a testable and applicable modeling framework to a broad community of epidemiologists for formulating scenarios of landscape change consequences on vector dynamics, with potential implications for their surveillance and control. PMID:25102068

Rebaudo, Francois; Costa, Jane; Almeida, Carlos E.; Silvain, Jean-Francois; Harry, Myriam; Dangles, Olivier

2014-01-01

311

Applications of Population Genetics to Animal Breeding, from Wright, Fisher and Lush to Genomic Prediction  

PubMed Central

Although animal breeding was practiced long before the science of genetics and the relevant disciplines of population and quantitative genetics were known, breeding programs have mainly relied on simply selecting and mating the best individuals on their own or relatives’ performance. This is based on sound quantitative genetic principles, developed and expounded by Lush, who attributed much of his understanding to Wright, and formalized in Fisher’s infinitesimal model. Analysis at the level of individual loci and gene frequency distributions has had relatively little impact. Now with access to genomic data, a revolution in which molecular information is being used to enhance response with “genomic selection” is occurring. The predictions of breeding value still utilize multiple loci throughout the genome and, indeed, are largely compatible with additive and specifically infinitesimal model assumptions. I discuss some of the history and genetic issues as applied to the science of livestock improvement, which has had and continues to have major spin-offs into ideas and applications in other areas. PMID:24395822

Hill, William G.

2014-01-01

312

The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events  

PubMed Central

Background Due to human variations in genetic susceptibility, vaccination often triggers adverse events in a small population of vaccinees. Based on our previous work on ontological modeling of genetic susceptibility to disease, we developed an Ontology of Genetic Susceptibility Factors (OGSF), a biomedical ontology in the domain of genetic susceptibility and genetic susceptibility factors. The OGSF framework was then applied in the area of vaccine adverse events (VAEs). Results OGSF aligns with the Basic Formal Ontology (BFO). OGSF defines ‘genetic susceptibility’ as a subclass of BFO:disposition and has a material basis ‘genetic susceptibility factor’. The ‘genetic susceptibility to pathological bodily process’ is a subclasses of ‘genetic susceptibility’. A VAE is a type of pathological bodily process. OGSF represents different types of genetic susceptibility factors including various susceptibility alleles (e.g., SNP and gene). A general OGSF design pattern was developed to represent genetic susceptibility to VAE and associated genetic susceptibility factors using experimental results in genetic association studies. To test and validate the design pattern, two case studies were populated in OGSF. In the first case study, human gene allele DBR*15:01 is susceptible to influenza vaccine Pandemrix-induced Multiple Sclerosis. The second case study reports genetic susceptibility polymorphisms associated with systemic smallpox VAEs. After the data of the Case Study 2 were represented using OGSF-based axioms, SPARQL was successfully developed to retrieve the susceptibility factors stored in the populated OGSF. A network of data from the Case Study 2 was constructed by using ontology terms and individuals as nodes and ontology relations as edges. Different social network analys is (SNA) methods were then applied to verify core OGSF terms. Interestingly, a SNA hub analysis verified all susceptibility alleles of SNPs and a SNA closeness analysis verified the susceptibility genes in Case Study 2. These results validated the proper OGSF structure identified different ontology aspects with SNA methods. Conclusions OGSF provides a verified and robust framework for representing various genetic susceptibility types and genetic susceptibility factors annotated from experimental VAE genetic association studies. The RDF/OWL formulated ontology data can be queried using SPARQL and analyzed using centrality-based network analysis methods. PMID:24963371

2014-01-01

313

Applications of Genetically Modified Tools to Safety Assessment in Drug Development  

PubMed Central

The process of new drug development consists of several stages; after identifying potential candidate compounds, preclinical studies using animal models link the laboratory and human clinical trials. Among many steps in preclinical studies, toxicology and safety assessments contribute to identify potential adverse events and provide rationale for setting the initial doses in clinical trials. Gene modulation is one of the important tools of modern biology, and is commonly employed to examine the function of genes of interest. Advances in new drug development have been achieved by exploding information on target selection and validation using genetically modified animal models as well as those of cells. In this review, a recent trend of genetically modified methods is discussed with reference to safety assessments, and the exemplary applications of gene-modulating tools to the tests in new drug development were summarized. PMID:24278499

Kay, Hee Yeon; Wu, Hongmin; Lee, Seo In

2010-01-01

314

Gene genealogies for genetic association mapping, with application to Crohn's disease.  

PubMed

A gene genealogy describes relationships among haplotypes sampled from a population. Knowledge of the gene genealogy for a set of haplotypes is useful for estimation of population genetic parameters and it also has potential application in finding disease-predisposing genetic variants. As the true gene genealogy is unknown, Markov chain Monte Carlo (MCMC) approaches have been used to sample genealogies conditional on data at multiple genetic markers. We previously implemented an MCMC algorithm to sample from an approximation to the distribution of the gene genealogy conditional on haplotype data. Our approach samples ancestral trees, recombination and mutation rates at a genomic focal point. In this work, we describe how our sampler can be used to find disease-predisposing genetic variants in samples of cases and controls. We use a tree-based association statistic that quantifies the degree to which case haplotypes are more closely related to each other around the focal point than control haplotypes, without relying on a disease model. As the ancestral tree is a latent variable, so is the tree-based association statistic. We show how the sampler can be used to estimate the posterior distribution of the latent test statistic and corresponding latent p-values, which together comprise a fuzzy p-value. We illustrate the approach on a publicly-available dataset from a study of Crohn's disease that consists of genotypes at multiple SNP markers in a small genomic region. We estimate the posterior distribution of the tree-based association statistic and the recombination rate at multiple focal points in the region. Reassuringly, the posterior mean recombination rates estimated at the different focal points are consistent with previously published estimates. The tree-based association approach finds multiple sub-regions where the case haplotypes are more genetically related than the control haplotypes, and that there may be one or multiple disease-predisposing loci. PMID:24348515

Burkett, Kelly M; Greenwood, Celia M T; McNeney, Brad; Graham, Jinko

2013-01-01

315

Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture  

PubMed Central

Controlling the sex ratio is essential in finfish farming. A balanced sex ratio is usually good for broodstock management, since it enables to develop appropriate breeding schemes. However, in some species the production of monosex populations is desirable because the existence of sexual dimorphism, primarily in growth or first time of sexual maturation, but also in color or shape, can render one sex more valuable. The knowledge of the genetic architecture of sex determination (SD) is convenient for controlling sex ratio and for the implementation of breeding programs. Unlike mammals and birds, which show highly conserved master genes that control a conserved genetic network responsible for gonad differentiation (GD), a huge diversity of SD mechanisms has been reported in fish. Despite theory predictions, more than one gene is in many cases involved in fish SD and genetic differences have been observed in the GD network. Environmental factors also play a relevant role and epigenetic mechanisms are becoming increasingly recognized for the establishment and maintenance of the GD pathways. Although major genetic factors are frequently involved in fish SD, these observations strongly suggest that SD in this group resembles a complex trait. Accordingly, the application of quantitative genetics combined with genomic tools is desirable to address its study and in fact, when applied, it has frequently demonstrated a multigene trait interacting with environmental factors in model and cultured fish species. This scenario has notable implications for aquaculture and, depending upon the species, from chromosome manipulation or environmental control techniques up to classical selection or marker assisted selection programs, are being applied. In this review, we selected four relevant species or fish groups to illustrate this diversity and hence the technologies that can be used by the industry for the control of sex ratio: turbot and European sea bass, two reference species of the European aquaculture, and salmonids and tilapia, representing the fish for which there are well established breeding programs. PMID:25324858

Martínez, Paulino; Viñas, Ana M.; Sánchez, Laura; Díaz, Noelia; Ribas, Laia; Piferrer, Francesc

2014-01-01

316

Genetic Counseling Program Information  

E-print Network

Genetic Counseling Program Information for Potential Applicants #12;Wayne State Genetic Counseling Program Overview "Genetic counseling is the process of helping people understand and adapt to the medical, psychological, and familial implications of genetic contributions to disease. The process integrates

Berdichevsky, Victor

317

Lattice-based clustering and genetic programming for coordinate transformation in GPS applications  

NASA Astrophysics Data System (ADS)

Coordinate transformation is essential in many georeferencing applications. Level-wised transformation can be considered as a regression problem and done by machine-learning approaches. However, inaccurate and biased results are usually derived when training data do not uniformly distribute. In this paper, the performance of regression-based coordinate transformation for GPS applications is discussed. A lattice-based clustering method is developed and integrated with genetic programming for building better regression models of coordinate transformation. The GPS application area is first partitioned into lattices with lattice sizes being determined by the geographic locations and distribution of the GPS reference points. Clustering is then performed on lattices, not on data points. Each cluster of lattices serves as a training data set for a genetic regression model of coordinate transformation. In this manner, the data points contained in the different lattices can be considered to be of the same importance. Biased regression results caused by the imbalanced distribution of data can also be eliminated. The experimental results show that the proposed method can further improve the positioning accuracy than previous methods.

Wu, Chih-Hung; Su, Wei-Han

2013-03-01

318

Enhanced conjugation of Candida rugosa lipase onto multiwalled carbon nanotubes using reverse micelles as attachment medium and application in nonaqueous biocatalysis.  

PubMed

Three liquid phases (viz. aqueous, nonaqueous, and reverse micelles) were scrutinized as medium for attachment of the enzyme Candida rugosa lipase (CRL) onto multiwalled carbon nanotubes (CNTs). The nanotubes were functionalized to attain carboxyl and amino groups on their surfaces before enzyme conjugation. Transmission electron microscopy and Fourier transformation infrared spectroscopic studies were used for characterization of the nanotubes during the course of functionalization. High enzyme loadings associated with the functionalized CNTs were observed when reverse micelles were used as the attachment medium. In addition, high activity in terms of ester synthesis in organic solvents was also observed while using those preparations. The nanobioconjugates prepared using reverse micelles were found to be highly sturdy and exhibited appreciable operational stability of around 95 ± 3% at 20th cycle (in case of carboxylated nanotubes) and 90 ± 5% at 10th cycle (in case of aminated nanotubes) for esterification. This shows the potential application of reverse micelles as the attachment medium for surface active enzymes such as CRL onto CNTs. PMID:24828252

Raghavendra, Tripti; Vahora, Uzma; Shah, Amita R; Madamwar, Datta

2014-01-01

319

Application of Homozygosity Haplotype Analysis to Genetic Mapping with High-Density SNP Genotype Data  

PubMed Central

Background In families segregating a monogenic genetic disorder with a single disease gene introduction, patients share a mutation-carrying chromosomal interval with identity-by-descent (IBD). Such a shared chromosomal interval or haplotype, surrounding the actual pathogenic mutation, is typically detected and defined by multipoint linkage and phased haplotype analysis using microsatellite or SNP genotype data. High-density SNP genotype data presents a computational challenge for conventional genetic analyses. A novel non-parametric method termed Homozygosity Haplotype (HH) was recently proposed for the genome-wide search of the autosomal segments shared among patients using high density SNP genotype data. Methodology/Principal Findings The applicability and the effectiveness of HH in identifying the potential linkage of disease causative gene with high-density SNP genotype data were studied with a series of monogenic disorders ascertained in eastern Canadian populations. The HH approach was validated using the genotypes of patients from a family affected with a rare autosomal dominant disease Schnyder crystalline corneal dystrophy. HH accurately detected the ?1 Mb genomic interval encompassing the causative gene UBIAD1 using the genotypes of only four affected subjects. The successful application of HH to identify the potential linkage for a family with pericentral retinal disorder indicates that HH can be applied to perform family-based association analysis by treating affected and unaffected family members as cases and controls respectively. A new strategy for the genome-wide screening of known causative genes or loci with HH was proposed, as shown the applications to a myoclonus dystonia and a renal failure cohort. Conclusions/Significance Our study of the HH approach demonstrates that HH is very efficient and effective in identifying potential disease linked region. HH has the potential to be used as an efficient alternative approach to sequencing or microsatellite-based fine mapping for screening the known causative genes in genetic disease study. PMID:19399176

Jiang, Haiyan; Orr, Andrew; Guernsey, Duane L.; Robitaille, Johane; Asselin, Géraldine; Samuels, Mark E.; Dubé, Marie-Pierre

2009-01-01

320

The Systems Genetics Resource: A Web Application to Mine Global Data for Complex Disease Traits  

PubMed Central

The Systems Genetics Resource (SGR) (http://systems.genetics.ucla.edu) is a new open-access web application and database that contains genotypes and clinical and intermediate phenotypes from both human and mouse studies. The mouse data include studies using crosses between specific inbred strains and studies using the Hybrid Mouse Diversity Panel. SGR is designed to assist researchers studying genes and pathways contributing to complex disease traits, including obesity, diabetes, atherosclerosis, heart failure, osteoporosis, and lipoprotein metabolism. Over the next few years, we hope to add data relevant to deafness, addiction, hepatic steatosis, toxin responses, and vascular injury. The intermediate phenotypes include expression array data for a variety of tissues and cultured cells, metabolite levels, and protein levels. Pre-computed tables of genetic loci controlling intermediate and clinical phenotypes, as well as phenotype correlations, are accessed via a user-friendly web interface. The web site includes detailed protocols for all of the studies. Data from published studies are freely available; unpublished studies have restricted access during their embargo period. PMID:23730305

van Nas, Atila; Pan, Calvin; Ingram-Drake, Leslie A.; Ghazalpour, Anatole; Drake, Thomas A.; Sobel, Eric M.; Papp, Jeanette C.; Lusis, Aldons J.

2013-01-01

321

Insights into the biology of Borrelia burgdorferi gained through the application of molecular genetics.  

PubMed

Borrelia burgdorferi, the vector-borne bacterium that causes Lyme disease, was first identified in 1982. It is known that much of the pathology associated with Lyme borreliosis is due to the spirochete's ability to infect, colonize, disseminate, and survive within the vertebrate host. Early studies aimed at defining the biological contributions of individual genes during infection and transmission were hindered by the lack of adequate tools and techniques for molecular genetic analysis of the spirochete. The development of genetic manipulation techniques, paired with elucidation and annotation of the B. burgdorferi genome sequence, has led to major advancements in our understanding of the virulence factors and the molecular events associated with Lyme disease. Since the dawn of this genetic era of Lyme research, genes required for vector or host adaptation have garnered significant attention and highlighted the central role that these components play in the enzootic cycle of this pathogen. This chapter covers the progress made in the Borrelia field since the application of mutagenesis techniques and how they have allowed researchers to begin ascribing roles to individual genes. Understanding the complex process of adaptation and survival as the spirochete cycles between the tick vector and vertebrate host will lead to the development of more effective diagnostic tools as well as identification of novel therapeutic and vaccine targets. In this chapter, the Borrelia genes are presented in the context of their general biological roles in global gene regulation, motility, cell processes, immune evasion, and colonization/dissemination. PMID:24377854

Groshong, Ashley M; Blevins, Jon S

2014-01-01

322

Field application of a genetically engineered microorganism for polycyclic aromatic hydrocarbon bioremediation process monitoring and control  

SciTech Connect

On October 30, 1996, the US Environmental Protection Agency (EPA) commenced the first test release of genetically engineered microorganisms (GEMs) for use in bioremediation. The specific objectives of the investigation were multifaceted and include (1) testing the hypothesis that a GEM can be successfully introduced and maintained in a bioremediation process, (2) testing the concept of using, at the field scale, reporter organisms for direct bioremediation process monitoring and control, and (3) acquiring data that can be used in risk assessment decision making and protocol development for future field release applications of GEMs. The genetically engineered strain under investigation is Pseudomonas fluorescens strain HK44 (King et al., 1990). The original P. fluorescens parent strain was isolated from polycyclic aromatic hydrocarbon (PAH) contaminated manufactured gas plant soil. Thus, this bacterium is able to biodegrade naphthalene (as well as other substituted naphthalenes and other PAHs) and is able to function as a living bioluminescent reporter for the presence of naphthalene contamination, its bioavailability, and the functional process of biodegradation. A unique component of this field investigation was the availability of an array of large subsurface soil lysimeters. This article describes the experience associated with the release of a genetically modified microorganism, the lysimeter facility and its associated instrumentation, as well as representative data collected during the first eighteen months of operation.

Sayler, G.S.; Cox, C.D.; Ripp, S.; Nivens, D.E.; Werner, C.; Ahn, Y.; Matrubutham, U. [Univ. of Tennessee, Knoxville, TN (United States); Burlage, R. [Oak Ridge National Lab., TN (United States). Environmental Sciences Div.

1998-11-01

323

Optimality and stability of symmetric evolutionary games with applications in genetic selection.  

PubMed

Symmetric evolutionary games, i.e., evolutionary games with symmetric fitness matrices, have important applications in population genetics, where they can be used to model for example the selection and evolution of the genotypes of a given population. In this paper, we review the theory for obtaining optimal and stable strategies for symmetric evolutionary games, and provide some new proofs and computational methods. In particular, we review the relationship between the symmetric evolutionary game and the generalized knapsack problem, and discuss the first and second order necessary and sufficient conditions that can be derived from this relationship for testing the optimality and stability of the strategies. Some of the conditions are given in different forms from those in previous work and can be verified more efficiently. We also derive more efficient computational methods for the evaluation of the conditions than conventional approaches. We demonstrate how these conditions can be applied to justifying the strategies and their stabilities for a special class of genetic selection games including some in the study of genetic disorders. PMID:25811551

Huang, Yuanyuan; Hao, Yiping; Wang, Min; Zhou, Wen; Wu, Zhijun

2015-06-01

324

Hybrid Algorithms for Fuzzy Reverse Supply Chain Network Design  

PubMed Central

In consideration of capacity constraints, fuzzy defect ratio, and fuzzy transport loss ratio, this paper attempted to establish an optimized decision model for production planning and distribution of a multiphase, multiproduct reverse supply chain, which addresses defects returned to original manufacturers, and in addition, develops hybrid algorithms such as Particle Swarm Optimization-Genetic Algorithm (PSO-GA), Genetic Algorithm-Simulated Annealing (GA-SA), and Particle Swarm Optimization-Simulated Annealing (PSO-SA) for solving the optimized model. During a case study of a multi-phase, multi-product reverse supply chain network, this paper explained the suitability of the optimized decision model and the applicability of the algorithms. Finally, the hybrid algorithms showed excellent solving capability when compared with original GA and PSO methods. PMID:24892057

Che, Z. H.; Chiang, Tzu-An; Kuo, Y. C.

2014-01-01

325

Hybrid algorithms for fuzzy reverse supply chain network design.  

PubMed

In consideration of capacity constraints, fuzzy defect ratio, and fuzzy transport loss ratio, this paper attempted to establish an optimized decision model for production planning and distribution of a multiphase, multiproduct reverse supply chain, which addresses defects returned to original manufacturers, and in addition, develops hybrid algorithms such as Particle Swarm Optimization-Genetic Algorithm (PSO-GA), Genetic Algorithm-Simulated Annealing (GA-SA), and Particle Swarm Optimization-Simulated Annealing (PSO-SA) for solving the optimized model. During a case study of a multi-phase, multi-product reverse supply chain network, this paper explained the suitability of the optimized decision model and the applicability of the algorithms. Finally, the hybrid algorithms showed excellent solving capability when compared with original GA and PSO methods. PMID:24892057

Che, Z H; Chiang, Tzu-An; Kuo, Y C; Cui, Zhihua

2014-01-01

326

Reversible Sterilization  

ERIC Educational Resources Information Center

Notes that difficult questions arise concerning the use of sterilization for alleged eugenic and euthenic purposes. Thus, how reversible sterilization will be used with relation to the poor, mentally ill, mentally retarded, criminals, and minors, is questioned. (Author/AM)

Largey, Gale

1977-01-01

327

Genetic algorithm for the design of high frequency diffraction gratings for high power laser applications  

NASA Astrophysics Data System (ADS)

We present a genetic algorithm with small population sizes for the design of diffraction gratings in the rigorous domain. A general crossover and mutation scheme is defined, forming fifteen offspring from 3 parents, which enables the algorithm to be used for designing gratings with diverse optical properties by careful definition of the merit function. The initial parents are randomly selected and the parents of the subsequent generations are selected by survival of the fittest. The performance of the algorithm is demonstrated by designing diffraction gratings with specific application to high power laser beam lines. Gratings are designed that act as beam deflectors, polarisers, polarising beam splitters, harmonic separation gratings and pulse compression gratings. By imposing fabrication constraints within the design process, we determine which of these elements have true potential for application within high power laser beam lines.

Thomson, Martin J.; Waddie, Andrew J.; Taghizadeh, Mohammad R.

2006-04-01

328

Protective efficacy of reverse genetics based on inactivated American and Asian neuraminidase DIVA marker vaccines against highly pathogenic H5N1 avian influenza viruses in chickens  

Technology Transfer Automated Retrieval System (TEKTRAN)

Asian H5N1 highly pathogenic avian influenza has become endemic in several countries, and vaccination is commonly being used. Vaccination can affect surveillance, and therefore there is considerable interest in DIVA (differentiate infected from vaccinated animals) vaccine strategies. Using reverse...

329

Technological Advances in Bifidobacterial Molecular Genetics: Application to Functional Genomics and Medical Treatments  

PubMed Central

Bifidobacteria are well known as beneficial intestinal bacteria that exert health-promoting effects in humans. In addition to physiological and immunological investigations, molecular genetic technologies have been developed and have recently started to be applied to clarify the molecular bases of host-Bifidobacterium interactions. These technologies include transformation technologies and Escherichia coli-Bifidobacterium shuttle vectors that enable heterologous gene expression. In this context, a plasmid artificial modification method that protects the introduced plasmid from the restriction system in host bifidobacteria has recently been developed to increase transformation efficiency. On the other hand, targeted gene inactivation systems, which are vital for functional genomics, seemed far from being practically applicable in bifidobacteria. However, remarkable progress in this technology has recently been achieved, enabling functional genomics in bifidobacteria. Integrated use of these molecular genetic technologies with omics-based analyses will surely boost characterization of the molecular basis underlying beneficial effects of bifidobacteria. Applications of recombinant bifidobacteria to medical treatments have also progressed. PMID:24936345

FUKIYA, Satoru; HIRAYAMA, Yosuke; SAKANAKA, Mikiyasu; KANO, Yasunobu; YOKOTA, Atsushi

2012-01-01

330

A School-Based Application of Modified Habit Reversal for Tourette Syndrome via a Translator: A Case Study  

ERIC Educational Resources Information Center

A school-based modified habit reversal intervention was utilized with an adolescent diagnosed with Tourette syndrome who recently immigrated from Mexico. Because the student possessed little proficiency of the English language, an interpreter was needed to help implement the procedure. The frequency of motor tics markedly decreased from baseline…

Gilman, Rich; Connor, Nancy; Haney, Michelle

2005-01-01

331

An Application of Reverse Engineering to Automatic Item Generation: A Proof of Concept Using Automatically Generated Figures  

ERIC Educational Resources Information Center

A reverse engineering approach to automatic item generation (AIG) was applied to a figure-based publicly released test item from the Organisation for Economic Cooperation and Development (OECD) Programme for International Student Assessment (PISA) mathematical literacy cognitive instrument as part of a proof of concept. The author created an item…

Lorié, William A.

2013-01-01

332

Genetic programming  

Microsoft Academic Search

The paper presents essays on genetic programming which involve topics such as: the artificial evolution of computer code, human-competitive machine intelligence by means of genetic programming, GP as automatic programming, GP application, the evolution of arbitrary computational processes and the art of genetic programming

Wolfgang Banzhaf; J. R. Koza; C. Ryan; L. Spector; C. Jacob

2000-01-01

333

Dissociable Effects of 5-HT2C Receptor Antagonism and Genetic Inactivation on Perseverance and Learned Non-Reward in an Egocentric Spatial Reversal Task  

PubMed Central

Cognitive flexibility can be assessed in reversal learning tests, which are sensitive to modulation of 5-HT2C receptor (5-HT2CR) function. Successful performance in these tests depends on at least two dissociable cognitive mechanisms which may separately dissipate associations of previous positive and negative valence. The first is opposed by perseverance and the second by learned non-reward. The current experiments explored the effect of reducing function of the 5-HT2CR on the cognitive mechanisms underlying egocentric reversal learning in the mouse. Experiment 1 used the 5-HT2CR antagonist SB242084 (0.5 mg/kg) in a between-groups serial design and Experiment 2 used 5-HT2CR KO mice in a repeated measures design. Animals initially learned to discriminate between two egocentric turning directions, only one of which was food rewarded (denoted CS+, CS?), in a T- or Y-maze configuration. This was followed by three conditions; (1) Full reversal, where contingencies reversed; (2) Perseverance, where the previous CS+ became CS? and the previous CS? was replaced by a novel CS+; (3) Learned non-reward, where the previous CS? became CS+ and the previous CS+ was replaced by a novel CS-. SB242084 reduced perseverance, observed as a decrease in trials and incorrect responses to criterion, but increased learned non-reward, observed as an increase in trials to criterion. In contrast, 5-HT2CR KO mice showed increased perseverance. 5-HT2CR KO mice also showed retarded egocentric discrimination learning. Neither manipulation of 5-HT2CR function affected performance in the full reversal test. These results are unlikely to be accounted for by increased novelty attraction, as SB242084 failed to affect performance in an unrewarded novelty task. In conclusion, acute 5-HT2CR antagonism and constitutive loss of the 5-HT2CR have opposing effects on perseverance in egocentric reversal learning in mice. It is likely that this difference reflects the broader impact of 5HT2CR loss on the development and maintenance of cognitive function. PMID:24204954

Nilsson, Simon R. O.; Somerville, Elizabeth M.; Clifton, Peter G.

2013-01-01

334

Genetics and evolution: an iOS application to supplement introductory courses in transmission and evolutionary genetics.  

PubMed

Students in college courses struggle to understand many concepts fundamental to transmission and evolutionary genetics, including multilocus inheritance, recombination, Hardy-Weinberg, and genetic drift. These students consistently ask for more demonstrations and more practice problems. With this demand in mind, the "Genetics and Evolution" app was designed to help students (and their instructors) by providing a suite of tools granting them the ability to: (1) simulate genetic crosses with varying numbers of genes and patterns of inheritance, (2) simulate allele frequency changes under natural selection and/ or genetic drift, (3) quiz themselves to reinforce terminology (customizable by any instructor for their whole classroom), *4) solve various problems (recombination fractions, Hardy-Weinberg, heritability, population growth), and (5) generate literally an infinite number of practice problems in all of these areas to try on their own. Although some of these functions are available elsewhere, the alternatives do not have the ability to instantly generate new practice problems or achieve these diverse functions in devices that students carry in their pockets every day. PMID:24727286

Myers, Russell B; Millman, Brandon; Noor, Mohamed A F

2014-05-01

335

Genetics and Evolution: An iOS Application to Supplement Introductory Courses in Transmission and Evolutionary Genetics  

PubMed Central

Students in college courses struggle to understand many concepts fundamental to transmission and evolutionary genetics, including multilocus inheritance, recombination, Hardy-Weinberg, and genetic drift. These students consistently ask for more demonstrations and more practice problems. With this demand in mind, the “Genetics and Evolution” app was designed to help students (and their instructors) by providing a suite of tools granting them the ability to: (1) simulate genetic crosses with varying numbers of genes and patterns of inheritance, (2) simulate allele frequency changes under natural selection and/ or genetic drift, (3) quiz themselves to reinforce terminology (customizable by any instructor for their whole classroom), *4) solve various problems (recombination fractions, Hardy-Weinberg, heritability, population growth), and (5) generate literally an infinite number of practice problems in all of these areas to try on their own. Although some of these functions are available elsewhere, the alternatives do not have the ability to instantly generate new practice problems or achieve these diverse functions in devices that students carry in their pockets every day. PMID:24727286

Myers, Russell B.; Millman, Brandon; Noor, Mohamed A. F.

2014-01-01

336

PT-Flax (phenotyping and TILLinG of flax): development of a flax (Linum usitatissimum L.) mutant population and TILLinG platform for forward and reverse genetics  

PubMed Central

Background Flax (Linum usitatissimum L.) is an economically important fiber and oil crop that has been grown for thousands of years. The genome has been recently sequenced and transcriptomics are providing information on candidate genes potentially related to agronomically-important traits. In order to accelerate functional characterization of these genes we have generated a flax EMS mutant population that can be used as a TILLinG (Targeting Induced Local Lesions in Genomes) platform for forward and reverse genetics. Results A population of 4,894 M2 mutant seed families was generated using 3 different EMS concentrations (0.3%, 0.6% and 0.75%) and used to produce M2 plants for subsequent phenotyping and DNA extraction. 10,839 viable M2 plants (4,033 families) were obtained and 1,552 families (38.5%) showed a visual developmental phenotype (stem size and diameter, plant architecture, flower-related). The majority of these families showed more than one phenotype. Mutant phenotype data are organised in a database and can be accessed and searched at UTILLdb (http://urgv.evry.inra.fr/UTILLdb). Preliminary screens were also performed for atypical fiber and seed phenotypes. Genomic DNA was extracted from 3,515 M2 families and eight-fold pooled for subsequent mutant detection by ENDO1 nuclease mis-match cleavage. In order to validate the collection for reverse genetics, DNA pools were screened for two genes coding enzymes of the lignin biosynthesis pathway: Coumarate-3-Hydroxylase (C3H) and Cinnamyl Alcohol Dehydrogenase (CAD). We identified 79 and 76 mutations in the C3H and CAD genes, respectively. The average mutation rate was calculated as 1/41?Kb giving rise to approximately 9,000 mutations per genome. Thirty-five out of the 52 flax cad mutant families containing missense or codon stop mutations showed the typical orange-brown xylem phenotype observed in CAD down-regulated/mutant plants in other species. Conclusions We have developed a flax mutant population that can be used as an efficient forward and reverse genetics tool. The collection has an extremely high mutation rate that enables the detection of large numbers of independant mutant families by screening a comparatively low number of M2 families. The population will prove to be a valuable resource for both fundamental research and the identification of agronomically-important genes for crop improvement in flax. PMID:24128060

2013-01-01

337

The partially reversible formation of Li-metal particles on a solid Li electrolyte: applications toward nanobatteries  

SciTech Connect

The feasibility of large-scale implementation of Li-air batteries (LABs) hinges on understanding the thermodynamic and kinetic factors that control charge-discharge rates, efficiency and life times. Here, the kinetics of bias-induced reactions is explored locally on the surface of Li-ion conductive glass ceramics, a preferred electrolyte for LABs, using direct current-voltage and strain spectroscopies. Above a critical bias, particle growth kinetics were found to be linear in both the bias and time domains. Partial reversibility was observed for Li particles as evidenced by the presence of anodic peaks following the Li{sup +} reduction, as well an associated reduction in particle height. The degree of reversibility was highest for the smallest particles formed. These observations thus suggest the possibility of producing nanobatteries with an active anode volume of the order of 0.1 al.

Arruda, Thomas M [ORNL; Kumar, Amit [ORNL; Kalinin, Sergei V [ORNL; Jesse, Stephen [ORNL

2012-01-01

338

PWP-073 Stochastic Models of Energy Commodity Prices and Their Applications: Mean-reversion with Jumps and Spikes  

Microsoft Academic Search

I propose several mean-reversion jump-di#usion models to describe spot prices of energy commoditiesthat maybevery costly to store. I incorporate multiple jumps, regime-switchingand stochastic volatilityinto these models in order to capture the salient features of energycommodity prices due to physical characteristics of energy commodities. Prices of variousenergy commodity derivatives are derived under each model using the Fourier transformmethods. In the context

Shijie Deng

1999-01-01

339

Orbits Homoclinic to Exponentially Small Periodic Orbits for a Class of Reversible Systems. Application to Water Waves  

Microsoft Academic Search

:   In this paper a class of reversible analytic vector fields is investigated near an equilibrium. For these vector fields,\\u000a the part of the spectrum of the differential at the equilibrium which lies near the imaginary axis comes from the perturbation\\u000a of a double eigenvalue 0 and two simple eigenvalues , .\\u000a \\u000a \\u000a In the first part of this paper, we

Eric Lombardi

1997-01-01

340

A microfluidic gel valve device using reversible sol–gel transition of methyl cellulose for biomedical application  

Microsoft Academic Search

We have fabricated a microfluidic gel valve device that used reversible sol–gel transition of methyl cellulose (MC). A microheater\\u000a and a microtemperature sensor were implemented in each microchannel in the gel valve device. Before evaluating the performance\\u000a of the gel valve device, various properties of the MC solution were investigated using viscometer, spectrophotometer, and\\u000a NMR. Gelation temperature was increased as

Dae Sung Yoon; Yoon-Kyoung Cho; Kwang W. Oh; Sunhee Kim; Young Ah Kim; Jung Im Han; Geunbae Lim

2006-01-01

341

Application of regression analysis based on genetic particle swarm algorithm in financial analysis  

Microsoft Academic Search

Slow convergence speed and premature are two key problems existing in the regression analysis techniques based on genetic algorithm. To overcome the shortcomings,this paper proposes an improved regression analysis based on the genetic particle swarm algorithm. The basic principle is that a new operator is constructed to use PSO. This algorithm has the choice of genetic algorithms and genetic features,

Xiaorong Cheng; Lin Sun; Ping Liu

2010-01-01

342

Improvement on the genetic algorithm and its application in employee performance evaluation  

Microsoft Academic Search

Aiming at the deficiencies of standard genetic algorithm, an improved algorithm is presented. Through improvement and expansion of genetic operators of standard genetic algorithm, the study enhances the operating efficiency and accuracy of fuzzy clustering analytical method which based on the improved genetic algorithm, applies it in the human resource management system, and conducts scientific and reasonable evaluation of employee

Minying Huang; Rui Mou

2010-01-01

343

MONITORING MYCOTOXIN PRODUCTION AT THE GENETIC LEVEL ON VARIOUS GROWTH SUBSTRATES USING QUANTITATIVE REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION?EXPERIMENT DESIGN  

EPA Science Inventory

The paper describes a method of analyzing the production of mycotoxins at the genetic level by monitoring the intracellular levels of messenger RNA (mRNA). Initial work will focus on threshing out the mycotoxin gene clusters in Stachybotrys chartarum followed by analysis of toxin...

344

Likelihood ratio testing for admixture models with application to genetic linkage analysis.  

PubMed

We consider likelihood ratio tests (LRT) and their modifications for homogeneity in admixture models. The admixture model is a two-component mixture model, where one component is indexed by an unknown parameter while the parameter value for the other component is known. This model is widely used in genetic linkage analysis under heterogeneity in which the kernel distribution is binomial. For such models, it is long recognized that testing for homogeneity is nonstandard, and the LRT statistic does not converge to a conventional??(2) ?distribution. In this article, we investigate the asymptotic behavior of the LRT for general admixture models and show that its limiting distribution is equivalent to the supremum of a squared Gaussian process. We also discuss the connection and comparison between LRT and alternative approaches such as modifications of LRT and score tests, including the modified LRT (Fu, Chen, and Kalbfleisch, 2006,?Statistica Sinica?16, 805-823). The LRT is an omnibus test that is powerful to detect general alternative hypotheses. In contrast, alternative approaches may be slightly more powerful to detect certain type of alternatives, but much less powerful for others. Our results are illustrated by simulation studies and an application to a genetic linkage study of schizophrenia. PMID:21385166

Di, Chong-Zhi; Liang, Kung-Yee

2011-12-01

345

The evolution of colorectal cancer genetics—Part 2: clinical implications and applications  

PubMed Central

The genetic understanding of colorectal cancer (CRC) continues to grow, and it is now estimated that 10% of the population has a known hereditary CRC syndrome. This article will examine the evolving surgical and medical management of hereditary CRC syndromes, and the impact of tumor genetics on therapy. This review will focus on the most common hereditary CRC-prone diseases seen in clinical practice, which include Lynch syndrome (LS), familial adenomatous polyposis (FAP) & attenuated FAP (AFAP), MutYH-associated polyposis (MAP), and serrated polyposis syndrome (SPS). Each section will review the current recommendations in the evaluation and treatment of these syndromes, as well as review surgical management and operative planning. A highly detailed multigeneration cancer family history with verified genealogy and pathology documentation whenever possible, coupled with germline mutation testing when indicated, is critically important to management decisions. Although caring for patients with these syndromes remains complex, the application of this knowledge facilitates better treatment of both individuals and their affected family members for generations to come. PMID:25276406

Schlussel, Andrew T.; Gagliano, Ronald A.; Eggerding, Faye; Donlon, Timothy; Berenberg, Jeffrey; Lynch, Henry T.

2014-01-01

346

AUTOMATIC CREATION OF A GENETIC NETWORK FOR THE lac OPERON FROM OBSERVED DATA BY MEANS OF GENETIC PROGRAMMING  

E-print Network

to automatically create (reverse engineer) a computer program representing the logic underlying the genetic network "reverse engineer" the logic underlying a genetic network. This reverse engineering entails creating bothAUTOMATIC CREATION OF A GENETIC NETWORK FOR THE lac OPERON FROM OBSERVED DATA BY MEANS OF GENETIC

Fernandez, Thomas

347

The Genetic Algorithm and Its Application to Calibrating Conceptual Rainfall-Runoff Models  

NASA Astrophysics Data System (ADS)

The genetic algorithm is a search procedure based on the mechanics of natural selection and natural genetics, which combines an artificial survival of the fittest with genetic operators abstracted from nature. In this paper, a genetic algorithm for function optimization is introduced and applied to calibration of a conceptual rainfall-runoff model for data from a particular catchment. All seven parameters of the model are optimized. The results show that the genetic algorithm can be efficient and robust.

Wang, Q. J.

1991-09-01

348

Optimisation of halogenase enzyme activity by application of a genetic algorithm.  

PubMed

A genetic algorithm (GA) was applied for the optimisation of an enzyme assay composition respectively the enzyme activity of a recombinantly produced FADH(2)-dependent halogenating enzyme. The examined enzyme belongs to the class of halogenases and is capable to halogenate tryptophan regioselective in position 5. Therefore, the expressed trp-5-halogenase can be an interesting tool in the manufacturing of serotonin precursors. The application of stochastic search strategies (e.g. GAs) is well suited for fast determination of the global optimum in multidimensional search spaces, where statistical approaches or even the popular classical one-factor-at-a-time method often failures by misleading to local optima. The concentrations of six different medium components were optimised and the maximum yield of the halogenated tryptophan could be increased from 3.5 up to 65%. PMID:16919347

Muffler, Kai; Retzlaff, Marco; van Pée, Karl-Heinz; Ulber, Roland

2007-01-10

349

Using distance covariance for improved variable selection with application to learning genetic risk models.  

PubMed

Variable selection is of increasing importance to address the difficulties of high dimensionality in many scientific areas. In this paper, we demonstrate a property for distance covariance, which is incorporated in a novel feature screening procedure together with the use of distance correlation. The approach makes no distributional assumptions for the variables and does not require the specification of a regression model and hence is especially attractive in variable selection given an enormous number of candidate attributes without much information about the true model with the response. The method is applied to two genetic risk problems, where issues including uncertainty of variable selection via cross validation, subgroup of hard-to-classify cases, and the application of a reject option are discussed. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25640961

Kong, Jing; Wang, Sijian; Wahba, Grace

2015-05-10

350

Application of Genetic Algorithm to the Design Optimization of Complex Energy Saving Glass Coating Structure  

NASA Astrophysics Data System (ADS)

Attenuation of GSM, GPS and personal communication signal leads to poor communication inside the building using regular shapes of energy saving glass coating. Thus, the transmission is very low. A brand new type of band pass frequency selective surface (FSS) for energy saving glass application is presented in this paper for one unit cell. Numerical Periodic Method of Moment approach according to a previous study has been applied to determine the new optimum design of one unit cell energy saving glass coating structure. Optimization technique based on the Genetic Algorithm (GA) is used to obtain an improved in return loss and transmission signal. The unit cell of FSS is designed and simulated using the CST Microwave Studio software at based on industrial, scientific and medical bands (ISM). A unique and irregular shape of an energy saving glass coating structure is obtained with lower return loss and improved transmission coefficient.

Johar, F. M.; Azmin, F. A.; Shibghatullah, A. S.; Suaidi, M. K.; Ahmad, B. H.; Abd Aziz, M. Z. A.; Salleh, S. N.; Shukor, M. Md

2014-04-01

351

Application of genetic algorithms to the optimization design of electron optical system  

NASA Astrophysics Data System (ADS)

The application of Genetic Algorithms (GAs) to the optimization design method, such as Simplex method and Powell method etc, can determine the final optimum structure and electric parameters of an electron optical system from given electron optical properties, but it may be landed in the localization of optimum search process. The GAs is a novel direct search optimization method based on principles of natural selection and survival of the fittest from natural evolution. Through the reproduction, crossover, and mutation iterative process, GAs can search the global optimum result. We applied the GAs to optimize an electron emission system and an extended field lens (EFL) respectively. The optimal structure and corresponding electrical parameters with a criterion of minimum objective function value, crossover radius for electron emission system and spherical aberration coefficient for EFL, have been searched and presented in this paper. The GAs, as a direct search method and an adaptive search technique, has significant advantage in the optimization design of electron optical systems.

Gu, Changxin; Wu, M. Q.; Shan, Liying; Lin, G.

2001-12-01

352

Genetically modified Plasmodium parasites as a protective  

E-print Network

.............................................................. Genetically modified Plasmodium that are only expressed in the pre-erythrocytic stages of the parasite4,5 . Here, we show by reverse genetics is sustained and stage specific. Our findings demonstrate that a safe and effective, genetically attenuated

Arnold, Jonathan

353

Reversible concentric ring microfluidic interconnects  

E-print Network

A reversible, Chip-to-Chip microfluidic interconnect was designed for use in high temperature, high pressure applications such as chemical microreactor systems. The interconnect uses two sets of concentric, interlocking ...

Thompson, Mary Kathryn, 1980-

2004-01-01

354

Reverse osmosis reverses conventional wisdom with Superfund cleanup success  

SciTech Connect

Although widely recognized as the most efficient means of water purification, reverse osmosis has not been considered effective for remediating hazardous wastewater. Scaling and fouling, which can cause overruns and downtime, and require membrane replacement, have inhibited success in high-volume wastewater applications. Despite this background, a reverse osmosis technology developed in Europe recently was used successfully to treat large volumes of contaminated water at a major Superfund site in Texas. The technology's success there may increase the chances for reverse osmosis to find wider use in future cleanups and other waste treatment applications.

Collins, M. (French Ltd. Task Group, Crosby, TX (United States)); Miller, K. (Rochem Environmental Inc., Houston, TX (United States))

1994-09-01

355

Generalized predictive control using genetic algorithms (GAGPC). An application to control of a non-linear process with model uncertainty  

Microsoft Academic Search

Predictive Control is one of the most powerful techniques in process control, but its application in non-linear processes is challenging. This is basically because the optimization method commonly used limits the kind of functions which can be minimized. The aim of this work is to show how the combination of Genetic Algorithms (GA) and Generalized Predictive Control (GPC), what we

Xavier Blasco; Miguel Martinez; Juan Senent; Javier Sanchis

356

Global-scale genetic identification of hammerhead sharks: Application to assessment of the international fin trade and law enforcement  

E-print Network

Global-scale genetic identification of hammerhead sharks: Application to assessment, fin trade, hammerhead sharks, shark conservation, Sphyrna, Abstract The future status of sharks-bodied hammerhead sharks, Sphyrna lewini, S. mokarran and S. zygaena, even in regions where some management occurs

357

Application of Interactive Genetic Algorithm to Fashion Design Hee-Su Kim and Sung-Bae Cho  

E-print Network

- 1 - Application of Interactive Genetic Algorithm to Fashion Design Hee-Su Kim and Sung-Bae Cho. This approach, however, can neither deal with continuous change of fashion nor reflect personal taste well to be applied to artistic domains, and we propose a fashion design aid system using it. Unlike the previous

Cho, Sung-Bae

358

Synthesis of nonuniformly spaced linear array for GSM\\/DCS\\/WCDMA base station application using genetic algorithm  

Microsoft Academic Search

The design of a nonuniformly spaced linear array suitable for a GSM\\/DCS\\/WCDMA base station application is presented. In the design, both the interspacing between array elements and the feeding Wilkinson power divider for a triband antenna array are facilitated using a genetic algorithm. The simulation results show the nonuniformly spaced linear array fed by an 8-way Wilkinson power divider is

An-Shyi Liu; Ruey-Beei Wu; Yi-Chen Lin; Hsueh-Jyh Li

2004-01-01

359

Applications of Genetically-Encoded Biosensors for the Construction and Control of Biosynthetic Pathways  

PubMed Central

Cells are filled with biosensors, molecular systems that measure the state of the cell and respond by regulating host processes. In much the same way that an engineer would monitor a chemical reactor, the cell uses these sensors to monitor changing intracellular environments and produce consistent behavior despite the variable environment. While natural systems derive a clear benefit from pathway regulation, past research efforts in engineering cellular metabolism have focused on introducing new pathways and removing existing pathway regulation. Synthetic biology is a rapidly growing field that focuses on the development of new tools that support the design, construction, and optimization of biological systems. Recent advances have been made in the design of genetically-encoded biosensors and the application of this class of molecular tools for optimizing and regulating heterologous pathways. Biosensors to cellular metabolites can be taken directly from natural systems, engineered from natural sensors, or constructed entirely in vitro. When linked to reporters, such as antibiotic resistance markers, these metabolite sensors can be used to report on pathway productivity, allowing high-throughput screening for pathway optimization. Future directions will focus on the application of biosensors to introduce feedback control into metabolic pathways, providing dynamic control strategies to increase the efficient use of cellular resources and pathway reliability. PMID:21946159

Michener, Josh K.; Thodey, Kate; Liang, Joe C.; Smolke, Christina D.

2011-01-01

360

Reverse Osmosis  

NSDL National Science Digital Library

North Dakota State University presents the theories behind reverse osmosis and how it affects household water supplies. The site addresses the impurities which are removed by this process. It also speaks of testing, the process itself and even the disadvantages of this process. A fairly encompassing site is what amounts from the work done by the University, it gives a clear and concise viewpoint of this process.

361

Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies  

PubMed Central

Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management. PMID:24808959

Abdul-Muneer, P. M.

2014-01-01

362

Vasectomy reversal.  

PubMed

A vasovasostomy may be performed on an outpatient basis with local anesthesia, but also may be performed on an outpatient basis with epidural or general anesthesia. Local anesthesia is preferred by most of my patients, the majority of whom choose this technique. With proper preoperative and intraoperative sedation, patients sleep lightly through most of the procedure. Because of the length of time often required for bilateral microsurgical vasoepididymostomy, epidural or general anesthesia and overnight hospitalization are usually necessary. Factors influencing the preoperative choice for vasovasostomy or vasoepididymostomy in patients undergoing vasectomy reversal are considered. The preoperative planned choice of vasovasostomy or vasoepididymostomy for patients having vasectomy reversal described herein does not have the support of all urologists who regularly perform these procedures. My present approach has evolved as the data reported in Tables 1 and 2 have become available, but it may change as new information is evaluated. However, it offers a logical method for planning choices of anesthesia and inpatient or outpatient status for patients undergoing vasectomy reversal procedures. PMID:3811050

Belker, A M

1987-02-01

363

A kernel machine method for detecting effects of interaction between multidimensional variable sets: An imaging genetics application.  

PubMed

Measurements derived from neuroimaging data can serve as markers of disease and/or healthy development, are largely heritable, and have been increasingly utilized as (intermediate) phenotypes in genetic association studies. To date, imaging genetic studies have mostly focused on discovering isolated genetic effects, typically ignoring potential interactions with non-genetic variables such as disease risk factors, environmental exposures, and epigenetic markers. However, identifying significant interaction effects is critical for revealing the true relationship between genetic and phenotypic variables, and shedding light on disease mechanisms. In this paper, we present a general kernel machine based method for detecting effects of the interaction between multidimensional variable sets. This method can model the joint and epistatic effect of a collection of single nucleotide polymorphisms (SNPs), accommodate multiple factors that potentially moderate genetic influences, and test for nonlinear interactions between sets of variables in a flexible framework. As a demonstration of application, we applied the method to the data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) to detect the effects of the interactions between candidate Alzheimer's disease (AD) risk genes and a collection of cardiovascular disease (CVD) risk factors, on hippocampal volume measurements derived from structural brain magnetic resonance imaging (MRI) scans. Our method identified that two genes, CR1 and EPHA1, demonstrate significant interactions with CVD risk factors on hippocampal volume, suggesting that CR1 and EPHA1 may play a role in influencing AD-related neurodegeneration in the presence of CVD risks. PMID:25600633

Ge, Tian; Nichols, Thomas E; Ghosh, Debashis; Mormino, Elizabeth C; Smoller, Jordan W; Sabuncu, Mert R

2015-04-01

364

Genetic polymorphism near HIV-1 reverse transcriptase resistance-associated codons is a major obstacle for the line probe assay as an alternative method to sequence analysis.  

PubMed

The performance of the line probe assay (LIPA) for the detection of mutations conferring resistance to nucleoside inhibitors of HIV-1 reverse transcriptase was evaluated in comparison with sequence analysis. The tests were undertaken on plasma samples from 63 patients (61 receiving combination therapy and 2 without treatment at the time of inclusion). In 27 cases (43%) which included codons 41, 69, 70, 74, 184 and 215, the sequence of the RT gene was distinct from the hybridization probes used in LIPA. Correspondingly, LIPA gave uninterpretable results in 15, 30 and 41% of cases for codons 184, 215 and 41, respectively. Overall, the concordance between LIPA and sequence analysis varied from 52% (codons 41 and 215) to 85% (codon 70). These data show that the polymorphism of the nucleotide sequence near resistance-associated codons is a major shortcoming of LIPA. PMID:10403673

Koch, N; Yahi, N; Colson, P; Fantini, J; Tamalet, C

1999-06-01

365

Volume 10, Issue 1 2011 Article 46 Statistical Applications in Genetics  

E-print Network

Genetic Linkage Analysis in the Presence of Germline Mosaicism Omer Weissbrod, Technion - Israel Institute and Geiger, Dan (2011) "Genetic Linkage Analysis in the Presence of Germline Mosaicism," Statistical;Genetic Linkage Analysis in the Presence of Germline Mosaicism Omer Weissbrod and Dan Geiger Abstract

Friedman, Nir

366

GENETIC ACTIVITY PROFILES--APPLICATION IN ASSESSING POTENTIAL CARCINOGENICITY OF COMPLEX ENVIRONMENTAL MIXTURES  

EPA Science Inventory

Some knowledge of the potential genetic activity of a complex environmental mixture may be gained from an assessment of the genetic activity of its component chemicals. he expanded Genetic Activity Profile (GAP) data base provides a computer generated graphic representation of ge...

367

An application of genetic algorithm to DNA sequencing by oligonucleotide hybridization  

Microsoft Academic Search

The authors propose a sequencing algorithm for oligonucleotide hybridization using the genetic algorithm. The target DNA sequence reconstructed by the hybridization method is relatively long for genetic algorithm (GA), so special setups of the genetic operation are necessary. The authors introduce the grouping GA and a special crossover method for this problem. They carried out some experiments of sequence reconstruction,

H. Douzono; S. Hara; Y. Noguchi

1998-01-01

368

Vaxign: The First Web-Based Vaccine Design Program for Reverse Vaccinology and Applications for Vaccine Development  

PubMed Central

Vaxign is the first web-based vaccine design system that predicts vaccine targets based on genome sequences using the strategy of reverse vaccinology. Predicted features in the Vaxign pipeline include protein subcellular location, transmembrane helices, adhesin probability, conservation to human and/or mouse proteins, sequence exclusion from genome(s) of nonpathogenic strain(s), and epitope binding to MHC class I and class II. The precomputed Vaxign database contains prediction of vaccine targets for >70 genomes. Vaxign also performs dynamic vaccine target prediction based on input sequences. To demonstrate the utility of this program, the vaccine candidates against uropathogenic Escherichia coli (UPEC) were predicted using Vaxign and compared with various experimental studies. Our results indicate that Vaxign is an accurate and efficient vaccine design program. PMID:20671958

He, Yongqun; Xiang, Zuoshuang; Mobley, Harry L. T.

2010-01-01

369

Principles of genetics and their clinical application in the neonatal intensive care unit.  

PubMed

The neonate born with a genetic defect or fetal anomaly presents a challenge to the neonatal intensive care unit team. Typically genetic disorders are thought of as being rare; however, this is not true, and it is becoming increasingly evident as knowledge and technology progress. A definitive diagnosis is essential for management and care of the neonate and the neonate's family. An evidence-based approach to the neonate who has a suspected genetic anomaly is essential to provide accurate diagnosis and to guide ongoing care. This article gives an overview of basic genetics and genetic counseling, and applies the principles to two case studies. PMID:19237045

Schiefelbein, Julieanne H; Cheeseman, Susan E

2009-03-01

370

Network Reverse Engineering Approach in Synthetic Biology  

NASA Astrophysics Data System (ADS)

Synthetic biology is a new branch of interdisciplinary science that has been developed in recent years. The main purpose of synthetic biology is to apply successful principles that have been developed in electronic and chemical engineering to develop basic biological functional modules, and through rational design, develop man-made biological systems that have predicted useful functions. Here, we discuss an important principle in rational design of functional biological circuits: the reverse engineering design. We will use a research project that was conducted at Peking University for the International Genetic Engineering Machine Competition (iGEM) to illustrate the principle: synthesis a cell which has a semi-log dose-response to the environment. Through this work we try to demonstrate the potential application of network engineering in synthetic biology.

Zhang, Haoqian; Liu, Ao; Lu, Yuheng; Sheng, Ying; Wu, Qianzhu; Yin, Zhenzhen; Chen, Yiwei; Liu, Zairan; Pan, Heng; Ouyang, Qi

2013-12-01

371

[Genetic algorithm application to multi-focus patterns of 256-element phased array for focused ultrasound surgery].  

PubMed

The genetic optimal algorithm and sound field calculation approach for the spherical-section phased array are presented in this paper. The in-house manufactured 256-element phased array focused ultrasound surgery system is briefly described. The on-axis single focus and off-axis single focus are simulated along with the axis-symmetric six-focus patter and the axis-asymmetric four-focus pattern using a 256-element phased array and the genetic optimal algorithm and sound field calculation approach. The experimental results of the described 256-element phased array focused ultrasound surgery system acting on organic glass and phantom are also analyzed. The results of the simulations and experiments confirm the applicability of the genetic algorithm and field calculation approaches in accurately steering three dimensional foci and focus. PMID:19024453

Xu, Feng; Wan, Mingxi; Lu, Mingzhu

2008-10-01

372

Genetic algorithm based input selection for a neural network function approximator with applications to SSME health monitoring  

NASA Technical Reports Server (NTRS)

A genetic algorithm is used to select the inputs to a neural network function approximator. In the application considered, modeling critical parameters of the space shuttle main engine (SSME), the functional relationship between measured parameters is unknown and complex. Furthermore, the number of possible input parameters is quite large. Many approaches have been used for input selection, but they are either subjective or do not consider the complex multivariate relationships between parameters. Due to the optimization and space searching capabilities of genetic algorithms they were employed to systematize the input selection process. The results suggest that the genetic algorithm can generate parameter lists of high quality without the explicit use of problem domain knowledge. Suggestions for improving the performance of the input selection process are also provided.

Peck, Charles C.; Dhawan, Atam P.; Meyer, Claudia M.

1991-01-01

373

Optimization of reversible sequential circuits  

E-print Network

In recent years reversible logic has been considered as an important issue for designing low power digital circuits. It has voluminous applications in the present rising nanotechnology such as DNA computing, Quantum Computing, low power VLSI and quantum dot automata. In this paper we have proposed optimized design of reversible sequential circuits in terms of number of gates, delay and hardware complexity. We have designed the latches with a new reversible gate and reduced the required number of gates, garbage outputs, and delay and hardware complexity. As the number of gates and garbage outputs increase the complexity of reversible circuits, this design will significantly enhance the performance. We have proposed reversible D-latch and JK latch which are better than the existing designs available in literature.

Sayem, Abu Sadat Md

2010-01-01

374

Application of genetic algorithms for the extraction of electrical parameters of multicrystalline silicon  

NASA Astrophysics Data System (ADS)

The application of the genetic algorithms (GAs) concept in measurements science deals with a fitting procedure used for the numerical prediction of physical parameters from an experimental data curve. In this work, GAs were applied for the extraction of electrical parameters of multicrystalline silicon solar cells. The experimental technique used is the light-beam-induced-current (LBIC). From LBIC measurements, we deduced the values of the diffusion length L and the grain boundary recombination velocity Vr of the minority carriers of the multicrystalline silicon wafers using the fitting procedure. The nonlinear fitting procedure is based on the minimization of the standard deviation of the theoretical LBIC profile from the experimental one. However, this criterion is not convex, and using traditional deterministic optimization algorithms leads to local minima solutions. To overcome this problem, the nonlinear least-square minimization technique was computed with the GAs strategy, increasing the probability of obtaining the best minimum value of the cost function in very reasonable time. The results of the proposed algorithm are presented and compared with the Levenberg-Marquardt algorithm and the Gauss-Newton method. The GAs-based numerical technique was found to be a promising and a powerful technique for numerical evaluation of the electrical parameters of silicon solar cells.

Sellami, A.; Zagrouba, M.; Bouaïcha, M.; Bessaïs, B.

2007-05-01

375

Linear genetic programming application for successive-station monthly streamflow prediction  

NASA Astrophysics Data System (ADS)

In recent decades, artificial intelligence (AI) techniques have been pronounced as a branch of computer science to model wide range of hydrological phenomena. A number of researches have been still comparing these techniques in order to find more effective approaches in terms of accuracy and applicability. In this study, we examined the ability of linear genetic programming (LGP) technique to model successive-station monthly streamflow process, as an applied alternative for streamflow prediction. A comparative efficiency study between LGP and three different artificial neural network algorithms, namely feed forward back propagation (FFBP), generalized regression neural networks (GRNN), and radial basis function (RBF), has also been presented in this study. For this aim, firstly, we put forward six different successive-station monthly streamflow prediction scenarios subjected to training by LGP and FFBP using the field data recorded at two gauging stations on Çoruh River, Turkey. Based on Nash-Sutcliffe and root mean squared error measures, we then compared the efficiency of these techniques and selected the best prediction scenario. Eventually, GRNN and RBF algorithms were utilized to restructure the selected scenario and to compare with corresponding FFBP and LGP. Our results indicated the promising role of LGP for successive-station monthly streamflow prediction providing more accurate results than those of all the ANN algorithms. We found an explicit LGP-based expression evolved by only the basic arithmetic functions as the best prediction model for the river, which uses the records of the both target and upstream stations.

Danandeh Mehr, Ali; Kahya, Ercan; Yerdelen, Cahit

2014-09-01

376

Construction and application of a protein and genetic interaction network (yeast interactome)  

PubMed Central

Cytoscape is a bioinformatic data analysis and visualization platform that is well-suited to the analysis of gene expression data. To facilitate the analysis of yeast microarray data using Cytoscape, we constructed an interaction network (interactome) using the curated interaction data available from the Saccharomyces Genome Database (www.yeastgenome.org) and the database of yeast transcription factors at YEASTRACT (www.yeastract.com). These data were formatted and imported into Cytoscape using semi-automated methods, including Linux-based scripts, that simplified the process while minimizing the introduction of processing errors. The methods described for the construction of this yeast interactome are generally applicable to the construction of any interactome. Using Cytoscape, we illustrate the use of this interactome through the analysis of expression data from a recent yeast diauxic shift experiment. We also report and briefly describe the complex associations among transcription factors that result in the regulation of thousands of genes through coordinated changes in expression of dozens of transcription factors. These cells are thus able to sensitively regulate cellular metabolism in response to changes in genetic or environmental conditions through relatively small changes in the expression of large numbers of genes, affecting the entire yeast metabolome. PMID:19273534

Stuart, Gregory R.; Copeland, William C.; Strand, Micheline K.

2009-01-01

377

Application of reverse-phase HPLC to quantify oligopeptide acetylation eliminates interference from unspecific acetyl CoA hydrolysis  

PubMed Central

Protein acetylation is a common modification that plays a central role in several cellular processes. The most widely used methods to study these modifications are either based on the detection of radioactively acetylated oligopetide products or an enzyme-coupled reaction measuring conversion of the acetyl donor acetyl CoA to the product CoASH. Due to several disadvantages of these methods, we designed a new method to study oligopeptide acetylation. Based on reverse phase HPLC we detect both reaction products in a highly robust and reproducible way. The method reported here is also fully compatible with subsequent product analysis, e.g. by mass spectroscopy. The catalytic subunit, hNaa30p, of the human NatC protein N-acetyltransferase complex was used for N-terminal oligopeptide acetylation. We show that unacetylated and acetylated oligopeptides can be efficiently separated and quantified by the HPLC-based analysis. The method is highly reproducible and enables reliable quantification of both substrates and products. It is therefore well-suited to determine kinetic parameters of acetyltransferases. PMID:19660098

Evjenth, Rune; Hole, Kristine; Ziegler, Mathias; Lillehaug, Johan R

2009-01-01

378

Judaism, Genetic Screening and Genetic Therapy  

Microsoft Academic Search

Genetic screening, gene therapy and other applications of genetic engineering are permissible in Judaism when used for the treatment, cure, or prevention of disease. Such genetic manipulation is not considered to be a violation of God's natural law, but a legitimate implementation of the biblical mandate to heal. If Tay-Sachs disease, diabetes, hemophilia, cystic fibrosis, Huntington's disease or other genetic

FRED ROSNER

379

Reverse genetic characterization of two paralogous acetoacetyl CoA thiolase genes in Arabidopsis reveals their importance in plant growth and development  

SciTech Connect

Acetoacetyl CoA thiolase (AACT, EC 2.3.1.9) catalyzes the condensation of two acetyl?CoA molecules to form acetoacetyl?CoA. Two AACT?encoding genes, At5g47720 (AACT1) and At5g48230 (AACT2), were functionally identified in the Arabidopsis genome by direct enzymological assays and functional expression in yeast. Promoter::GUS fusion experiments indicated that AACT1 is primarily expressed in the vascular system and AACT2 is highly expressed in root tips, young leaves, top stems and anthers. Characterization of T?DNA insertion mutant alleles at each AACT locus established that AACT2 function is required for embryogenesis and for normal male gamete transmission. In contrast, plants lacking AACT1 function are completely viable and show no apparent growth phenotypes, indicating that AACT1 is functionally redundant with respect to AACT2 function. RNAi lines that express reduced levels of AACT2 show pleiotropic phenotypes, including reduced apical dominance, elongated life span and flowering duration, sterility, dwarfing, reduced seed yield and shorter root length. Microscopic analysis reveals that the reduced stature is caused by a reduction in cell size and fewer cells, and male sterility is caused by loss of the pollen coat and premature degeneration of the tapetal cells. Biochemical analyses established that the roots of AACT2 RNAi plants show quantitative and qualitative alterations in phytosterol profiles. These phenotypes and biochemical alterations are reversed when AACT2 RNAi plants are grown in the presence of mevalonate, which is consistent with the role of AACT2 in generating the bulk of the acetoacetyl?CoA precursor required for the cytosol?localized, mevalonate?derived isoprenoid biosynthetic pathway.

Jin, Huanan; Song, Zhihong; Nikolau, Basil J.

2012-03-31

380

High capacity, reversible alloying reactions in SnSb/C nanocomposites for Na-ion battery applications  

SciTech Connect

A new SnSb/C nanocomposite based on Na alloying reactions is demonstrated as anode for Na-ion battery applications. The electrode can achieve an exceptionally high capacity (544 mA h g?1, almost double that of intercalation carbon materials), good rate capacity and cyclability (80% capacity retention over 50 cycles) for Na-ion storage.

Xiao, Lifen; Cao, Yuliang; Xiao, Jie; Wang, Wei; Kovarik, Libor; Nie, Zimin; Liu, Jun

2012-04-04

381

Reversible simulation of irreversible computation  

NASA Astrophysics Data System (ADS)

Computer computations are generally irreversible while the laws of physics are reversible. This mismatch is penalized by among other things generating excess thermic entropy in the computation. Computing performance has improved to the extent that efficiency degrades unless all algorithms are executed reversibly, for example by a universal reversible simulation of irreversible computations. All known reversible simulations are either space hungry or time hungry. The leanest method was proposed by Bennett and can be analyzed using a simple ‘reversible’ pebble game. The reachable reversible simulation instantaneous descriptions (pebble configurations) of such pebble games are characterized completely. As a corollary we obtain the reversible simulation by Bennett and, moreover, show that it is a space-optimal pebble game. We also introduce irreversible steps and give a theorem on the tradeoff between the number of allowed irreversible steps and the memory gain in the pebble game. In this resource-bounded setting the limited erasing needs to be performed at precise instants during the simulation. The reversible simulation can be modified so that it is applicable also when the simulated computation time is unknown.

Li, Ming; Tromp, John; Vitányi, Paul

1998-09-01

382

Application of pre-stack reverse time migration based on FWI velocity estimation to ground penetrating radar data  

NASA Astrophysics Data System (ADS)

Reverse-time migration (RTM) is used for subsurface imaging to handle complex velocity models including steeply dipping interfaces and dramatic lateral variations and promises better imaging results compared to traditional migration method such as Kirchhoff migration algorithm. RTM has been increasingly used in seismic surveys for hydrocarbon resource explorations. Based on the similarity of kinematics and dynamics between electromagnetic wave and elastic wave, we develop pre-stack RTM method and apply it to process ground penetrating radar (GPR) data. Finite-difference time domain (FDTD) numerical method is used to simulate the electromagnetic wave propagation including forward and backward extrapolations, the cross-correlation imaging condition is used to obtain the final image. In order to provide a velocity model with relatively higher accuracy as the initial velocity model for RTM, we apply a full waveform inversion (FWI) in time domain to estimate the subsurface velocity structure based on reflection radar data. For testing the effectiveness of the algorithm, we have constructed a complex geological model, common-offset radar data and common-shot profile (CSP) radar reflection data are synthesized. All data are migrated with traditional Kirchhoff migration method and pre-stack RTM method separately, the migration results from pre-stack RTM show better coincidence with the true model. Furthermore, we have performed a physical experiment in a sandbox where a polyvinyl chloride (PVC) box is buried in the sand, the obtained common-offset radar data and common-shot radar data are migrated by using Kirchhoff migration method and pre-stack RTM algorithm separately, the pre-stack RTM result shows that RTM algorithm could get better imaging results.

Liu, Sixin; Lei, Linlin; Fu, Lei; Wu, Junjun

2014-08-01

383

Phylogenetic and genetic analysis of feline immunodeficiency virus gag, pol, and env genes from domestic cats undergoing nucleoside reverse transcriptase inhibitor treatment or treatment-naïve cats in Rio de Janeiro, Brazil.  

PubMed

Feline immunodeficiency virus (FIV) is the Lentivirus responsible for an immunodeficiency-like disease in domestic cats (Felis catus). FIV is divided into five phylogenetic subtypes (A, B, C, D, and E), based on genetic diversity. Knowledge of the geographical distribution of subtypes is relevant for understanding different disease progressions and for vaccine development. In this study, viral sequences of 26 infected cats from Rio de Janeiro, 8 undergoing treatment with zidovudine (AZT) for at least 5 years, were successfully amplified from blood specimens. gag capsid (CA), pol reverse transcriptase (RT), and env gp120 (V3-V4) regions were analyzed to determine subtypes and to evaluate potential mutations related to antiretroviral drug resistance among treated cats. Subtyping based on phylogenetic analysis was performed by the neighbor-joining and maximum likelihood methods. All of the sequences clustered with subtype B in the three regions, exhibiting low genetic variability. Additionally, we found evidence that the same virus is circulating in animals in close contact. The analysis of FIV RT sequences identified two new putative mutations related to drug resistance located in the RT "finger" domain, which has 60% identity to human immunodeficiency virus (HIV) sequence. Amino acid change K-->R at codons 64 and 69 was found in 25% and 37.5% of the treated animals, respectively. These signatures were comparable to K65R and K70R thymidine-associated mutations found in the HIV-1 HXB2 counterpart. This finding strongly suggests a position correlation between the mutations found in FIV and the K65R and K70R substitutions from drug-resistant HIV-1 strains. PMID:18550661

Martins, Angelica N; Medeiros, Sheila O; Simonetti, Jose P; Schatzmayr, Hermann G; Tanuri, Amílcar; Brindeiro, Rodrigo M

2008-08-01

384

Application of reversed-phase high-performance liquid chromatography with fluorimetric detection for simultaneous assessment of global DNA and total RNA methylation in Lepidium sativum: effect of plant exposure to Cd(II) and Se(IV).  

PubMed

In the present work, application of the previously established reversed-phase liquid chromatography procedure based on fluorescent labeling of cytosine and methylcytosine moieties with 2-bromoacetophenone (HPLC-FLD) is presented for simultaneous evaluation of global DNA and total RNA methylation at cytosine carbon 5. The need for such analysis was comprehended from the recent advances in the field of epigenetics that highlight the importance of non-coding RNAs in DNA methylation and suggest that RNA methylation might play a similar role in the modulation of genetic information, as previously demonstrated for DNA. In order to adopt HPLC-FLD procedure for DNA and RNA methylation analysis in a single biomass extract, two extraction procedures with different selectivity toward nucleic acids were examined, and a simplified calibration was designed allowing for evaluation of methylation percentage based on the ratio of chromatographic peak areas: cytidine/5-methylcytidine for RNA and 2'-deoxycytidine/5-methyl-2'-deoxycytidine for DNA. As a proof of concept, global DNA and total RNA methylation were determined in Lepidium sativum hydroponically grown in the presence of different Cd(II) or Se(IV) concentrations, expecting that plant exposure to abiotic stress might affect not only global DNA but also total RNA methylation. The results obtained showed the increase of DNA methylation in the treated plants up to concentration levels 2 mg L(-1) Cd and 1 mg L(-1) Se in the growth medium. For higher stressors' concentration, global DNA methylation tended to decrease. Most importantly, an inverse correlation was found between DNA and RNA methylation levels (r = -0.6788, p = 0.031), calling for further studies of this particular modification of nucleic acids in epigenetic context. PMID:23322354

Yanez Barrientos, Eunice; Wrobel, Kazimierz; Lopez Torres, Adolfo; Gutiérrez Corona, Felix; Wrobel, Katarzyna

2013-03-01

385

Applications and Implications of Advances in Human Genetics: Perspectives from a Group of Black Americans  

Microsoft Academic Search

Objectives: We explored the opinions of 40 Black Americans regarding: (1) what they thought most Blacks and Whites believe about genetic causes for perceived race differences in human traits, and (2) the impact of genetic science on them, their families, and Black people. Methods: We conducted in-depth telephone interviews with 40 self-identified Black men and women. Transcripts of the interviews

Jane P. Sheldon; Toby Epstein Jayaratne; Merle B. Feldbaum; Courtney D. DiNardo; Elizabeth M. Petty

2007-01-01

386

Application of the microsatellite technique for analyzing genetic diversity in shrimp breeding programs  

Microsoft Academic Search

The microsatellite technique was employed to demonstrate the use of genetic markers as a genetic analysis tool to manage breeding programs of cultured species. This technique was used on a total of 312 P. vannamei shrimp from Population 1 (Sinaloa, Mexico), Population 2 (Ecuador), Population 3 (hybrid of Population 1 X Population 2), Population 4 (Oaxaca, Mexico), a Guatemalan stock,

Greg M. Wolfus; Denise K. Garcia; Acacia Alcivar-Warren

1997-01-01

387

Genetic algorithm and the application for Job-Shop group scheduling  

Microsoft Academic Search

Genetic algorithm (GA) is a heuristic and random search technique mimicking nature. This paper first presents the basic principle of GA, the definition and the function of the genetic operators, and the principal character of GA. On the basis of these, the paper proposes using GA as a new solution method of the job-shop group scheduling problem, discusses the coded

Jianzhong Mao; Zhiming Wu

1995-01-01

388

Genetic testing for pharmacogenetics and its clinical application in drug therapy  

Microsoft Academic Search

There is wide individual variation in drug responses and adverse effects. As the main causes of the variation in drug responses, attention has focused on the genetic polymorphisms that encode metabolic enzymes regulating pharmacodynamics and receptors modulating the affinity with the responsive sites. Tailor-made drug therapy analyzes genetic polymorphisms involved in drug responses before drug administration and selects drugs and

Masahiro Hiratsuka; Takamitsu Sasaki; Michinao Mizugaki

2006-01-01

389

Application of Genetic Algorithm in the Optimization of Water Pollution Control Scheme  

Microsoft Academic Search

Genetic Algorithm (Genetic Algorithm Chine write for the GA) is a kind of hunting Algorithm bionic global optimization imitating the Darwinian biological evolution theories, is advancing front of complex nonlinear science and artificial intelligence science. In the basic of introducing the GA basic principle and optimization Algorithm, this text leads the GA into the domain of the water pollution control

Rui-Ming Zhao; Dong-Ping Qian

2007-01-01

390

Teaching Applied Genetics and Molecular Biology to Agriculture Engineers. Application of the European Credit Transfer System  

ERIC Educational Resources Information Center

We have been teaching applied molecular genetics to engineers and adapted the teaching methodology to the European Credit Transfer System. We teach core principles of genetics that are universal and form the conceptual basis of most molecular technologies. The course then teaches widely used techniques and finally shows how different techniques…

Weiss, J.; Egea-Cortines, M.

2008-01-01

391

Offering predictive testing for Huntington disease in a medical genetics clinic: Practical applications  

Microsoft Academic Search

Predictive testing for Huntington disease is presently offered in a select few medical genetics centers in the United States. This is in part due to the labor intensive counseling and psychological testing suggested by the research protocols. We discuss some specific suggestions for establishing programs for Huntington disease predictive testing within pre-existing medical genetics clinics to encourage more centers to

Robin L. Bennett; Thomas D. Bird; Linda Teri

1993-01-01

392

GENETIC NEURAL NETWORK BASED DATA MINING AND APPLICATION IN CASE ANALYSIS OF POLICE OFFICE  

Microsoft Academic Search

This paper puts forward a method that combines the learning algorithm of BP neural network with genetic algorithm to train BP network and optimize the weight values of the network in a global scale. This method is featured as global optimization, high accuracy and fast convergence. The data-mining model based on genetic neural network has been widely applied to the

LIU Han-li; LI Lin; ZHU Hai-hong

393

Application of elevator group control system based on genetic algorithm optimize BP fuzzy neural network  

Microsoft Academic Search

Its deficiency was revealed because of traffic pattern identification method of elevator group control system based on using BP neural network, and a new traffic patten identification model is proposed which is based on optimizing fuzzy neural network by genetic algorithm. The genetic algorithm is used to train fuzzy BP neural network, which can overcome the shortcoming of local minimum

Yanqiu Wang; Jian Zhang; Yueling Zhao; Yu Wang

2008-01-01

394

First successful application of preimplantation genetic diagnosis and haplotyping for congenital hyperinsulinism  

Microsoft Academic Search

Congenital hyperinsulinism is the most common cause of persistent hypoglycaemia in infancy. Early surgical intervention is usually required to prevent brain damage. The prevention of the transmission to the offspring is important in families carrying the mutated gene. Preimplantation genetic diagnosis (PGD) is an early genetic testing procedure for couples at risk of transmitting inherited diseases. A 36-year-old Saudi woman

Wafa Qubbaj; Abdulrahman Al-Swaid; Saad Al-Hassan; Khalid Awartani; Hesham Deek; Serdar Coskun

2011-01-01

395

Novel Design for Reversible Arithmetic Logic Unit  

NASA Astrophysics Data System (ADS)

Reversible logic circuits are of high interests to calculate with minimum energy consumption having applications in low-power CMOS design, optical computing and nanotechnology, especially in quantum computer. Quantum computer requires quantum arithmetic. A new design of a reversible arithmetic logic unit (reversible ALU) for quantum arithmetic has been proposed in this article. As we known, ALU is an important part of central processing unit (CPU) as the execution unit. So this article provides explicit construction of reversible ALU effecting basic arithmetic operations. By provided the corresponding control unit, the proposed reversible ALU can combine the classical arithmetic and logic operation in a reversible integrated system. This article provides a new more powerful ALU which contains more functions and it will make contribute to the realization of reversible Programmable Logic Device (RPLD) in future using reversible ALU.

Zhou, Rigui; Li, Yancheng; Zhang, Manqun; Hu, BenQiong

2015-02-01

396

Application of Long-Range and Binding Reverse Transcription-Quantitative PCR To Indicate the Viral Integrities of Noroviruses  

PubMed Central

This study intends to establish and apply methods evaluating both viral capsid and genome integrities of human noroviruses (NoVs), which thus far remain nonculturable. Murine norovirus 1 (MNV-1) and human NoV GII.4 in phosphate-buffered saline suspensions were treated with heat, UV light, or ethanol and detected by reverse transcription-quantitative PCR (RT-qPCR), long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR. For MNV-1 heated at 60°C for 2 and 30 min, limited reductions of genomic copies (<0.3-log) were obtained by RT-qPCR and long-range RT-qPCR, while the cell-binding pretreatments obtained higher reductions (>1.89-log reduction after 60°C for 30 min by binding long-range RT-qPCR). The human NoV GII.4 was found to be more heat resistant than MNV-1. For both MNV-1 and human NoV GII.4 after UV treatments of 20 and 200 mJ/cm2, no significant difference (P > 0.05) was observed between the dose-dependent reductions obtained by the four detection methodologies. Treatment of 70% ethanol for 1 min was shown to be more effective for inactivation of both MNV-1 and human NoV GII.4 than the heat and UV treatments used in this study. Subsequently, eight raspberry and four shellfish samples previously shown to be naturally contaminated with human NoVs by RT-qPCR (GI and GII; thus, 24 RT-qPCR signals) were subjected to comparison by this method. RT-qPCR, long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR detected 20/24, 14/24, 24/24, and 23/24 positive signals, respectively, indicating the abundant presence of intact NoV particles. PMID:25107982

De Keuckelaere, Ann; Uyttendaele, Mieke

2014-01-01

397

Application of long-range and binding reverse transcription-quantitative PCR to indicate the viral integrities of noroviruses.  

PubMed

This study intends to establish and apply methods evaluating both viral capsid and genome integrities of human noroviruses (NoVs), which thus far remain nonculturable. Murine norovirus 1 (MNV-1) and human NoV GII.4 in phosphate-buffered saline suspensions were treated with heat, UV light, or ethanol and detected by reverse transcription-quantitative PCR (RT-qPCR), long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR. For MNV-1 heated at 60°C for 2 and 30 min, limited reductions of genomic copies (<0.3-log) were obtained by RT-qPCR and long-range RT-qPCR, while the cell-binding pretreatments obtained higher reductions (>1.89-log reduction after 60°C for 30 min by binding long-range RT-qPCR). The human NoV GII.4 was found to be more heat resistant than MNV-1. For both MNV-1 and human NoV GII.4 after UV treatments of 20 and 200 mJ/cm(2), no significant difference (P > 0.05) was observed between the dose-dependent reductions obtained by the four detection methodologies. Treatment of 70% ethanol for 1 min was shown to be more effective for inactivation of both MNV-1 and human NoV GII.4 than the heat and UV treatments used in this study. Subsequently, eight raspberry and four shellfish samples previously shown to be naturally contaminated with human NoVs by RT-qPCR (GI and GII; thus, 24 RT-qPCR signals) were subjected to comparison by this method. RT-qPCR, long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR detected 20/24, 14/24, 24/24, and 23/24 positive signals, respectively, indicating the abundant presence of intact NoV particles. PMID:25107982

Li, Dan; De Keuckelaere, Ann; Uyttendaele, Mieke

2014-10-01

398

Control of Wettability of Carbon Nanotube Array by Reversible Dry Oxidation for Superhydrophobic Coating and Supercapacitor Applications  

NASA Astrophysics Data System (ADS)

In this thesis, dry chemical modification methods involving UV/ozone, oxygen plasma, and vacuum annealing treatments are explored to precisely control the wettability of CNT arrays. The effect of oxidation using UV/ozone and oxygen plasma treatments is highly reversible as long as the O/C ratio of the CNT arrays is kept below 18%. At O/C ratios higher than 18%, the effect of oxidation is no longer reversible. This irreversible oxidation is caused by irreversible changes to the CNT atomic structure during the oxidation process. During the oxidation process, CNT arrays undergo three different processes. For CNT arrays with O/C ratios lower than 40%, the oxidation process results in the functionalization of CNT outer walls by oxygenated groups. Although this functionalization process introduces defects, vacancies and micropores opening, the graphitic structure of the CNT is still largely intact. For CNT arrays with O/C ratios between 40% and 45%, the oxidation process results in the etching of CNT outer walls. This etching process introduces large scale defects and holes that can be obviously seen under TEM at high magnification. Most of these holes are found to be several layers deep and, in some cases, a large portion of the CNT side walls are cut open. For CNT arrays with O/C ratios higher than 45%, the oxidation process results in the exfoliation of the CNT walls and amorphization of the remaining CNT structure. This amorphization process can be implied from the disappearance of C-C sp2 peak in the XPS spectra associated with the pi-bond network. The impact behavior of water droplet impinging on superhydrophobic CNT arrays in a low viscosity regime is investigated for the first time. Here, the experimental data are presented in the form of several important impact behavior characteristics including critical Weber number, volume ratio, restitution coefficient, and maximum spreading diameter. As observed experimentally, three different impact regimes are identified while another impact regime is proposed. These regimes are partitioned by three critical Weber numbers, two of which are experimentally observed. The volume ratio between the primary and the secondary droplets is found to decrease with the increase of Weber number in all impact regimes other than the first one. In the first impact regime, this is found to be independent of Weber number since the droplet remains intact during and subsequent to the impingement. Experimental data show that the coefficient of restitution decreases with the increase of Weber number in all impact regimes. The rate of decrease of the coefficient of restitution in the high Weber number regime is found to be higher than that in the low and moderate Weber number. Experimental data also show that the maximum spreading factor increases with the increase of Weber number in all impact regimes. The rate of increase of the maximum spreading factor in the high Weber number regime is found to be higher than that in the low and moderate Weber number. Phenomenological approximations and interpretations of the experimental data, as well as brief comparisons to the previously proposed scaling laws, are shown here. Dry oxidation methods are used for the first time to characterize the influence of oxidation on the capacitive behavior of CNT array EDLCs. The capacitive behavior of CNT array EDLCs can be tailored by varying their oxygen content, represented by their O/C ratio. The specific capacitance of these CNT arrays increases with the increase of their oxygen content in both KOH and Et4NBF4/PC electrolytes. As a result, their gravimetric energy density increases with the increase of their oxygen content. However, their gravimetric power density decreases with the increase of their oxygen content. The optimally oxidized CNT arrays are able to withstand more than 35,000 charge/discharge cycles in Et4NBF4/PC at a current density of 5 A/g while only losing 10% of their original capacitance. (Abstract shortened by UMI.)

Aria, Adrianus Indrat

399

Random frog: an efficient reversible jump Markov Chain Monte Carlo-like approach for variable selection with applications to gene selection and disease classification.  

PubMed

The identification of disease-relevant genes represents a challenge in microarray-based disease diagnosis where the sample size is often limited. Among established methods, reversible jump Markov Chain Monte Carlo (RJMCMC) methods have proven to be quite promising for variable selection. However, the design and application of an RJMCMC algorithm requires, for example, special criteria for prior distributions. Also, the simulation from joint posterior distributions of models is computationally extensive, and may even be mathematically intractable. These disadvantages may limit the applications of RJMCMC algorithms. Therefore, the development of algorithms that possess the advantages of RJMCMC methods and are also efficient and easy to follow for selecting disease-associated genes is required. Here we report a RJMCMC-like method, called random frog that possesses the advantages of RJMCMC methods and is much easier to implement. Using the colon and the estrogen gene expression datasets, we show that random frog is effective in identifying discriminating genes. The top 2 ranked genes for colon and estrogen are Z50753, U00968, and Y10871_at, Z22536_at, respectively. (The source codes with GNU General Public License Version 2.0 are freely available to non-commercial users at: http://code.google.com/p/randomfrog/.). PMID:22840646

Li, Hong-Dong; Xu, Qing-Song; Liang, Yi-Zeng

2012-08-31

400

Isolobal analogies in intermetallics: the reversed approximation MO approach and applications to CrGa4- and Ir3Ge7-type phases.  

PubMed

Intermetallic phases offer a wealth of unique and unexplained structural features, which pose exciting challenges for the development of new bonding concepts. In this article, we present a straightforward approach to rapidly building bonding descriptions of such compounds: the reversed approximation Molecular Orbital (raMO) method. In this approach, we reverse the usual technique of using linear combinations of simple functions to approximate true wave functions and employ the fully occupied crystal orbitals of a compound as a basis set for the determination of the eigenfunctions of a simple, chemically transparent model Hamiltonian. The solutions fall into two sets: (1) a series of functions representing the best-possible approximations to the model system's eigenstates constructible from the occupied crystal orbitals and (2) a second series of functions that are orthogonal to the bonding picture represented by the model Hamiltonian. The electronic structure of a compound is thus quickly resolved into a series of orthogonal bonding subsystems. We first demonstrate the raMO analysis on a familiar molecule, 1,3-butadiene, and then move to illustrating its use in discovering new bonding phenomena through applications to three intermetallic phases: the PtHg4-type CrGa4 and the Ir3Ge7-type compounds Os3Sn7 and Ir3Sn7. For CrGa4, a density of states (DOS) minimum coinciding with its Fermi energy is traced to 18-electron configurations on the Cr atoms. For Os3Sn7 and Ir3Sn7, 18-electron configurations also underlie DOS pseudogaps. This time, however, the 18-electron counts involve multicenter interactions isolobal with classical Ir-Ir or Os-Os covalent bonds, as well as Sn-Sn single bonds serving as electron reservoirs. Our results are based on DFT-calibrated Hückel calculations, but in principle the raMO analysis can be implemented in any method employing one-electron wave functions. PMID:24555770

Yannello, Vincent J; Kilduff, Brandon J; Fredrickson, Daniel C

2014-03-01

401

An application of LOH analysis for detecting the genetic influences of space environmental radiation  

NASA Astrophysics Data System (ADS)

To detect the genetic influence of space environmental radiation at the chromosome level we proposed an application of loss of heterozygosity LOH analysis system for the mutations induced in human lymphoblastoid TK6 cells Surprisingly we succeeded the mutation detection in the frozen dells which were exposed to a low-dose 10 cGy of carbon-ion beam irradiation Mutation assays were performed within a few days or after about one month preservation at --80 r C following irradiation The results showed an increase in mutation frequency at the thymidine kinase TK gene locus 1 6-fold 2 5 X 10 -6 to 3 9 X 10 -6 and 2 1-fold 2 5 X 10 -6 to 5 3 X 10 -6 respectively Although the relative distributions of mutation classes were not changed by the radiation exposure in either assay an interesting characteristic was detected using this LOH analysis system two TK locus markers and eleven microsatellite loci spanning chromosome 17 The radiation-specific patterns of interstitial deletions were observed in the hemizygous LOH mutants which were considered as a result of end-joining repair of carbon ion-induced DNA double-strand breaks These results clearly demonstrate that this analysis can be used for the detection of low-dose ionizing radiation effects in the frozen cells In addition we performed so called adaptive response experiments in which TK6 cells were pre-irradiated with low-dose 2 5 sim 10 cGy of X-ray and then exposed to challenging dose 2Gy of X-rays Interestingly the

Yatagai, F.; Umebayashi, Y.; Honma, M.; Abe, T.; Suzuki, H.; Shimazu, T.; Ishioka, N.; Iwaki, M.

402

Applications of Improved Multi-Agent Genetic Algorithm to Water Pollution Control System Planning  

NASA Astrophysics Data System (ADS)

Combining the ability of apperception and counteractive to environment of agent with search method of genetic algorithm, an improved multi-agent genetic algorithm (MAGA) is advanced. It ensures diversity of population and improves local search ability of genetic algorithm by simulating competition, cooperate and self-study of different agents using neighboring cross operator, aberrance operator and self-learning operator of agent. The algorithm is applied to the optimal planning for the waste treatment system of Urumqi, Xinjiang. Results demonstrate an improved performance in finding the global minimum when water quality requirements have been fulfilled. The result demonstrates nicer performance and factual value of MAGA.

Dong, Qianjin; Lu, Fan; Gao, Shichun

2010-05-01

403

Genome metabolome integrated network analysis to uncover connections between genetic variants and complex traits: an application to obesity  

PubMed Central

Current studies of phenotype diversity by genome-wide association studies (GWAS) are mainly focused on identifying genetic variants that influence level changes of individual traits without considering additional alterations at the system-level. However, in addition to level alterations of single phenotypes, differences in association between phenotype levels are observed across different physiological states. Such differences in molecular correlations between states can potentially reveal information about the system state beyond that reported by changes in mean levels alone. In this study, we describe a novel methodological approach, which we refer to as genome metabolome integrated network analysis (GEMINi) consisting of a combination of correlation network analysis and genome-wide correlation study. The proposed methodology exploits differences in molecular associations to uncover genetic variants involved in phenotype variation. We test the performance of the GEMINi approach in a simulation study and illustrate its use in the context of obesity and detailed quantitative metabolomics data on systemic metabolism. Application of GEMINi revealed a set of metabolic associations which differ between normal and obese individuals. While no significant associations were found between genetic variants and body mass index using a standard GWAS approach, further investigation of the identified differences in metabolic association revealed a number of loci, several of which have been previously implicated with obesity-related processes. This study highlights the advantage of using molecular associations as an alternative phenotype when studying the genetic basis of complex traits and diseases. PMID:24573330

Valcárcel, Beatriz; Ebbels, Timothy M. D.; Kangas, Antti J.; Soininen, Pasi; Elliot, Paul; Ala-Korpela, Mika; Järvelin, Marjo-Riitta; de Iorio, Maria

2014-01-01

404

Genome metabolome integrated network analysis to uncover connections between genetic variants and complex traits: an application to obesity.  

PubMed

Current studies of phenotype diversity by genome-wide association studies (GWAS) are mainly focused on identifying genetic variants that influence level changes of individual traits without considering additional alterations at the system-level. However, in addition to level alterations of single phenotypes, differences in association between phenotype levels are observed across different physiological states. Such differences in molecular correlations between states can potentially reveal information about the system state beyond that reported by changes in mean levels alone. In this study, we describe a novel methodological approach, which we refer to as genome metabolome integrated network analysis (GEMINi) consisting of a combination of correlation network analysis and genome-wide correlation study. The proposed methodology exploits differences in molecular associations to uncover genetic variants involved in phenotype variation. We test the performance of the GEMINi approach in a simulation study and illustrate its use in the context of obesity and detailed quantitative metabolomics data on systemic metabolism. Application of GEMINi revealed a set of metabolic associations which differ between normal and obese individuals. While no significant associations were found between genetic variants and body mass index using a standard GWAS approach, further investigation of the identified differences in metabolic association revealed a number of loci, several of which have been previously implicated with obesity-related processes. This study highlights the advantage of using molecular associations as an alternative phenotype when studying the genetic basis of complex traits and diseases. PMID:24573330

Valcárcel, Beatriz; Ebbels, Timothy M D; Kangas, Antti J; Soininen, Pasi; Elliot, Paul; Ala-Korpela, Mika; Järvelin, Marjo-Riitta; de Iorio, Maria

2014-05-01

405

Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)  

PubMed Central

Molecular markers are a highly valuable tool for creating genetic maps. Like in many other crops, sugar beet (Beta vulgaris L.) breeding is increasingly supported by the application of such genetic markers. Single nucleotide polymorphism (SNP) based markers have a high potential for automated analysis and high-throughput genotyping. We developed a bioinformatics workflow that uses Sanger and 2nd-generation sequence data for detection, evaluation and verification of new transcript-associated SNPs from sugar beet. RNAseq data from one parent of an established mapping population were produced by 454-FLX sequencing and compared to Sanger ESTs derived from the other parent. The workflow established for SNP detection considers the quality values of both types of reads, provides polymorphic alignments as well as selection criteria for reliable SNP detection and allows painless generation of new genetic markers within genes. We obtained a total of 14,323 genic SNPs and InDels. According to empirically optimised settings for the quality parameters, we classified these SNPs into four usability categories. Validation of a subset of the in silico detected SNPs by genotyping the mapping population indicated a high success rate of the SNP detection. Finally, a total of 307 new markers were integrated with existing data into a new genetic map of sugar beet which offers improved resolution and the integration of terminal markers. PMID:25302600

Holtgräwe, Daniela; Sörensen, Thomas Rosleff; Viehöver, Prisca; Schneider, Jessica; Schulz, Britta; Borchardt, Dietrich; Kraft, Thomas; Himmelbauer, Heinz; Weisshaar, Bernd

2014-01-01

406

Design and analysis of genetical genomics studies and their potential applications in livestock research   

E-print Network

Quantitative Trait Loci (QTL) mapping has been widely used to identify genetic loci attributable to the variation observed in complex traits. In recent years, gene expression phenotypes have emerged as a new type of ...

Lam, Alex C.

2009-01-01

407

Genetics of Type 2 Diabetes: Insights into the Pathogenesis and Its Clinical Application  

PubMed Central

With rapidly increasing prevalence, diabetes has become one of the major causes of mortality worldwide. According to the latest studies, genetic information makes substantial contributions towards the prediction of diabetes risk and individualized antidiabetic treatment. To date, approximately 70 susceptibility genes have been identified as being associated with type 2 diabetes (T2D) at a genome-wide significant level (P < 5 × 10?8). However, all the genetic loci identified so far account for only about 10% of the overall heritability of T2D. In addition, how these novel susceptibility loci correlate with the pathophysiology of the disease remains largely unknown. This review covers the major genetic studies on the risk of T2D based on ethnicity and briefly discusses the potential mechanisms and clinical utility of the genetic information underlying T2D. PMID:24864266

Sun, Xue; Yu, Weihui; Hu, Cheng

2014-01-01

408

Application of Genetic Algorithms and Thermogravimetry to Determine the Kinetics of Polyurethane Foam in Smoldering Combustion   

E-print Network

In this work, the kinetic parameters governing the thermal and oxidative degradation of flexible polyurethane foam are determined using thermogravimetric data and a genetic algorithm. These kinetic parameters are needed ...

Rein, Guillermo; Lautenberger, Chris; Fernandez-Pello, Carlos; Torero, Jose L; Urban, David

409

Application of genetic-based neural networks to thermal unit commitment  

Microsoft Academic Search

A new approach using genetic algorithms based neural networks and dynamic programming (GANN-DP) to solve power system unit commitment problems is proposed in this paper. A set of feasible generator commitment schedules is first formulated by genetic-enhanced neural networks. These pre-committed schedules are then optimized by the dynamic programming technique. By the proposed approach, learning stagnation is avoided. The neural

Shyh-Jier-Huang; Ching-Lien Huang

1997-01-01

410

Microsatellite loci in the carcinogenic liver fluke, Opisthorchis viverrini and their application as population genetic markers.  

PubMed

Opisthorchis viverrini is a carcinogenic foodborne trematode endemic in Southeast Asia especially in Thailand and the Lao People's Democratic Republic. Opisthorchiasis causes hepatobiliary diseases and cholangiocarcinoma (bile duct cancer). Currently there is substantial evidence on genetic variation of O. viverrini but the information on population genetic structure is lacking. Because microsatellite DNA of this parasite is not available, we for the first time isolated and utilized microsatellite DNA as genetic markers to examine genetic diversity and the population structure of O. viverrini. Partial genomic DNA libraries were constructed by conventional and enrichment methods which yielded microsatellite-containing clones of 0.18-0.25% and 16.84%, respectively. Within 41 microsatellite loci isolated 36.59% were perfect, 60.98% were interrupted and 2.44% were compound microsatellites. The CA repetitions were the most frequent, followed by GT and CAT. Primers specific to the flanking regions of 12 microsatellite loci were developed to genotype 150 O. viverrini individuals from geographical localities in Thailand and Lao PDR. Allele numbers per locus ranged from 2 to 15, with the mean expected heterozygosity of 0.03-0.66. Analyses of O. viverrini from 5 localities revealed a high level of genetic diversity and had significant deviation from Hardy-Weinberg equilibrium. Significant heterozygote deficiency as well as heterozygote excess was detected across all localities indicating the possibility of selfing (inbreeding) as a predominant reproductive mode. Significant genetic differentiation (F(ST)) was also detected between worms from different localities with varying levels of genetic heterogeneity. We discuss our results in terms of what these novel microsatellite markers reveal about the epidemiology and transmission dynamics of this medically important parasite, both in terms of the current study and their potential for future comprehensive population genetic studies O. viverrini sensu lato in Southeast Asia. PMID:19900579

Laoprom, Nonglak; Sithithaworn, Paiboon; Ando, Katsuhiko; Sithithaworn, Jiraporn; Wongkham, Sopit; Laha, Thewarach; Klinbunga, Sirawut; Webster, Joanne P; Andrews, Ross H

2010-01-01

411

The Use of Prior Distributions to Learn Genetic Olivier Gevaert1  

E-print Network

of a struc- ture prior for reverse-engineering genetic networks with Bayesian network models can improve more reliable models of genetic networks. 1 Introduction Reverse engineering genetic networks has been and extensions of Bayesian networks are popular models for reverse engineering genetic networks ([5, 15, 9, 10

412

Analysis of Genetic Variation and Potential Applications in Genome-Scale Metabolic Modeling  

PubMed Central

Genetic variation is the motor of evolution and allows organisms to overcome the environmental challenges they encounter. It can be both beneficial and harmful in the process of engineering cell factories for the production of proteins and chemicals. Throughout the history of biotechnology, there have been efforts to exploit genetic variation in our favor to create strains with favorable phenotypes. Genetic variation can either be present in natural populations or it can be artificially created by mutagenesis and selection or adaptive laboratory evolution. On the other hand, unintended genetic variation during a long term production process may lead to significant economic losses and it is important to understand how to control this type of variation. With the emergence of next-generation sequencing technologies, genetic variation in microbial strains can now be determined on an unprecedented scale and resolution by re-sequencing thousands of strains systematically. In this article, we review challenges in the integration and analysis of large-scale re-sequencing data, present an extensive overview of bioinformatics methods for predicting the effects of genetic variants on protein function, and discuss approaches for interfacing existing bioinformatics approaches with genome-scale models of cellular processes in order to predict effects of sequence variation on cellular phenotypes. PMID:25763369

Cardoso, João G. R.; Andersen, Mikael Rørdam; Herrgård, Markus J.; Sonnenschein, Nikolaus

2015-01-01

413

Using needs-based frameworks for evaluating new technologies: an application to genetic tests.  

PubMed

Given the multitude of newly available genetic tests in the face of limited healthcare budgets, the European Society of Human Genetics assessed how genetic services can be prioritized fairly. Using (health) benefit maximizing frameworks for this purpose has been criticized on the grounds that rather than maximization, fairness requires meeting claims (e.g. based on medical need) equitably. This study develops a prioritization score for genetic tests to facilitate equitable allocation based on need-based claims. It includes attributes representing health need associated with hereditary conditions (severity and progression), a genetic service's suitability to alleviate need (evidence of benefit and likelihood of positive result) and costs to meet the needs. A case study for measuring the attributes is provided and a suggestion is made how need-based claims can be quantified in a priority function. Attribute weights can be informed by data from discrete-choice experiments. Further work is needed to measure the attributes across the multitude of genetic tests and to determine appropriate weights. The priority score is most likely to be considered acceptable if developed within a decision process which meets criteria of procedural fairness and if the priority score is interpreted as "strength of recommendation" rather than a fixed cut-off value. PMID:25488566

Rogowski, Wolf H; Schleidgen, Sebastian

2015-02-01

414

A Novel Genetic Score Approach Using Instruments to Investigate Interactions between Pathways and Environment: Application to Air Pollution  

PubMed Central

Air pollution has been associated with increased systemic inflammation markers. We developed a new pathway analysis approach to investigate whether gene variants within relevant pathways (oxidative stress, endothelial function, and metal processing) modified the association between particulate air pollution and fibrinogen, C-reactive protein (CRP), intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1). Our study population consisted of 822 elderly participants of the Normative Aging Study (1999–2011). To investigate the role of biological mechanisms and to reduce the number of comparisons in the analysis, we created pathway-specific scores using gene variants related to each pathway. To select the most appropriate gene variants, we used the least absolute shrinkage and selection operator (Lasso) to relate independent outcomes representative of each pathway (8-hydroxydeoxyguanosine for oxidative stress, augmentation index for endothelial function, and patella lead for metal processing) to gene variants. A high genetic score corresponds to a higher allelic risk profile. We fit mixed-effects models to examine modification by the genetic score of the weekly air pollution association with the outcome. Among participants with higher genetic scores within the oxidative stress pathway, we observed significant associations between particle number and fibrinogen, while we did not find any association among participants with lower scores (pinteraction?=?0.04). Compared to individuals with low genetic scores of metal processing gene variants, participants with higher scores had greater effects of particle number on fibrinogen (pinteraction?=?0.12), CRP (pinteraction?=?0.02), and ICAM-1 (pinteraction?=?0.08). This two-stage penalization method is easy to implement and can be used for large-scale genetic applications. PMID:24755831

Bind, Marie-Abele; Coull, Brent; Suh, Helen; Wright, Robert; Baccarelli, Andrea; Vokonas, Pantel; Schwartz, Joel

2014-01-01

415

Low electric field, easily reversible electrical set and reset processes in a Ge15Te83Si2 glass for phase change memory applications  

NASA Astrophysics Data System (ADS)

We report here an easily reversible set-reset process in a new Ge15Te83Si2 glass that could be a promising candidate for phase change random access memory applications. The I-V characteristics of the studied sample show a comparatively low threshold electric field (Eth) of 7.3 kV/cm. Distinct differences in the type of switching behavior are achieved by means of controlling the on state current. It enables the observation of a threshold type for less than 0.7 mA beyond memory type (set) switching. The set and reset processes have been achieved with a similar magnitude of 1 mA, and with a triangular current pulse for the set process and a short duration rectangular pulse of 10 msec width for the reset operation. Further, a self-resetting effect is seen in this material upon excitation with a saw-tooth/square pulse, and their response of leading and trailing edges are discussed. About 6.5 × 104 set-reset cycles have been undertaken without any damage to the device.

Anbarasu, M.; Asokan, S.

2011-04-01

416

Ant Colony Optimization with Genetic Operation and Its Application to Traveling Salesman Problem  

NASA Astrophysics Data System (ADS)

Ant colony optimization (ACO) algorithms are a recently developed, population-based approach which has been successfully applied to optimization problems. However, in the ACO algorithms it is difficult to adjust the balance between intensification and diversification and thus the performance is not always very well. In this work, we propose an improved ACO algorithm in which some of ants can evolve by performing genetic operation, and the balance between intensification and diversification can be adjusted by numbers of ants which perform genetic operation. The proposed algorithm is tested by simulating the Traveling Salesman Problem (TSP). Experimental studies show that the proposed ACO algorithm with genetic operation has superior performance when compared to other existing ACO algorithms.

Wang, Rong-Long; Zhou, Xiao-Fan; Okazaki, Kozo

417

Reverse-Genetic Analysis of the Two Biotin-Containing Subunit Genes of the Heteromeric Acetyl-Coenzyme A Carboxylase in Arabidopsis Indicates a Unidirectional Functional Redundancy1[C][W][OA  

PubMed Central

The heteromeric acetyl-coenzyme A carboxylase catalyzes the first and committed reaction of de novo fatty acid biosynthesis in plastids. This enzyme is composed of four subunits: biotin carboxyl-carrier protein (BCCP), biotin carboxylase, ?-carboxyltransferase, and ?-carboxyltransferase. With the exception of BCCP, single-copy genes encode these subunits in Arabidopsis (Arabidopsis thaliana). Reverse-genetic approaches were used to individually investigate the physiological significance of the two paralogous BCCP-coding genes, CAC1A (At5g16390, codes for BCCP1) and CAC1B (At5g15530, codes for BCCP2). Transfer DNA insertional alleles that completely eliminate the accumulation of BCCP2 have no perceptible effect on plant growth, development, and fatty acid accumulation. In contrast, transfer DNA insertional null allele of the CAC1A gene is embryo lethal and deleteriously affects pollen development and germination. During seed development the effect of the cac1a null allele first becomes apparent at 3-d after flowering, when the synchronous development of the endosperm and embryo is disrupted. Characterization of CAC1A antisense plants showed that reducing BCCP1 accumulation to 35% of wild-type levels, decreases fatty acid accumulation and severely affects normal vegetative plant growth. Detailed expression analysis by a suite of approaches including in situ RNA hybridization, promoter:reporter transgene expression, and quantitative western blotting reveal that the expression of CAC1B is limited to a subset of the CAC1A-expressing tissues, and CAC1B expression levels are only about one-fifth of CAC1A expression levels. Therefore, a likely explanation for the observed unidirectional redundancy between these two paralogous genes is that whereas the BCCP1 protein can compensate for the lack of BCCP2, the absence of BCCP1 cannot be tolerated as BCCP2 levels are not sufficient to support heteromeric acetyl-coenzyme A carboxylase activity at a level that is required for normal growth and development. PMID:21030508

Li, Xu; Ilarslan, Hilal; Brachova, Libuse; Qian, Hui-Rong; Li, Ling; Che, Ping; Wurtele, Eve Syrkin; Nikolau, Basil J.

2011-01-01

418

Characterization of Reverse Genetics-Derived Cold-Adapted Master Donor Virus A/Leningrad/134/17/57 (H2N2) and Reassortants with H5N1 Surface Genes in a Mouse Model  

PubMed Central

Live attenuated influenza vaccines (LAIV) offer significant advantages over subunit or split inactivated vaccines to mitigate an eventual influenza pandemic, including simpler manufacturing processes and more cross-protective immune responses. Using an established reverse genetics (rg) system for wild-type (wt) A/Leningrad/134/1957 and cold-adapted (ca) A/Leningrad/134/17/1957 (Len17) master donor virus (MDV), we produced and characterized three rg H5N1 reassortant viruses carrying modified HA and intact NA genes from either A/Vietnam/1203/2004 (H5N1, VN1203, clade 1) or A/Egypt/321/2007 (H5N1, EG321, clade 2) virus. A mouse model of infection was used to determine the infectivity and tissue tropism of the parental wt viruses compared to the ca master donor viruses as well as the H5N1 reassortants. All ca viruses showed reduced replication in lungs and enhanced replication in nasal epithelium. In addition, the H5N1 HA and NA enhanced replication in lungs unless it was restricted by the internal genes of the ca MDV. Mice inoculated twice 4 weeks apart with the H5N1 reassortant LAIV candidate viruses developed serum hemagglutination inhibition HI and IgA antibody titers to the homologous and heterologous viruses consistent with protective immunity. These animals remained healthy after challenge inoculation with a lethal dose with homologous or heterologous wt H5N1 highly pathogenic avian influenza (HPAI) viruses. The profiles of viral replication in respiratory tissues and the immunogenicity and protective efficacy characteristics of the two ca H5N1 candidate LAIV viruses warrant further development into a vaccine for human use. PMID:24648485

Isakova-Sivak, Irina; Chen, Li-Mei; Bourgeois, Melissa; Matsuoka, Yumiko; Voeten, J. Theo M.; Heldens, Jacco G. M.; van den Bosch, Han; Klimov, Alexander; Rudenko, Larisa; Cox, Nancy J.

2014-01-01

419

Characterization of reverse genetics-derived cold-adapted master donor virus A/Leningrad/134/17/57 (H2N2) and reassortants with H5N1 surface genes in a mouse model.  

PubMed

Live attenuated influenza vaccines (LAIV) offer significant advantages over subunit or split inactivated vaccines to mitigate an eventual influenza pandemic, including simpler manufacturing processes and more cross-protective immune responses. Using an established reverse genetics (rg) system for wild-type (wt) A/Leningrad/134/1957 and cold-adapted (ca) A/Leningrad/134/17/1957 (Len17) master donor virus (MDV), we produced and characterized three rg H5N1 reassortant viruses carrying modified HA and intact NA genes from either A/Vietnam/1203/2004 (H5N1, VN1203, clade 1) or A/Egypt/321/2007 (H5N1, EG321, clade 2) virus. A mouse model of infection was used to determine the infectivity and tissue tropism of the parental wt viruses compared to the ca master donor viruses as well as the H5N1 reassortants. All ca viruses showed reduced replication in lungs and enhanced replication in nasal epithelium. In addition, the H5N1 HA and NA enhanced replication in lungs unless it was restricted by the internal genes of the ca MDV. Mice inoculated twice 4 weeks apart with the H5N1 reassortant LAIV candidate viruses developed serum hemagglutination inhibition HI and IgA antibody titers to the homologous and heterologous viruses consistent with protective immunity. These animals remained healthy after challenge inoculation with a lethal dose with homologous or heterologous wt H5N1 highly pathogenic avian influenza (HPAI) viruses. The profiles of viral replication in respiratory tissues and the immunogenicity and protective efficacy characteristics of the two ca H5N1 candidate LAIV viruses warrant further development into a vaccine for human use. PMID:24648485

Isakova-Sivak, Irina; Chen, Li-Mei; Bourgeois, Melissa; Matsuoka, Yumiko; Voeten, J Theo M; Heldens, Jacco G M; van den Bosch, Han; Klimov, Alexander; Rudenko, Larisa; Cox, Nancy J; Donis, Ruben O

2014-05-01

420

Molecular Studies in Horses with SRY-Positive XY Sex Reversal  

E-print Network

determination genes lead to various abnormal sexual phenotypes, including sex reversal syndrome in which the genetic and phenotypic sex do not match. Sex reversal syndrome has been reported in humans, mouse, and several domestic species. In horses, SRY...

Fang, Erica

2012-02-14

421

Clinical genetic testing for male factor infertility: current applications and future directions.  

PubMed

Spermatogenesis involves the aggregated action of up to 2300 genes, any of which, could, potentially, provide targets for diagnostic tests of male factor infertility. Contrary to the previously proposed common variant hypothesis for common diseases such as male infertility, genome-wide association studies and targeted gene sequencing in cohorts of infertile men have identified only a few gene polymorphisms that are associated with male infertility. Unfortunately, the search for genetic variants associated with male infertility is further hampered by the lack of viable animal models of human spermatogenesis, difficulty in robustly phenotyping infertile men and the complexity of pedigree studies in male factor infertility. In this review, we describe basic genetic principles involved in understanding the genetic basis of male infertility and examine the utility and proper clinical use of the proven genetic assays of male factor infertility, specifically Y chromosome microdeletions, chromosomal translocations, karyotype, cystic fibrosis transmembrane conductance regulator mutation analysis and sperm genetic tests. Unfortunately, these tests are only able to diagnose the cause of about 20% of male factor infertility. The remainder of the review will be devoted to examining novel tests and diagnostic tools that have the potential to explain the other 80% of male factor infertility that is currently classified as idiopathic. Those tests include epigenetic analysis of the spermatozoa and the evaluation of rare genetic variants and copy number variations in patients. Success in advancing to the implementation of such areas is not only dependent on technological advances in the laboratory, but also improved phenotyping in the clinic. PMID:24711280

Hotaling, J; Carrell, D T

2014-05-01

422

Mining Genetic Epidemiology Data with Bayesian Networks Application to APOE Gene Variation and Plasma Lipid Levels  

Microsoft Academic Search

There is a critical need for data-mining methods that can identify SNPs that predict among-individual variation in a phenotype of interest and reverse-engineer the biological network of relationships between SNPs, phenotypes, and other factors. This problem is both challenging and important in light of the large number of SNPs in many genes of interest and across the human genome. A

Andrei S. Rodin; Thomas H. Mosley Jr.; Andrew G. Clark; Charles F. Sing; Eric Boerwinkle

2005-01-01

423

Forward and reverse mutagenesis in C. elegans  

PubMed Central

Mutagenesis drives natural selection. In the lab, mutations allow gene function to be deciphered. C. elegans is highly amendable to functional genetics because of its short generation time, ease of use, and wealth of available gene-alteration techniques. Here we provide an overview of historical and contemporary methods for mutagenesis in C. elegans, and discuss principles and strategies for forward (genome-wide mutagenesis) and reverse (target-selected and gene-specific mutagenesis) genetic studies in this animal. PMID:24449699

Kutscher, Lena M.; Shaham, Shai

2014-01-01

424

Application of exome sequencing in the search for genetic causes of rare disorders of copper metabolism.  

PubMed

The genetic defect in a number of rare disorders of metal metabolism remains elusive. The limited number of patients with these disorders impedes the identification of the causative gene through positional cloning, which requires numerous families with multiple affected individuals. However, with next-generation sequencing all coding DNA (exomes) or whole genomes of patients can be sequenced to identify genes that are consistently mutated in patients. With this strategy only a limited number of patients and/or pedigrees is needed, bringing the elucidation of the genetic cause of even very rare diseases within reach. The main challenge associated with whole exome sequencing is the identification of the disease-causing mutation(s) among abundant genetic candidate variants. We describe several strategies to manage this data wealth, including comparison with control databases, increasing the number of patients and controls, and reducing the genomic region under investigation through homozygosity mapping. In this review we introduce a number of rare disorders of copper metabolism, with a suspected but yet unknown monogenetic cause, as an attractive target for this strategy. We anticipate that use of these novel techniques will identify the basic defect in the disorders described in this review, as well as in other genetic disorders of metal metabolism, in the next few years. PMID:22555275

Fuchs, Sabine A; Harakalova, Magdalena; van Haaften, Gijs; van Hasselt, Peter M; Cuppen, Edwin; Houwen, Roderick H J

2012-07-01

425

The Application of Genetically Engineered Herpes Simplex Viruses to the Treatment of Experimental Brain Tumors  

Microsoft Academic Search

Due to lack of effective therapy, primary brain tumors are the focus of intense investigation of novel experimental approaches that use vectors and recombinant viruses. Therapeutic approaches have been both indirect, whereby vectors are used, or direct to allow for direct cell killing by the introduced virus. Genetically engineered herpes simplex viruses are currently being evaluated as an experimental approach

Samita S. Andreansky; Bin He; G. Yancey Gillespie; Liliana Soroceanu; James Markert; Joany Chou; Bernard Roizman; Richard J. Whitley

1996-01-01

426

Optimisation of halogenase enzyme activity by application of a genetic algorithm  

Microsoft Academic Search

A genetic algorithm (GA) was applied for the optimisation of an enzyme assay composition respectively the enzyme activity of a recombinantly produced FADH2-dependent halogenating enzyme. The examined enzyme belongs to the class of halogenases and is capable to halogenate tryptophan regioselective in position 5. Therefore, the expressed trp-5-halogenase can be an interesting tool in the manufacturing of serotonin precursors. The

Kai Muffler; Marco Retzlaff; Karl-Heinz van Pée; Roland Ulber

2007-01-01

427

Intracerebral Hemorrhage in Mice: Model Characterization and Application for Genetically Modified Mice  

Microsoft Academic Search

Gene knockout or transgenic animals may assist in elucidating the mechanisms of brain injury after intracerebral hemorrhage (ICH). However, almost all commercially available transgenic or knockout animals are mice. The purpose of this study was to develop an ICH model in mice and to investigate the influence of gender and complement C5 genetic differences on outcome after ICH. Male and

Takehiro Nakamura; Guohua Xi; Ya Hua; Timothy Schallert; Julian T. Hoff; Richard F. Keep

2004-01-01

428

Genetic Vectors as a Tool in Association Studies: Definitions and Application for Study of Rheumatoid Arthritis  

PubMed Central

To identify putative relations between different genetic factors in the human genome in the development of common complex disease, we mapped the genetic data to an ensemble of spin chains and analysed the data as a quantum system. Each SNP is considered as a spin with three states corresponding to possible genotypes. The combined genotype represents a multispin state, described by the product of individual-spin states. Each person is characterized by a single genetic vector (GV) and individuals with identical GVs comprise the GV group. This consolidation of genotypes into GVs provides integration of multiple genetic variants for a single statistical test and excludes ambiguity of biological interpretation known for allele and haplotype associations. We analyzed two independent cohorts, with 2633 rheumatoid arthritis cases and 2108 healthy controls, and data for 6 SNPs from the HTR2A locus plus shared epitope allele. We found that GVs based on selected markers are highly informative and overlap for 98.3% of the healthy population between two cohorts. Interestingly, some of the GV groups contain either only controls or only cases, thus demonstrating extreme susceptibility or protection features. By using this new approach we confirmed previously detected univariate associations and demonstrated the most efficient selection of SNPs for combined analyses for functional studies.

Sandalov, Igor; Padyukov, Leonid

2015-01-01

429

Polymorphic Simple Sequence Repeat Regions in Chloroplast Genomes: Applications to the Population Genetics of Pines  

Microsoft Academic Search

Simple sequence repeats (SSRs), consisting of tandemly repeated multiple copies of mono-, di-, tri-, or tetranucleotide motifs, are ubiquitous in eukaryotic genomes and are frequently used as genetic markers, taking advantage of their length polymorphism. We have examined the polymorphism of such sequences in the chloroplast genomes of plants, by using a PCR-based assay. GenBank searches identified the presence of

W. Powell; M. Morgante; R. McDevitt; G. G. Vendramin; J. A. Rafalski

1995-01-01

430

Application of Mutation Only Genetic Algorithm for the Extraction of Investment Strategy in Financial Time Series  

Microsoft Academic Search

We use the recently introduced method of mutation only genetic algorithm (MOGA) to search for good strategies of investment in financial time series, as measured by the yield over a fixed period of investment. The rules for buy, sell or hold are introduced as conditional statements involving inequalities of various moving averages, and encoded in a string representation chromosomes in

Xia Pan; Jian Zhang; K. Y. Szeto

2005-01-01

431

Optimization Using Genetic Algorithms: An Application to the Real Business Cycle Model  

Microsoft Academic Search

This paper uses genetic algorithms (GAs) to find the optimal parameter values in the solution of the Real Business Cycle model. To generate the policy functions of the individual, we approximate the conditional expectation of the Euler equation using an exponential polynomial function, based on the method proposed by Marcet (1991). The ambiguity in the selection of the starting values

Christian Johnson

1997-01-01

432

Application of genetic algorithms to fault diagnosis in nuclear power plants  

Microsoft Academic Search

A nuclear power plant (NPP) is a complex and highly reliable special system. Without expert knowledge, fault confirmation in the NPP can be prevented by illusive and real-time signals. A new method of fault diagnosis, based on genetic algorithms (GAs) has been developed to resolve this problem. This NPP fault diagnosis method combines GAs and classical probability with an expert

Zhou Yangping; Zhao Bingquan; Wu DongXin

2000-01-01

433

An application of genetic and tabu searches to the freight railroad operating plan problem  

Microsoft Academic Search

This paper addresses the joint train-scheduling and demand-flow problem for a major US freight railroad. No efficient optimization techniques are known to solve the NP-hard combinatorial optimization problem. Genetic search is used to find acceptable solutions; however, its performance is found to deteriorate as the problem size grows. A \\

Michael Francis Gorman

1998-01-01

434

A Genetic Algorithm for Finite State Automata Induction with an Application to Phonotactics  

Microsoft Academic Search

This paper presents a genetic algorithm for the automatic construction of finite-state automata from positive data. The algorithm is suitable for constructing automata from complete and incomplete presentation of data. In the case of incomplete presentation of data, different degrees of generalisation can be achieved with a set of search parameters. This paper describes the algorithm, and presents results for

Anja Belz; Berkan Eskikaya

1998-01-01

435

The application of Mahalanobis's generalized distance to measure genetic divergence in Durum wheat  

Microsoft Academic Search

Mahalanobis's generalized distance analysis of days to flowering, days to physiological maturity, height, lodging, and grain yield data pertaining to ten cultivars of durum wheat (Triticum turgidum L. var. durum) revealed no association between genetic divergence and geographic origin. The analysis, however, succeeded in differentiating between those cultivars of tropical origin adapted to short daylength and those of temperate origin

J. Lee; P. J. Kaltsikes

1973-01-01

436

A genetic linkage map of the mouse: Current applications and future prospects  

Microsoft Academic Search

Technological advances have made possible the development of high-resolution genetic linkage maps for the mouse. These maps in turn offer exciting prospects for understanding mammalian genome evolution through comparative mapping, for developing mouse models of human disease, and for identifying the function of all genes in the organism.

Neal G. Copeland; Nancy A. Jenkins; Debra J. Gilbert; Janan T. Eppig; L. J. Maltais; J. H. Nadeau; J. C. Miller; W. F. Dietrich; A. Weaver; S. E. Lincoln; R. G. Steen; L. D. Steing; Eric S. Lander

1993-01-01

437

RESPONSE TO AN ASYMMETRIC DEMAND FOR ATTRIBUTES: AN APPLICATION TO THE MARKET FOR GENETICALLY MODIFIED CROPS  

Microsoft Academic Search

A framework is developed for examining the price and welfare effects of the introduction of genetically modified (GM) crops. In the short run, non-GM grain generally becomes another niche product. However, more profound market effects are observed under some reasonable parameterizations. In the long run, consumer and producer welfare are usually greater after the introduction of GM technology. Nevertheless, in

Sergio H. Lence; Dermot J. Hayes

2001-01-01

438

Neural Network Model Predictive Control with Genetic Algorithm Optimization and Its Application to Turbofan Engine Starting  

Microsoft Academic Search

Turbofan engine starting is one of the most important procedures during the whole process of job, but also very complicated due to its nonlinear dynamic working procedure. Recognizing the weaknesses of predict model and traditional algorithm for rolling optimization to deal with strong nonlinear systems, this paper presents neural network model predictive control method with genetic algorithm optimization, and uses

Yu Bo; Zhu Jihong

2010-01-01

439

Genetic switchboard for synthetic biology applications Jarred M. Calluraa,b,c  

E-print Network

RNA levels of the riboregulated genes, shifts in the activities of the relevant enzymes and pathways, an RNA-based gene-expression sys- tem, and noted its orthogonal expression capabilities (7, 8). Here, we and linking electrical circuits. Here, we define a ge- netic switchboard as an assembly of orthogonal, genetic

Collins, James J.

440

On the Application of Markov Chain Monte Carlo Methods to Genetic Analyses on Complex Pedigrees  

Microsoft Academic Search

Summary Markov chain Monte Carlo methods are frequently used in the analyses of genetic data on pedigrees for the estimation of probabilities and likelihoods which cannot be calculated by existing exact methods. In the case of discrete data, the underlying Markov chain may be reducible and care must be taken to ensure that reliable estimates are obtained. Potential reducibility thus

N. A. Sheehan

2000-01-01

441

New microsatellite loci for the mandarin fish Siniperca chuatsi and their application in population genetic analysis.  

PubMed

The mandarin fish is a popular fresh water food fish in China. Fifty-three polymorphic microsatellite markers were isolated through construction of an enriched library of genomic DNA of Siniperca chuatsi (Percichthyidae). We found 2 to 7 alleles per locus. The observed and expected heterozygosity values varied from 0.059 to 1.000 and from 0.305 to 0.818, respectively. The polymorphic information content value varied from 0.255 to 0.782. Twelve microsatellite loci deviated significantly from Hardy-Weinberg equilibrium after Bonferroni's correction. These markers were evaluated in five species of sinipercine fish; 98% of the 265 locus/taxon combinations tested gave cross-amplification. Eight polymorphic microsatellite markers were randomly selected for genetic characterization of three S. chuatsi populations. The Ganjiang River and Yuanjiang River populations had moderate levels of genetic diversity, while the Mudanjiang River population had a relatively low level genetic diversity. Genetic distance-based cluster analysis showed clustering of the Ganjiang River and Yuanjiang River populations in a single group and the Mudanjiang River population in a separate group. Based on these results, we suggest that S. chuatsi from the Yangtze River watershed are distinct from the Mudanjiang River population. These SSR markers will be useful for diversity, mapping and marker assisted studies of S. chuatsi and other sinipercine fishes. PMID:24535883

Tian, C X; Liang, X-F; Yang, M; Dou, Y Q; Zheng, H Z; Cao, L; Yuan, Y C; Zhao, C

2014-01-01

442

Application of domain evolution model-based genetic algorithm with fuzzy environment factor to system optimization  

Microsoft Academic Search

Genetic algorithms are able to search very large, variable complex spaces and locate the global optimum. However, there exist many difficulties in applying GA to large-scale nonlinear system optimization or “GA hard” problems. This paper presents an improved GA based on domain evolution model and fuzzy environment factor. Simulation study shows that it is a powerful search technique which can

Zhang Yale; Chen Wu; Xu Bowen; Fang Chongzhi

1996-01-01

443

Genetic variation and its maintenance  

SciTech Connect

This book contains several papers divided among three sections. The section titles are: Genetic Diversity--Its Dimensions; Genetic Diversity--Its Origin and Maintenance; and Genetic Diversity--Applications and Problems of Complex Characters.

Roberts, D.F.; De Stefano, G.F.

1986-01-01

444

(10, k) Reversible Multiples  

E-print Network

We consider the integers having the property of reversing when multiplied by a specific integer k. First, we proved that k should be either 1, 4 or 9. Second, we classify these integers as (10, 1)- reverse multiples, (10, 4)- reverse multiples and (10, 9)- reverse