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1

[Applications of reverse genetics in studying classical swine fever virus].  

PubMed

Classical swine fever (CSF), caused by classical swine fever virus (CSFV), has been epidemic or endemic in many countries, and causes great economical losses to pig industry worldwide. Attenuated vaccines (such as C-strain) have played an important role in the control of CSF. Recently some new phenomena appear, such as atypical and persistent infections of CSF, immunization failure and so on. Meanwhile, eradication programs have been implemented in many countries, restricting the widespread applications of attenuated vaccines. Thus, currently the priority is to strengthen the research in pathogenesis and transmission mechanisms, as well as to develop marker vaccines. Recently, the applications of reverse genetics technology open up a new way for research of structure and function of CSFV proteins and development of novel vaccines against CSF. This review focuses on the progress of applications of reverse genetics in the functional analysis and marker vaccine development of CSFV, and also discusses the problems confronted now and prospective aspects in the study of CSFV. PMID:20112686

Liu, Dafei; Sun, Yuan; Qiu, Huaji

2009-10-01

2

Application of Genetic Algorithm on Remanufacturing Reverse Logistics Network Model  

Microsoft Academic Search

For the goal of energy-saving and environmental protection and increasing the re-utilization of recycling products for enterprises, the paper discusses an open-loop remanufacturing reverse logistics network which has a location selection of two layers, then constructs a mixed integer linear programming model to achieve the overall minimum cost including the freight between nodes, the fixed cost, the disposal cost and

Bo Yan; Danyu Lee

2008-01-01

3

Reverse Genetics with Animal Viruses  

Microsoft Academic Search

New strategies to genetically manipulate the genomes of several important animal pathogens have been established in recent\\u000a years. This article focuses on the reverse genetics techniques, which enables genetic manipulation of the genomes of non-segmented\\u000a negative-sense RNA viruses. Recovery of a negative-sense RNA virus entirely from cDNA was first achieved for rabies virus\\u000a in 1994. Since then, reverse genetic systems

Teshome Mebatsion

4

Reverse genetics in eukaryotes  

PubMed Central

Reverse genetics consists in the modification of the activity of a target gene to analyse the phenotypic consequences. Four main approaches are used toward this goal and will be explained in this review. Two of them are centered on genome alterations. Mutations produced by random chemical or insertional mutagenesis can be screened, to recover only mutants in a specific gene of interest. Alternatively, these alterations may be specifically targeted on a gene of interest by homologous recombination. The two other approaches are centered on mRNA. RNA interference is a powerful method to reduce the level of gene products, while morpholino antisense oligonucleotides alter mRNA metabolism or translation. Some model species, such as Drosophila, are amenable to most of these approaches, whereas other model species are restricted to one of them. For example, in mice and yeasts gene targeting by homologous recombination is prevalent, while in Xenopus and zebrafish morpholino oligonucleotides are mainly used. Genome-wide collections of mutants or inactivated models obtained in several species by these approaches have been made and will help decipher gene functions in the post-genome era.

Hardy, Serge; Legagneux, Vincent; Audic, Yann; Paillard, Luc

2010-01-01

5

Development and Application of a Reverse Genetics System for Japanese Encephalitis Virus  

PubMed Central

Japanese encephalitis virus (JEV) is a common agent of viral encephalitis that causes high mortality and morbidity among children. Molecular genetic studies of JEV are hampered by the lack of a genetically stable full-length infectious JEV cDNA clone. We describe here the development of such a clone. A JEV isolate was fully sequenced, and then its full-length cDNA was cloned into a bacterial artificial chromosome. This was then further engineered so that transcription of the cDNA in vitro would generate synthetic RNAs with authentic 5? and 3? ends. The synthetic RNAs thus produced were highly infectious in susceptible cells (>106 PFU/?g), and these cells rapidly generated a high titer of synthetic viruses (>5 × 106 PFU/ml). The recovered viruses were indistinguishable from the parental virus in terms of plaque morphology, growth kinetics, RNA accumulation, protein expression, and cytopathogenicity. Significantly, the structural and functional integrity of the cDNA was maintained even after 180 generations of growth in Escherichia coli. A single point mutation acting as a genetic marker was introduced into the cDNA and was found in the genome of the recovered virus, indicating that the cDNA can be manipulated. Furthermore, we showed that JEV is an attractive vector for the expression of heterologous genes in a wide variety of cell types. This novel reverse genetics system for JEV will greatly facilitate research into JEV biology. It will also be useful as a heterologous gene expression vector and will aid the development of a vaccine against JEV.

Yun, Sang-Im; Kim, Seok-Yong; Rice, Charles M.; Lee, Young-Min

2003-01-01

6

Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications  

PubMed Central

Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics.

Hilson, Pierre; Allemeersch, Joke; Altmann, Thomas; Aubourg, Sebastien; Avon, Alexandra; Beynon, Jim; Bhalerao, Rishikesh P.; Bitton, Frederique; Caboche, Michel; Cannoot, Bernard; Chardakov, Vasil; Cognet-Holliger, Cecile; Colot, Vincent; Crowe, Mark; Darimont, Caroline; Durinck, Steffen; Eickhoff, Holger; de Longevialle, Andeol Falcon; Farmer, Edward E.; Grant, Murray; Kuiper, Martin T.R.; Lehrach, Hans; Leon, Celine; Leyva, Antonio; Lundeberg, Joakim; Lurin, Claire; Moreau, Yves; Nietfeld, Wilfried; Paz-Ares, Javier; Reymond, Philippe; Rouze, Pierre; Sandberg, Goran; Segura, Maria Dolores; Serizet, Carine; Tabrett, Alexandra; Taconnat, Ludivine; Thareau, Vincent; Van Hummelen, Paul; Vercruysse, Steven; Vuylsteke, Marnik; Weingartner, Magdalena; Weisbeek, Peter J.; Wirta, Valtteri; Wittink, Floyd R.A.; Zabeau, Marc; Small, Ian

2004-01-01

7

Reverse Genetics of Floral Scent: Application of Tobacco Rattle Virus-Based Gene Silencing in Petunia1[OA  

PubMed Central

Floral fragrance is responsible for attracting pollinators as well as repelling pathogens and pests. As such, it is of immense biological importance. Molecular dissection of the mechanisms underlying scent production would benefit from the use of model plant systems with big floral organs that generate an array of volatiles and that are amenable to methods of forward and reverse genetics. One candidate is petunia (Petunia hybrida), which has emerged as a convenient model system, and both RNAi and overexpression approaches using transgenes have been harnessed for the study of floral volatiles. Virus-induced gene silencing (VIGS) is characterized by a simple inoculation procedure and rapid results relative to transgenesis. Here, we demonstrate the applicability of the tobacco rattle virus-based VIGS system to studies of floral scent. Suppression of the anthocyanin pathway via chalcone synthase silencing was used as a reporter, allowing easy visual identification of anthocyaninless silenced flowers/tissues with no effect on the level of volatile emissions. Use of tobacco rattle virus constructs containing target genes involved in phenylpropanoid volatile production, fused to the chalcone synthase reporter, allowed simple identification of flowers with suppressed activity of the target genes. The applicability of VIGS was exemplified with genes encoding S-adenosyl-l-methionine:benzoic acid/salicylic acid carboxyl methyltransferase, phenylacetaldehyde synthase, and the myb transcription factor ODORANT1. Because this high-throughput reverse-genetics approach was applicable to both structural and regulatory genes responsible for volatile production, it is expected to be highly instrumental for large-scale scanning and functional characterization of novel scent genes.

Spitzer, Ben; Zvi, Michal Moyal Ben; Ovadis, Marianna; Marhevka, Elena; Barkai, Oren; Edelbaum, Orit; Marton, Ira; Masci, Tania; Alon, Michal; Morin, Shai; Rogachev, Ilana; Aharoni, Asaph; Vainstein, Alexander

2007-01-01

8

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.

Stobart, Christopher C.; Moore, Martin L.

2014-01-01

9

RNA virus reverse genetics and vaccine design.  

PubMed

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

10

Comparative Analysis of Reoviridae Reverse Genetics Methods  

PubMed Central

Effective methods to engineer the segmented, double-stranded RNA genomes of Reoviridae viruses have only recently been developed. Mammalian orthoreoviruses (MRV) and bluetongue virus (BTV) can be recovered from entirely recombinant reagents, significantly improving the capacity to study the replication, pathogenesis, and transmission of these viruses. Conversely, rotaviruses (RVs), which are the major etiological agent of severe gastroenteritis in infants and children, have thus far only been modified using single-segment replacement methods. Reoviridae reverse genetics techniques universally rely on site-specific initiation of transcription by T7 RNA polymerase to generate the authentic 5? end of recombinant RNA segments, but they vary in how the RNAs are introduced into cells: recombinant BTV is recovered by transfection of in vitro transcribed RNAs, whereas recombinant MRV and RV RNAs are transcribed intracellularly from transfected plasmid cDNAs. Additionally, several parameters have been identified in each system that are essential for recombinant virus recovery. Generating recombinant BTV requires the use of 5? capped RNAs and is enhanced by multiple rounds of RNA transfection, suggesting that translation of viral proteins is likely the rate-limiting step. For RV, the efficiency of recovery is almost entirely dependent on the strength of the selection mechanism used to isolate the single-segment recombinant RV from the unmodified helper virus. The reverse genetics methods for BTV and RV will be presented and compared to the previously described MRV methods. Analysis and comparison of each method suggest several key lines of research that might lead to a reverse genetics system for RV, analogous to those used for MRV and BTV.

Trask, Shane D.; Boehme, Karl W.; Dermody, Terence S.; Patton, John T.

2012-01-01

11

Reverse genetics: Its origins and prospects  

SciTech Connect

The nucleotide sequence of a gene and its flanking segments alone will not tell us how its expression is regulated during development and differentiation, or in response to environmental changes. To comprehend the physiological significance of the molecular details requires biological analysis. Recombinant DNA techniques provide a powerful experimental approach. A strategy termed reverse genetics' utilizes the analysis of the activities of mutant and normal genes and experimentally constructed mutants to explore the relationship between gene structure and function thereby helping elucidate the relationship between genotype and phenotype.

Berg, P. (Stanford Univ., CA (United States))

1991-04-01

12

Development and application of a positive-negative selectable marker system for use in reverse genetics in Plasmodium  

Microsoft Academic Search

A limitation of transfection of malaria parasites is the availability of only a low number of positive selectable markers for selection of transformed mutants. This is exacerbated for the rodent parasite Plasmodium berghei as selection of mutants is performed in vivo in laboratory rodents. We here report the development and application of a negative selection system based upon transgenic expression

Joanna A. M. Braks; Blandine Franke-Fayard; Hans Kroeze; Chris J. Janse; Andrew P. Waters

2006-01-01

13

Arenavirus reverse genetics for vaccine development.  

PubMed

Arenaviruses are important human pathogens with no Food and Drug Administration (FDA)-licensed vaccines available and current antiviral therapy being limited to an off-label use of the nucleoside analogue ribavirin of limited prophylactic efficacy. The development of reverse genetics systems represented a major breakthrough in arenavirus research. However, rescue of recombinant arenaviruses using current reverse genetics systems has been restricted to rodent cells. In this study, we describe the rescue of recombinant arenaviruses from human 293T cells and Vero cells, an FDA-approved line for vaccine development. We also describe the generation of novel vectors that mediate synthesis of both negative-sense genome RNA and positive-sense mRNA species of lymphocytic choriomeningitis virus (LCMV) directed by the human RNA polymerases I and II, respectively, within the same plasmid. This approach reduces by half the number of vectors required for arenavirus rescue, which could facilitate virus rescue in cell lines approved for human vaccine production but that cannot be transfected at high efficiencies. We have shown the feasibility of this approach by rescuing both the Old World prototypic arenavirus LCMV and the live-attenuated vaccine Candid#1 strain of the New World arenavirus Junín. Moreover, we show the feasibility of using these novel strategies for efficient rescue of recombinant tri-segmented both LCMV and Candid#1. PMID:23364194

Ortiz-Riaño, Emilio; Cheng, Benson Yee Hin; Carlos de la Torre, Juan; Martínez-Sobrido, Luis

2013-06-01

14

An Inducible and Reversible Mouse Genetic Rescue System  

PubMed Central

Inducible and reversible regulation of gene expression is a powerful approach for uncovering gene function. We have established a general method to efficiently produce reversible and inducible gene knockout and rescue in mice. In this system, which we named iKO, the target gene can be turned on and off at will by treating the mice with doxycycline. This method combines two genetically modified mouse lines: a) a KO line with a tetracycline-dependent transactivator replacing the endogenous target gene, and b) a line with a tetracycline-inducible cDNA of the target gene inserted into a tightly regulated (TIGRE) genomic locus, which provides for low basal expression and high inducibility. Such a locus occurs infrequently in the genome and we have developed a method to easily introduce genes into the TIGRE site of mouse embryonic stem (ES) cells by recombinase-mediated insertion. Both KO and TIGRE lines have been engineered for high-throughput, large-scale and cost-effective production of iKO mice. As a proof of concept, we have created iKO mice in the apolipoprotein E (ApoE) gene, which allows for sensitive and quantitative phenotypic analyses. The results demonstrated reversible switching of ApoE transcription, plasma cholesterol levels, and atherosclerosis progression and regression. The iKO system shows stringent regulation and is a versatile genetic system that can easily incorporate other techniques and adapt to a wide range of applications.

Madisen, Linda; Pavlova, Maria N.; Gragerova, Galina; Rohde, Alex D.; Schimpf, Brian A.; Liang, Yuqiong; Ojala, Ethan; Kramer, Farah; Roth, Patricia; Slobodskaya, Olga; Dolka, Io; Southon, Eileen A.; Tessarollo, Lino; Bornfeldt, Karin E.; Gragerov, Alexander; Pavlakis, George N.; Gaitanaris, George A.

2008-01-01

15

Reverse genetics approaches to combat pathogenic arenaviruses  

PubMed Central

Several arenaviruses cause hemorrhagic fever (HF) in humans, and evidence indicates that the worldwide-distributed prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) is a neglected human pathogen of clinical significance. Moreover, arenaviruses pose a biodefense threat. No licensed anti-arenavirus vaccines are available, and current anti-arenavirus therapy is limited to the use of ribavirin, which is only partially effective and is associated with anemia and other side effects. Therefore, it is important to develop effective vaccines and better antiviral drugs to combat the dual threats of naturally occurring and intentionally introduced arenavirus infections. The development of arenavirus reverse genetic systems is allowing investigators to conduct a detailed molecular characterization of the viral cis-acting signals and trans-acting factors that control each of the steps of the arenavirus life cycle, including RNA synthesis, packaging and budding. Knowledge derived from these studies is uncovering potential novel targets for therapeutic intervention, as well as facilitating the establishment of assays to identify and characterize candidate antiviral drugs capable of interfering with specific steps of the virus life cycle. Likewise, the ability to generate predetermined specific mutations within the arenavirus genome and analyze their phenotypic expression would significantly contribute to the elucidation of arenavirus-host interactions, including the basis of their ability to cause severe HF. This, in turn, could lead to the development of novel, potent and safe arenavirus vaccines.

de la Torre, Juan C.

2008-01-01

16

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

17

A “reverse genetic” approach to autosomal dominant polycystic kidney disease  

Microsoft Academic Search

Biochemical, anatomical, pathophysiological and clinical studies of autosomal dominant “adult-type” polycystic kidney disease have cast little light on the underlying biochemical defect which causes the disease. The advent of recombinant DNA technology permits a novel approach to its pathophysiology. In this approach, termed “reverse genetics”, the mutation which produces the disease is first localised by genetic linkage. This is followed

Stephen T. Reeders

1987-01-01

18

Estimating Genome Reversal Distance by Genetic Algorithm  

Microsoft Academic Search

Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3\\/2- approximation algorithm. However, the problem of sorting signed permutation can be solved easily. Fast algorithms have been developed both for finding the sorting sequence and

Andy AuYeung; Ajith Abraham

2004-01-01

19

Estimating genome reversal distance by genetic algorithm  

Microsoft Academic Search

Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3\\/2-approximation algorithm. However, the problem of sorting signed permutation can be solved easily. Fast algorithms have been developed both for finding the sorting sequence and finding

A. Auyeung; Ajith Abraham

2003-01-01

20

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.

2011-01-01

21

The reverse genetics applied to fish RNA viruses.  

PubMed

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

Biacchesi, Stéphane

2011-01-01

22

Applications of reversible electrodeposition electrochromic devices  

Microsoft Academic Search

Electrochromic devices based upon the reversible electrodeposition of Bi are described. The electrochemistry, interface chemistry and spectroelectrochemistry of the system relevant to information display and smart windows applications are briefly reviewed. The detailed nucleation and growth behavior of the system are described to help explain electrochromic device performance. Electrochromic displays have been formulated to produce full RGB color, and switching

John P Ziegler; Bruce M Howard

1995-01-01

23

Reverse genetics for proteomics: from proteomic discovery to scientific content.  

PubMed

Proteomic strategies generally result in rather descriptive outcomes. Although proteomic patterns may lead to understanding of cellular function or failure, they do not provide insights into cellular mechanisms of normal physiology or molecular mechanisms of disease. The integration of single events or patterns into complex biological processes and signaling networks must be functionally validated by studying these processes in a dynamic physiological context. Effective methodologies, applied at the level of intact cells and model organisms that monitor their function, topology and interaction of proteins are necessary and essential. Reverse genetic strategies can greatly advance the understanding of patterns identified through proteomic analysis. RNAi as an accessible method for routine functional analysis of cells and whole model organisms represents a quantum leap in revolutionizing reverse genetics. This paper aims at describing an integrated workflow linking proteome-based discovery to molecular analysis of single genes and proteins by RNAi, potentially contributing to the advanced understanding of molecular mechanisms in neurodegenerative disease, including Parkinson's disease. PMID:16835688

Bauer, M; Ueffing, M

2006-08-01

24

Reverse polymeric micelles for pharmaceutical applications.  

PubMed

Star-shaped (4- to 8-arms) and linear poly(glycidyl methacrylate)s were synthesized by atom transfer radical polymerization as precursors of poly(glycerol methacrylate)s (PG(OH)MAs). The water-soluble PG(OH)MA backbones were modified through the esterification of pendant hydroxyl functions with acyl chlorides (12 to 18 carbons). Alkyated PG(OH)MAs were shown to self-assemble into reverse micelles (RMs) in organic solvents and/or oil. The resulting nanosized aggregates (20-60 nm) were able to reversibly extract anionic dyes from water and solubilise them in an organic phase. Furthermore, the encapsulation of vasopressin, a model peptide, in RMs significantly improved its solubility in an oily vehicle. This observation led to the development of water-free peptide formulations. In vitro release studies showed that the entrapped peptide slowly diffused out of an oily RM solution (<15% in 7 days). The release rate could be significantly increased upon emulsification of the oleaginous phase. In vivo, the subcutaneous administration of loaded RMs to rats significantly prolonged the pharmacological effect of vasopressin (>48 h vs. 8-10 h for an aqueous solution). These results highlight the ability of RMs to act as solubilizers for hydrophilic solutes in organic media, a property that may be exploited for applications in organic chemistry and pharmaceutical technology. PMID:18571266

Jones, Marie-Christine; Gao, Hui; Leroux, Jean-Christophe

2008-12-18

25

Mitigating Reversing Vulnerabilities in .Net Applications Using Virtualized Software Protection.  

National Technical Information Service (NTIS)

Protecting intellectual property contained in application source code and preventing tampering with application binaries are both major concerns for software developers. Simply by possessing an application binary, any user is able to attempt to reverse en...

M. A. Zimmerman

2008-01-01

26

OryGenesDB: a database for rice reverse genetics  

PubMed Central

Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics. We have developed OryGenesDB (), a database dedicated to rice reverse genetics. Insertion mutants of rice genes are catalogued by Flanking Sequence Tag (FST) information that can be readily accessed by this database. Our database presently contains 44166 FSTs generated by most of the rice insertional mutagenesis projects. The OryGenesDB genome browser is based on the powerful Generic Genome Browser (GGB) developed in the framework of the Generic Model Organism Project (GMOD). The main interface of our web site displays search and analysis interfaces to look for insertions in any candidate gene of interest. Several starting points can be used to exhaustively retrieve the insertions positions and associated genomic information using blast, keywords or gene name search. The toolbox integrated in our database also includes an ‘anchoring’ option that allows immediate mapping and visualization of up to 50 nucleic acid sequences in the rice Genome Browser of OryGenesDB. As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors.

Droc, G.; Ruiz, M.; Larmande, P.; Pereira, A.; Piffanelli, P.; Morel, J. B.; Dievart, A.; Courtois, B.; Guiderdoni, E.; Perin, C.

2006-01-01

27

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

28

Genetic Applications in Avian Conservation  

USGS Publications Warehouse

A fundamental need in conserving species and their habitats is defining distinct entities that range from individuals to species to ecosystems and beyond (Table 1; Ryder 1986, Moritz 1994, Mayden and Wood 1995, Haig and Avise 1996, Hazevoet 1996, Palumbi and Cipriano 1998, Hebert et al. 2004, Mace 2004, Wheeler et al. 2004, Armstrong and Ball 2005, Baker 2008, Ellis et al. 2010, Winker and Haig 2010). Rapid progression in this interdisciplinary field continues at an exponential rate; thus, periodic updates on theory, techniques, and applications are important for informing practitioners and consumers of genetic information. Here, we outline conservation topics for which genetic information can be helpful, provide examples of where genetic techniques have been used best in avian conservation, and point to current technical bottlenecks that prevent better use of genomics to resolve conservation issues related to birds. We hope this review will provide geneticists and avian ecologists with a mutually beneficial dialogue on how this integrated field can solve current and future problems.

Haig, Susan M.; Bronaugh, Whitcomb M.; Crowhurst, Rachel S.; D'Elia, Jesse; Eagles-Smith, Collin A.; Epps, Clinton W.; Knaus, Brian; Miller, Mark P.; Moses, Michael L.; Oyler-McCance, Sara; Robinson, W. Douglas; Sidlauskas, Brian

2011-01-01

29

Generation of Genetically Stable Recombinant Rotaviruses Containing Novel Genome Rearrangements and Heterologous Sequences by Reverse Genetics  

PubMed Central

The rotavirus (RV) genome consists of 11 segments of double-stranded RNA (dsRNA). Typically, each segment contains 5? and 3? untranslated regions (UTRs) that flank an open reading frame (ORF) encoding a single protein. RV variants with segments of atypical size owing to sequence rearrangements have been described. In many cases, the rearrangement originates from a partial head-to-tail sequence duplication that initiates after the stop codon of the ORF, leaving the protein product of the segment unaffected. To probe the limits of the RV genome to accommodate additional genetic sequence, we used reverse genetics to insert duplications (analogous to synthetic rearrangements) and heterologous sequences into the 3? UTR of the segment encoding NSP2 (gene 8). The approach allowed the recovery of recombinant RVs that contained sequence duplications (up to 200 bp) and heterologous sequences, including those for FLAG, the hepatitis C virus E2 epitope, and the internal ribosome entry site of cricket paralysis virus. The recombinant RVs grew to high titer (>107 PFU/ml) and remained genetically stable during serial passage. Despite their longer 3? UTRs, rearranged RNAs of recombinant RVs expressed wild-type levels of protein in vivo. Competitive growth experiments indicated that, unlike RV segments with naturally occurring sequence duplications, genetically engineered segments were less efficiently packaged into progeny viruses. Thus, features of naturally occurring rearranged segments, other than their increased length, contribute to their enhanced packaging phenotype. Our results define strategies for developing recombinant RVs as expression vectors, potentially leading to next-generation RV vaccines that induce protection against other infectious agents.

Navarro, Aitor; Trask, Shane D.

2013-01-01

30

Reverse genetic studies of the DNA damage response in the chicken B lymphocyte line DT40  

Microsoft Academic Search

In the ‘post-genome’ era, reverse genetics is one of the most informative and powerful means to investigate protein function. The chicken B lymphocyte line DT40 is widely used for reverse genetics because the cells have a number of advantages, including efficient gene targeting as well as a remarkably stable phenotype. Furthermore, the absence of functional p53 in DT40 cells enables

Mitsuyoshi Yamazoe; Eiichiro Sonoda; Helfrid Hochegger; Shunichi Takeda

2004-01-01

31

Applications of behavioural genetics: outpacing the science?  

Microsoft Academic Search

Human behavioural genetics is an established research discipline of the genomic age, and applications for behavioural genetic information are most likely to emerge in areas such as criminal justice, education, employment and insurance. However, behavioural genetic research into personality traits and antisocial behaviour poses several risks; for example, tentative or preliminary research findings might be misused in legal and commercial

Mark A. Rothstein

2005-01-01

32

Application of the Conditioned Reverse Path Method  

NASA Astrophysics Data System (ADS)

The conditioned reverse path (CRP) method has been applied to identify the non-linear behaviour of a beam-like structure, both ends clamped, one with a non-linear stiffness characteristic. The same method was already successfully applied to the identification of another COST benchmark, known as the VTT non-linear suspension. This benchmark shows the enhancements of the technique, now applied to a real multi-degree-of-freedom (mdof) system, with single-point excitation subject to bending modes; the non-linearity is acting on one end of the beam in terms of displacements. The CRP technique is based on the construction of a hierarchy of uncorrelated response components in the frequency domain, allowing the estimation of the coefficients of the non-linearities away from the location of the applied excitation and also the identification of the linear dynamic compliance matrix when the number of excitations is smaller than the number of response locations.

Garibaldi, L.

2003-01-01

33

Genetic algorithm dynamic performance evaluation for RFID reverse logistic management  

Microsoft Academic Search

Environmental awareness, green directives, liberal return policies, and recycling of materials are globally accepted by industry and the general public as an integral part of the product life cycle. Reverse logistics reflects the acceptance of new policies by analyzing the processes associated with the flow of products, components and materials from end users to re-users consisting of second markets and

Amy J. C. Trappey; Charles V. Trappey; Chang-Ru Wu

2010-01-01

34

Research into the engineering application of reverse engineering technology  

Microsoft Academic Search

Based on previous research on reverse engineering (RE) technology, the engineering application of RE is explored in this paper. The application environment of RE is built with coordinate measurement machine (CMM) and CAD\\/CAM software. Taking a core die of the inlet of a diesel engine as an example, this paper describes the processes of RE, from object digitization, CAD model

Yu Zhang

2003-01-01

35

Coarse-grained reverse engineering of genetic regulatory networks  

Microsoft Academic Search

We have modeled genetic regulatory networks in the framework of continuous-time recurrent neural networks. A method for determining the parameters of such networks, given expression level time series data, is introduced and evaluated using artificial data. The method is also applied to a set of actual expression data from the development of rat central nervous system.

Mattias Wahde; John Hertz

2000-01-01

36

Fly-TILL: reverse genetics using a living point mutation resource.  

PubMed

Mutagenesis with ethylmethanesulfonate (EMS) has been the standard for traditional genetic screens, and in recent years has been applied to reverse genetics. However, reverse-genetic strategies require maintaining a viable germline library so that mutations that are discovered can subsequently be recovered. In applying our TILLING (Targeting Induced Local Lesions IN Genomes) method to establish a Drosophila reverse-genetic service (Fly-TILL), we chose to screen the Zuker lines, a large collection of EMS-mutagenized second- and third-chromosome balanced lines that had been established for forward-genetic screening. For the past four years, our Fly-TILL service has screened this collection to provide approximately 150 allelic series of point mutations for the fly community. Our analysis of >2000 point mutations and indels have provided a glimpse into the population dynamics of this valuable genetic resource. We found evidence for selection and differential recovery of mutations, depending on distance from balancer breakpoints. Although this process led to variable mutational densities, we have nevertheless been able to deliver potentially valuable mutations in genes selected by Fly-TILL users. We anticipate that our findings will help guide the future implementation of point-mutation resources for the Drosophila community. PMID:19098435

Cooper, Jennifer L; Till, Bradley J; Henikoff, Steven

2008-01-01

37

Boron removal by reverse osmosis membranes in seawater desalination applications  

Microsoft Academic Search

Rapid development of seawater desalination applications using membrane technology in recent years has reignited the issue of boron in drinking water. This is reflected by an increasing number of scientific investigations on the removal of boron by reverse osmosis (RO) and to a lesser extent by nanofiltration (NF) membranes over the last decade. This review provides a summary of the

Kha L. Tu; Long D. Nghiem; Allan R. Chivas

2010-01-01

38

Freewheeling diode reverse-recovery failure modes in IGBT applications  

Microsoft Academic Search

In this paper, reverse-recovery failure modes in modern fast power diodes are investigated. By the aid of semiconductor device simulation tools, a better view is obtained for the physical process, and operating conditions at which both diode snappy recovery and dynamic avalanching occur during the recovery period in modern high-frequency power electronic applications. The work presented here confirms that the

Munaf T. Rahimo; Noel Y. A. Shammas

2001-01-01

39

Contributions to Reverse Logistics with Game theoretic Applications  

Microsoft Academic Search

The last two decades witnessed an increasing emphasis on reverse logistics (RL). Our thesis attempts to investigate two research problems in RL and explore game theoretic applications in this field.\\u000aIn Chapter 1, we introduce SCM, RL, relevant game theoretic applications, and the organizational structure of this thesis.\\u000aIn Chapter 2, we address a newsvendor problem with resalable returns. We

Sandy Huyu Wu

2012-01-01

40

New Generation Live Vaccines against Human Respiratory Syncytial Virus Designed by Reverse Genetics  

Microsoft Academic Search

Development of a live pediatric vaccine against human respiratory syncytial virus (RSV) is complicated by the need to immunize young infants and the difficulty in balancing attenuation and immuno- genicity. The ability to introduce desired mutations into infectious virus by reverse genetics provides a method for identifying and designinghighlydefinedattenuatingmutations.Thesecanbeintro- duced in combinations as desired to achieve gradations of attenua- tion.

Peter L. Collins; Brian R. Murphy

2005-01-01

41

Large-scale reverse docking profiles and their applications  

PubMed Central

Background Reverse docking approaches have been explored in previous studies on drug discovery to overcome some problems in traditional virtual screening. However, current reverse docking approaches are problematic in that the target spaces of those studies were rather small, and their applications were limited to identifying new drug targets. In this study, we expanded the scope of target space to a set of all protein structures currently available and developed several new applications of reverse docking method. Results We generated 2D Matrix of docking scores among all the possible protein structures in yeast and human and 35 famous drugs. By clustering the docking profile data and then comparing them with fingerprint-based clustering of drugs, we first showed that our data contained accurate information on their chemical properties. Next, we showed that our method could be used to predict the druggability of target proteins. We also showed that a combination of sequence similarity and docking profile similarity could predict the enzyme EC numbers more accurately than sequence similarity alone. In two case studies, 5-flurouracil and cycloheximide, we showed that our method can successfully find identifying target proteins. Conclusions By using a large number of protein structures, we improved the sensitivity of reverse docking and showed that using as many protein structure as possible was important in finding real binding targets.

2012-01-01

42

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

43

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

44

Construction of a Sonchus Yellow Net Virus Minireplicon: a Step toward Reverse Genetic Analysis of Plant Negative-Strand RNA Viruses  

PubMed Central

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.

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.

2013-01-01

45

Repository of Eurasian influenza virus hemagglutinin and neuraminidase reverse genetics vectors and recombinant viruses  

PubMed Central

Reverse genetics can be used to produce recombinant influenza A viruses containing virtually every desired combination of hemagglutinin (HA) and neuraminidase (NA) genes using the virus backbone of choice. Here, a repository of plasmids and recombinant viruses representing all contemporary Eurasian HA and NA subtypes, H1–H16 and N1–N9, was established. HA and NA genes were selected based on sequence analyses of influenza virus genes available from public databases. Prototype Eurasian HA and NA genes were cloned in bidirectional reverse genetics plasmids. Recombinant viruses based on the virus backbone of A/PR/8/34, and containing a variety of HA and NA genes were produced in 293T cells. Virus stocks were produced in MDCK cells and embryonated chicken eggs. These plasmids and viruses may be useful for numerous purposes, including influenza virus research projects, vaccination studies, and to serve as reference reagents in diagnostic settings.

Keawcharoen, J.; Spronken, M.I.J; Vuong, O.; Bestebroer, T.M.; Munster, V.J.; Osterhaus, A.D.M.E; Rimmelzwaan, G.F; Fouchier, R.A.M.

2010-01-01

46

[Application of documentary in teaching genetics].  

PubMed

This paper describes the advantages and the existing problems of the application of documentary in teaching genetics. Meanwhile, the corresponding improvement approaches were provided based on these problems. The advantages and function of documentary in teaching course will be fully developed and the teaching quality will be improved. PMID:22425958

Gao, Yong; Jian-Min, Chen

2012-03-01

47

Preparation of a standardized, efficacious agricultural H5N3 vaccine by reverse genetics  

Microsoft Academic Search

Options for the control of emerging and reemerging H5N1 influenza viruses include improvements in biosecurity and the use of inactivated vaccines. Commercially available H5N2 influenza vaccine prevents disease signs and reduces virus load but does not completely prevent virus shedding after challenge with H5N1 virus. By using reverse genetics, we prepared an H5N3 vaccine whose hemagglutinin is 99.6% homologous to

Ming Liu; John M Wood; Trevor Ellis; Scott Krauss; Patrick Seiler; Christie Johnson; Erich Hoffmann; Jennifer Humberd; Diane Hulse; Yun Zhang; Robert G Webster; Daniel R Perez

2003-01-01

48

46, XX male sex reversal syndrome: a case report and review of the genetic basis.  

PubMed

Sex reversal syndrome is a kind of human genetic disease about gender dysplasia, which is characterised by inconsistency between gonadal sexuality and chromosome sexuality; the incidence rate was about 1:20,000-100,000. The clinical manifestations, hormonal levels and cytogenetic findings in a patient of 46, XX male sex reversal syndrome retrospectively were analysed and related published reports were reviewed. The DNA fragments of sex-determining region Y (SRY) gene from the patient was found by polymerase chain reaction, but the fluorescent in situ hybridisation analysis revealed that the SRY translocated from Y to X chromosome. We concluded that the Y chromosomal SRY gene is required for the regulation of male sex determination. The detection of SRY is important for the clinical diagnosis of sex reversal syndrome. Translocation of SRY to X chromosome or other autosomes would be one of the key factors that induced XX male SRS. PMID:19143733

Wang, T; Liu, J H; Yang, J; Chen, J; Ye, Z Q

2009-02-01

49

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

50

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

PubMed Central

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

Santos, Jefferson Jose da Silva; Cordeiro, Marli Tenorio; Bertani, Giovani Rota; Marques, Ernesto Torres de Azevedo; Gil, Laura Helena Vega Gonzales

2013-01-01

51

A Reversible Programmable Logic Array (RPLA) Using Fredkin and Feynman Gates for Industrial Electronics and Applications  

Microsoft Academic Search

In recent years, reversible logic has emerged as a promising computing paradigm having application in low power CMOS, quantum computing, nanotechnology, and optical computing. The classical set of gates such as AND, OR, and EXOR are not reversible. In this paper, the authors have proposed reversible programmable logic array (RPLA) architecture using reversible Fredkin and Feynman gates. The proposed RPLA

Himanshu Thapliyal; Hamid R. Arabnia

2006-01-01

52

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.

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

2013-01-01

53

Genetic bases of instability of male sterility and fertility reversibility in photoperiod-sensitive genic male-sterile rice  

Microsoft Academic Search

Photoperiod-sensitive genetic male-sterile (PSGMS) rice, with its male fertility regulated by photoperiod length, is very\\u000a useful for hybrid rice development. However, breeding for new PSGMS lines has faced two major difficulties – the stability\\u000a of male sterility and the reversibility of male fertility. In this study we assessed the genetic bases of stability of sterility\\u000a and fertility reversibility using a

Y. Q. He; J. Yang; C. G. Xu; Z. G. Zhang; Q. Zhang

1999-01-01

54

Retention of induced mutations in a Drosophila reverse-genetic resource.  

PubMed

Targeting induced local lesions in genomes (TILLING) is a reverse-genetic method for identifying point mutations in chemically mutagenized populations. For functional genomics, it is ideal to have a stable collection of heavily mutagenized lines that can be screened over an extended period of time. However, long-term storage is impractical for Drosophila, so mutant strains must be maintained by continual propagation of live cultures. Here we evaluate a strategy in which ethylmethane sulfonate (EMS) mutagenized chromosomes were maintained as heterozygotes with balancer chromosomes for >100 generations before screening. The strategy yielded a spectrum of point mutations similar to those found in previous studies of EMS-induced mutations, as well as 2.4% indels (insertions and deletions). Our analysis of 1887 point mutations in 148 targets showed evidence for selection against deleterious lesions and differential retention of lesions among targets on the basis of their position relative to balancer breakpoints, leading to a broad distribution of mutational densities. Despite selection and differential retention, the success of a user-funded service based on screening a large collection several years after mutagenesis indicates sufficient stability for use as a long-term reverse-genetic resource. Our study has implications for the use of balancer chromosomes to maintain mutant lines and provides the first large-scale quantitative assessment of the limitations of using breeding populations for repositories of genetic variability. PMID:18780737

Cooper, Jennifer L; Greene, Elizabeth A; Till, Bradley J; Codomo, Christine A; Wakimoto, Barbara T; Henikoff, Steven

2008-09-01

55

Application of Time Reversed Acoustics for Seismic Source Characterization  

NASA Astrophysics Data System (ADS)

Traditionally an earthquake is located and the source mechanism is determined by using P and S phases. This uses only a limited portion of the information contained in a seismogram. A large part of the information carried by the waveform is not used. In this study we investigate the applicability of the Time Reversed Acoustics (TRA) technique, and thus the whole waveform of the recorded signal, for earthquake locations and source characterization. The basic concept involved in TRA is the fundamental symmetry of time reversal invariance. Injecting the recorded signal, with time running backwards, can focus the wave field to the source. TRA has emerged as an important technique in acoustics with applications to medicine, underwater sound, and many other disciplines. Numerical simulations show that the TRA technique can successfully locate a seismic source inside a layered earth model and can also recover the source time function. Finite difference modeling results show that TRA can determine the fault dip, rupture direction, and rupture length. The method is especially advantageous when data are available only from a sparse station network. Full seismograms contain source information from both waves radiated along the source-station ray path and from waves that radiated in all other directions but scattered toward the receivers. Application of the TRA technique to seismic source characterization requires the Green's function, which can be obtained in two ways. If the earth structure is known then the Green's function can be calculated numerically. To improve the efficiency, the method of constructing a medium response library is developed. This improves computation time significantly. The second approach uses small events (e.g., aftershocks) as an empirical Green's function. The performance of the TRA technique is demonstrated with data from real earthquakes.

Lu, R.; Toksöz, M.

2005-05-01

56

Identification of Host Genes Involved in Geminivirus Infection Using a Reverse Genetics Approach  

PubMed Central

Geminiviruses, like all viruses, rely on the host cell machinery to establish a successful infection, but the identity and function of these required host proteins remain largely unknown. Tomato yellow leaf curl Sardinia virus (TYLCSV), a monopartite geminivirus, is one of the causal agents of the devastating Tomato yellow leaf curl disease (TYLCD). The transgenic 2IRGFP N. benthamiana plants, used in combination with Virus Induced Gene Silencing (VIGS), entail an important potential as a tool in reverse genetics studies to identify host factors involved in TYLCSV infection. Using these transgenic plants, we have made an accurate description of the evolution of TYLCSV replication in the host in both space and time. Moreover, we have determined that TYLCSV and Tobacco rattle virus (TRV) do not dramatically influence each other when co-infected in N. benthamiana, what makes the use of TRV-induced gene silencing in combination with TYLCSV for reverse genetic studies feasible. Finally, we have tested the effect of silencing candidate host genes on TYLCSV infection, identifying eighteen genes potentially involved in this process, fifteen of which had never been implicated in geminiviral infections before. Seven of the analyzed genes have a potential anti-viral effect, whereas the expression of the other eleven is required for a full infection. Interestingly, almost half of the genes altering TYLCSV infection play a role in postranslational modifications. Therefore, our results provide new insights into the molecular mechanisms underlying geminivirus infections, and at the same time reveal the 2IRGFP/VIGS system as a powerful tool for functional reverse genetics studies.

Luna, Ana P.; Bejarano, Eduardo R.

2011-01-01

57

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

58

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

59

Delay of the reverse pedicled venous island flap: clinical applications.  

PubMed

In patients with hand or foot injuries, the delay procedure of the reverse pedicled venous flap was applied, including the loose areolar tissue around the pedicle vein. As preliminary clinical observations, five patients were treated with delay and the results compared with those of four patients without delay. The delay procedures were two types: type 1 was circumferential incision with ligature of the proximal vein, and type 2 was a bipedicled flap without ligature of the pedicle vein. Two weeks later, the flap was transferred to the defect. In the patients treated without delay, the maximum limit of the perfectly survived flap sizes was 4.0 × 2.0 cm. However, in the patients treated with delay, the perfectly survived sizes were 5.0 × 3.0 cm and 10 × 4.0 cm in type 1 delay and 12 × 5.0 cm in type 2 delay. The delay procedure appeared to stabilise the reverse pedicled venous flap and to expand its clinical applications. PMID:23710795

Ueda, Koichi; Nuri, Takashi; Akamatsu, Jun; Sugita, Naoya; Otani, Kazuhiro; Yamada, Akira

2013-10-01

60

Reverse genetic platform for inactivated and live-attenuated influenza vaccine.  

PubMed

Influenza vaccine strains have been traditionally developed by annual reassortment between vaccine donor strain and the epidemic virulent strains. The classical method requires screening and genotyping of the vaccine strain among various reassortant viruses, which are usually laborious and time-consuming. Here we developed an efficient reverse genetic system to generate the 6:2 reassortant vaccine virus from cDNAs derived from the influenza RNAs. Thus, cDNAs of the two RNAs coding for surface antigens, haemagglutinin and neuraminidase from the epidemic virus and the 6 internal genes from the donor strain were transfected into cells and the infectious viruses of 6:2 defined RNA ratio were rescued. X-31 virus (a high- growth virus in embryonated eggs) and its cold-adapted strain X-31 ca were judiciously chosen as donor strains for the generation of inactivated vaccine and live-attenuated vaccine, respectively. The growth properties of these recombinant viruses in embryonated chicken eggs and MDCK cell were indistinguishable as compared to those generated by classical reassortment process. Based on the reverse genetic system, we generated 6+2 reassortant avian influenza vaccine strains corresponding to the A/Chicken/Korea/ MS96 (H9N2) and A/Indonesia/5/2005 (H5N1). The results would serve as technical platform for the generation of both injectable inactivated vaccine and the nasal spray live attenuated vaccine for the prevention of influenza epidemics and pandemics. PMID:20054235

Jung, Eun Ju; Lee, Kwang Hee; Seong, Baik Lin

2010-02-28

61

A stabilized respiratory syncytial virus reverse genetics system amenable to recombination-mediated mutagenesis.  

PubMed

We describe the first example of combining bacterial artificial chromosome (BAC) recombination-mediated mutagenesis with reverse genetics for a negative strand RNA virus. A BAC-based respiratory syncytial virus (RSV) rescue system was established. An important advantage of this system is that RSV antigenomic cDNA was stabilized in the BAC vector. The RSV genotype chosen was A2-line19F, a chimeric strain previously shown to recapitulate in mice key features of RSV pathogenesis. We recovered two RSV reporter viruses, one expressing the red fluorescent protein monomeric Katushka 2 (A2-K-line19F) and one expressing Renilla luciferase (A2-RL-line19F). As proof of principle, we efficiently generated a RSV gene deletion mutant (A2-line19F?NS1/NS2) and a point mutant (A2-K-line19F-I557V) by recombination-mediated BAC mutagenesis. Together with sequence-optimized helper expression plasmids, BAC-RSV is a stable, versatile, and efficient reverse genetics platform for generation of a recombinant Pneumovirus. PMID:23062737

Hotard, Anne L; Shaikh, Fyza Y; Lee, Sujin; Yan, Dan; Teng, Michael N; Plemper, Richard K; Crowe, James E; Moore, Martin L

2012-12-01

62

A Stabilized Respiratory Syncytial Virus Reverse Genetics System Amenable to Recombination Mediated Mutagenesis  

PubMed Central

We describe the first example of combining bacterial artificial chromosome (BAC) recombination-mediated mutagenesis with reverse genetics for a negative strand RNA virus. A BAC-based respiratory syncytial virus (RSV) rescue system was established. An important advantage of this system is that RSV antigenomic cDNA was stabilized in the BAC vector. The RSV genotype chosen was A2-line19F, a chimeric strain previously shown to recapitulate in mice key features of RSV pathogenesis. We recovered two RSV reporter viruses, one expressing the red fluorescent protein monomeric Katushka 2 (A2-K-line19F) and one expressing Renilla luciferase (A2-RL-line19F). As proof of principle, we efficiently generated a RSV gene deletion mutant (A2-line19F?NS1/NS2) and a point mutant (A2-K-line19F-I557V) by recombination-mediated BAC mutagenesis. Together with sequence-optimized helper expression plasmids, BAC-RSV is a stable, versatile, and efficient reverse genetics platform for generation of a recombinant Pneumovirus.

Hotard, Anne L.; Shaikh, Fyza Y.; Lee, Sujin; Yan, Dan; Teng, Michael N.; Plemper, Richard K.; Crowe, James E.; Moore, Martin L.

2012-01-01

63

Research and Application of Reverse Mobile Commerce Platform  

Microsoft Academic Search

Reverse Mobile Commerce Platform is an innovative e-commerce mode that reverses the traditional business process of e-commerce. Commodities traded on such platform are invisible information such as certain public idea, opinion, knowledge, comment and experience etc. This paper sets out to put forward the ideology and system constitution of Reverse Mobile Commerce Platform, and make detailed description of its operational

Hu Zhiyong

2009-01-01

64

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.

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

2013-01-01

65

Evaluation of a genetically modified foot-and-mouth disease virus vaccine candidate generated by reverse genetics  

PubMed Central

Background Foot-and-mouth disease (FMD) is the most economically important and highly contagious disease of cloven-hoofed animals worldwide. Control of the disease has been mainly based on large-scale vaccinations with whole-virus inactivated vaccines. In recent years, a series of outbreaks of type O FMD occurred in China (including Chinese Taipei, Chinese Hong Kong) posed a tremendous threat to Chinese animal husbandry. Its causative agent, type O FMDV, has evolved into three topotypes (East–South Asia (ME-SA), Southeast Asia (SEA), Cathay (CHY)) in these regions, which represents an important obstacle to disease control. The available FMD vaccine in China shows generally good protection against ME-SA and SEA topotype viruses infection, but affords insufficient protection against some variants of the CHY topotype. Therefore, the choice of a new vaccine strain is of fundamental importance. Results The present study describes the generation of a full-length infectious cDNA clone of FMDV vaccine strain and a genetically modified virus with some amino acid substitutions in antigenic sites 1, 3, and 4, based on the established infectious clone. The recombinant viruses had similar growth properties to the wild O/HN/CHA/93 virus. All swine immunized with inactivated vaccine prepared from the O/HN/CHA/93 were fully protected from challenge with the viruses of ME-SA and SEA topotypes and partially protected against challenge with the virus of CHY topotype at 28?days post-immunization. In contrast, the swine inoculated with the genetically modified vaccine were completely protected from the infection of viruses of the three topotypes. Conclusions Some amino acid substitutions in the FMDV vaccine strain genome did not have an effect on the ability of viral replication in vitro. The vaccine prepared from genetically modified FMDV by reverse genetics significantly improved the protective efficacy to the variant of the CHY topotype, compared with the wild O/HN/CHA/93 virus. Thus, the full-length cDNA clone of FMDV can be a useful tool to develop genetically engineered FMDV vaccine candidates to help control porcinophilic FMD epidemics in China.

2012-01-01

66

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

67

Genetically modified plants for tactical systems applications  

NASA Astrophysics Data System (ADS)

Plants are ubiquitous in the environment and have the 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 tactical uses for this technology. Some obvious applications are using plants as sentinels for detecting biological and chemical warfare agents or their derivatives from a remote platform, as well as detecting explosives. Another tactical application is covert monitoring using individual plants. Different methods to detect GFP in transgenic plants will be discussed.

Stewart, C. Neal, Jr.

2002-08-01

68

The Application of Reverse Genetics to Polyploid Plant Species  

Microsoft Academic Search

Polyploidy events (polyploidization) followed by progressive loss of redundant genome components are a major feature of plant evolution, with new evidence suggesting that all flowering plants possess ancestral genome duplications. Furthermore, many of our most important crop plants have undergone additional, relatively recent, genome duplication events. Recent advances in DNA sequencing have made vast amounts of new genomic data available

Timothy L. Fitzgerald; Kemal Kazan; John M. Manners

2012-01-01

69

Improved dual promotor-driven reverse genetics system for influenza viruses.  

PubMed

Reverse genetic systems for influenza A virus (IAV) allow the generation of genetically manipulated infectious virus from a set of transfected plasmid DNAs encoding the eight genomic viral RNA segments (vRNA). For this purpose, cDNAs representing these eight vRNA segments are cloned into specific plasmid vectors that allow the generation of vRNA-like transcripts using polymerase I (Pol I). In addition, these plasmids support the transcription of viral mRNA by polymerase II (Pol II), leading to the expression of viral protein(s) encoded by the respective transcripts. In an effort to develop this system further, we constructed the bi-directional vector pMPccdB. It is based on pHW2000 (Hoffmann et al., 2000b) but contains additionally (i) the ccdB gene whose expression is lethal for most Escherichia coli strains and therefore used as a negative selection marker and (ii) more efficient AarI cloning sites that flank the ccdB gene on either side. Furthermore, we used a modified one-step restriction/ligation protocol to insert the desired cDNA into the respective pMPccdB vector DNA. Both the use of a negative selection marker and an improved cloning protocol were shown to facilitate the generation of genetically engineered IAV as illustrated in this study by the cloning and rescue of the 2009 pandemic isolate A/Giessen/6/2009 (Gi-H1N1). PMID:23886561

Mostafa, Ahmed; Kanrai, Pumaree; Ziebuhr, John; Pleschka, Stephan

2013-11-01

70

Convexity of reverse coherent information capacity and its application  

NASA Astrophysics Data System (ADS)

Reverse coherent information, as a symmetric counterpart of the coherent information, has been firstly defined by R. García-Patrón et al. This quantity allows to define reverse coherent information capacity which is additive. In this Letter, we prove the convexity of such capacity for a general quantum channel, and investigate the effect of convex decomposition of quantum channel on its (reverse) coherent information. Finally, we apply the convexity property to provide an upper bound on the reverse coherent information capacity for some important channels.

Wang, MinJie; Pan, Wei

2011-07-01

71

Application of time reversal acoustics focusing for nonlinear imaging ms  

NASA Astrophysics Data System (ADS)

Time reversal acoustic (TRA) focusing of ultrasound appears to be an effective tool for nonlinear imaging in industrial and medical applications because of its ability to efficiently concentrate ultrasonic energy (close to diffraction limit) in heterogeneous media. In this study, we used two TRA systems to focus ultrasonic beams with different frequencies in coinciding focal points, thus causing the generation of ultrasonic waves with combination frequencies. Measurements of the intensity of these combination frequency waves provide information on the nonlinear parameter of medium in the focal region. Synchronized stirring of two TRA focused beams enables obtaining 3-D acoustic nonlinearity images of the object. Each of the TRA systems employed an aluminum resonator with piezotransducers glued to its facet. One of the free facets of each resonator was submerged into a water tank and served as a virtual phased array capable of ultrasound focusing and beam steering. To mimic a medium with spatially varying acoustical nonlinearity a simplest model such as a microbubble column in water was used. Microbubbles were generated by electrolysis of water using a needle electrode. An order of magnitude increase of the sum frequency component was observed when the ultrasound beams were focused in the area with bubbles.

Sarvazyan, Armen; Sutin, Alexander

2001-05-01

72

Hybrid genetic algorithm research and its application in problem optimization  

Microsoft Academic Search

There is a lot of research in genetic algorithm about structural optimization. But as far as the large multi-goal program is concerned, it limits the application of genetic algorithm for the reason of its specialty and large calculation. In order to explore a new resolution, the author proposed a combining algorithm for structural optimization, which is based on genetic algorithm

Weijin Jiang I; Dingti Luol; Yusheng Xu; Xingming Sun

2004-01-01

73

Characterization of Influenza Virus NS1 Protein by Using a Novel Helper-Virus-Free Reverse Genetic System  

Microsoft Academic Search

We have developed a novel helper-virus-free reverse genetic system to genetically manipulate influenza A viruses. The RNPs, which were purified from the influenza A\\/WSN\\/33 (WSN) virus, were treated with RNase H in the presence of NS (nonstructural) cDNA fragments. This specifically digested the NS RNP. The NS- digested RNPs thus obtained were transfected into cells together with the in vitro-reconstituted

MASAYOSHI ENAMI; KAZUE ENAMI

2000-01-01

74

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.

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

2014-01-01

75

Universal influenza B virus genomic amplification facilitates sequencing, diagnostics, and reverse genetics.  

PubMed

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; Wentworth, David E

2014-05-01

76

A reverse genetics approach identifies novel mutants in light responses and anthocyanin metabolism in petunia.  

PubMed

Flower color and plant architecture are important commercially valuable features for ornamental petunias (Petunia x hybrida Vilm.). Photoperception and light signaling are the major environmental factors controlling anthocyanin and chlorophyll biosynthesis and shade-avoidance responses in higher plants. The genetic regulators of these processes were investigated in petunia by in silico analyses and the sequence information was used to devise a reverse genetics approach to probe mutant populations. Petunia orthologs of photoreceptor, light-signaling components and anthocyanin metabolism genes were identified and investigated for functional conservation by phylogenetic and protein motif analyses. The expression profiles of photoreceptor gene families and of transcription factors regulating anthocyanin biosynthesis were obtained by bioinformatic tools. Two mutant populations, generated by an alkalyting agent and by gamma irradiation, were screened using a phenotype-independent, sequence-based method by high-throughput PCR-based assay. The strategy allowed the identification of novel mutant alleles for anthocyanin biosynthesis (CHALCONE SYNTHASE) and regulation (PH4), and for light signaling (CONSTANS) genes. PMID:24554834

Berenschot, Amanda S; Quecini, Vera

2014-01-01

77

Genomic and Genetic Analysis of Bordetella Bacteriophages Encoding Reverse Transcriptase-Mediated Tropism-Switching Cassettes  

PubMed Central

Liu et al. recently described a group of related temperate bacteriophages that infect Bordetella subspecies and undergo a unique template-dependent, reverse transcriptase-mediated tropism switching phenomenon (Liu et al., Science 295: 2091-2094, 2002). Tropism switching results from the introduction of single nucleotide substitutions at defined locations in the VR1 (variable region 1) segment of the mtd (major tropism determinant) gene, which determines specificity for receptors on host bacteria. In this report, we describe the complete nucleotide sequences of the 42.5- to 42.7-kb double-stranded DNA genomes of three related phage isolates and characterize two additional regions of variability. Forty-nine coding sequences were identified. Of these coding sequences, bbp36 contained VR2 (variable region 2), which is highly dynamic and consists of a variable number of identical 19-bp repeats separated by one of three 5-bp spacers, and bpm encodes a DNA adenine methylase with unusual site specificity and a homopolymer tract that functions as a hotspot for frameshift mutations. Morphological and sequence analysis suggests that these Bordetella phage are genetic hybrids of P22 and T7 family genomes, lending further support to the idea that regions encoding protein domains, single genes, or blocks of genes are readily exchanged between bacterial and phage genomes. Bordetella bacteriophages are capable of transducing genetic markers in vitro, and by using animal models, we demonstrated that lysogenic conversion can take place in the mouse respiratory tract during infection.

Liu, Minghsun; Gingery, Mari; Doulatov, Sergei R.; Liu, Yichin; Hodes, Asher; Baker, Stephen; Davis, Paul; Simmonds, Mark; Churcher, Carol; Mungall, Karen; Quail, Michael A.; Preston, Andrew; Harvill, Eric T.; Maskell, Duncan J.; Eiserling, Frederick A.; Parkhill, Julian; Miller, Jeff F.

2004-01-01

78

Genome-wide association mapping combined with reverse genetics identifies new effectors of low water potential-induced proline accumulation in Arabidopsis.  

PubMed

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

79

Local reverse entropy and its application in small targets detection  

NASA Astrophysics Data System (ADS)

The detection of small targets that submerges in the homogeneous image background is a difficult problem in the design of small targets detection algorithm. The concept of local reverse entropy combining the concepts of local entropy with reverse entropy is proposed in this paper, which is to solve that problem by enhancing small targets. The norms of local signal-to-background ratio and elapsed time are used to demonstrate the performance of local reverse entropy map. Both quantitative analysis and qualitative comparison confirm the validity and efficiency of the presented approach.

Deng, He; Liu, Qingtang; Cheng, Lifang

2013-03-01

80

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

81

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.

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

82

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.

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

2012-01-01

83

Pharmacological and genetic reversal of age-dependent cognitive deficits attributable to decreased presenilin function.  

PubMed

Alzheimer's disease (AD) is the leading cause of cognitive loss and neurodegeneration in the developed world. Although its genetic and environmental causes are not generally known, familial forms of the disease (FAD) are attributable to mutations in a single copy of the Presenilin (PS) and amyloid precursor protein genes. The dominant inheritance pattern of FAD indicates that it may be attributable to gain or change of function mutations. Studies of FAD-linked forms of presenilin (psn) in model organisms, however, indicate that they are loss of function, leading to the possibility that a reduction in PS activity might contribute to FAD and that proper psn levels are important for maintaining normal cognition throughout life. To explore this issue further, we have tested the effect of reducing psn activity during aging in Drosophila melanogaster males. We have found that flies in which the dosage of psn function is reduced by 50% display age-onset impairments in learning and memory. Treatment with metabotropic glutamate receptor (mGluR) antagonists or lithium during the aging process prevented the onset of these deficits, and treatment of aged flies reversed the age-dependent deficits. Genetic reduction of Drosophila metabotropic glutamate receptor (DmGluRA), the inositol trisphosphate receptor (InsP(3)R), or inositol polyphosphate 1-phosphatase also prevented these age-onset cognitive deficits. These findings suggest that reduced psn activity may contribute to the age-onset cognitive loss observed with FAD. They also indicate that enhanced mGluR signaling and calcium release regulated by InsP(3)R as underlying causes of the age-dependent cognitive phenotypes observed when psn activity is reduced. PMID:20631179

McBride, Sean M J; Choi, Catherine H; Schoenfeld, Brian P; Bell, Aaron J; Liebelt, David A; Ferreiro, David; Choi, Richard J; Hinchey, Paul; Kollaros, Maria; Terlizzi, Allison M; Ferrick, Neal J; Koenigsberg, Eric; Rudominer, Rebecca L; Sumida, Ai; Chiorean, Stephanie; Siwicki, Kathleen K; Nguyen, Hanh T; Fortini, Mark E; McDonald, Thomas V; Jongens, Thomas A

2010-07-14

84

Molecular genetics and clinical applications for RH  

PubMed Central

Rhesus is the clinically most important protein-based blood group system. It represents the largest number of antigens and the most complex genetics of the 30 known blood group systems. The RHD and RHCE genes are strongly homologous. Some genetic complexity is explained by their close chromosomal proximity and unusual orientation, with their tail ends facing each other. The antigens are expressed by the RhD and the RhCE proteins. Rhesus exemplifies the correlation of genotype and phenotype, facilitating the understanding of general genetic mechanisms. For clinical purposes, genetic diagnostics of Rhesus antigens will improve the cost-effective development of transfusion medicine.

Flegel, Willy A.

2011-01-01

85

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

86

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

Microsoft Academic Search

Time reverse modeling (TRM) is applied to localize and characterize acoustic emission using a numerical concrete model. Aim is to transform a method within exploration geophysics to non-destructive testing. In contrast to previous time reverse applications, no single event or first onset time identification is applied. The method is described from a mathematical point of view. So-called source TRM with

Erik H. Saenger; Georg Karl Kocur; Roman Jud; Manuel Torrilhon

2011-01-01

87

A plasmid-based reverse genetics system for influenza A virus.  

PubMed Central

A reverse genetics system for negative-strand RNA viruses was first successfully developed for influenza viruses. This technology involved the transfection of in vitro-reconstituted ribonucleoprotein (RNP) complexes into influenza virus-infected cells. We have now developed a method that allows intracellular reconstitution of RNP complexes from plasmid-based expression vectors. Expression of a viral RNA-like transcript is achieved from a plasmid containing a truncated human polymerase I (polI) promoter and a ribozyme sequence that generates the desired 3' end by autocatalytic cleavage. The polI-driven plasmid is cotransfected into human 293 cells with polII-responsive plasmids that express the viral PB1, PB2, PA, and NP proteins. This exclusively plasmid-driven system results in the efficient transcription and replication of the viral RNA-like reporter and allows the study of cis- and trans-acting signals involved in the transcription and replication of influenza virus RNAs. Using this system, we have also been able to rescue a synthetic neuraminidase gene into a recombinant influenza virus. This method represents a convenient alternative to the previously established RNP transfection system.

Pleschka, S; Jaskunas, R; Engelhardt, O G; Zurcher, T; Palese, P; Garcia-Sastre, A

1996-01-01

88

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.

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

2001-01-01

89

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.

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

90

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

91

A Study of Reverse Osmosis Applicability to Light Water Reactor Radwaste Processing.  

National Technical Information Service (NTIS)

The use of membrane technology has demonstrated significant process potential in nuclear radioactive waste applications. Reverse osmosis and ultrafiltration can provide filtration capability without the need of filter aids, minimize the requirements of ch...

J. Markind T. Van Tran

1979-01-01

92

[Construction of eukaryotic expression vector of general type in reverse genetic systems of non-segmented negative strand RNA virus].  

PubMed

To construct eukaryotic expression vector of general type in reverse genetics systems of non-segmented negative strand RNA viruses, the multiple cloning site of the plasmid pVAX1 was replaced with HamRz cDNA sequence, a 9 sites linker and HdvRz cDNA sequence through the sequential addition of three adapters, the insertion of which could generate the correct 3' and 5' terminal sequences of the primary viral genomic RNA transcript and facilitate the assembly of the complete viral cDNA sequence. The sequences of the three adaptors were correct after identifying by restriction endonuclease digestions and sequencing. The constructed eukaryotic expression vector could not only be used to assemble viral genome, but also provide the basis for establishing the reverse genetic system rapidly. PMID:20329561

Huang, Ying; Tang, Qing; Zhang, Shou-Feng; Hu, Rong-Liang

2010-01-01

93

Protective efficacy in chickens, geese and ducks of an H5N1-inactivated vaccine developed by reverse genetics  

Microsoft Academic Search

We generated a high-growth H5N1\\/PR8 virus by plasmid-based reverse genetics. The virulence associated multiple basic amino acids of the HA gene were removed, and the resulting virus is attenuated for chickens and chicken eggs. A formalin-inactivated oil-emulsion vaccine was prepared from this virus. When SPF chickens were inoculated with 0.3 ml of the vaccine, the hemagglutinin-inhibition (HI) antibody became detectable

Guobin Tian; Suhua Zhang; Yanbing Li; Zhigao Bu; Peihong Liu; Jinping Zhou; Chengjun Li; Jianzhong Shi; Kangzhen Yu; Hualan Chen

2005-01-01

94

Semi-automatic Modeling of Reverse-Engineered Shapes through Design-by-Feature and Genetic Algorithms  

NASA Astrophysics Data System (ADS)

Reverse Engineering aims at constructing CAD models of existing objects starting from measurement data. In the classical approach a reverse engineering procedure completes in three main steps: data acquisition data processing and modeling. Herein we describe a novel semi-automatic approach for integrating CAD and reverse engineering. The basic idea consists in constructing a parametric and feature-based approximate model and matching it with measurement data to determine the unknown parameters. The approach is semi-automatic since part of the model is constructed manually by the user, while the exact values of the parameters are computed through an optimization procedure based on genetic algorithms. Two case studies are presented and critically discussed.

Bianconi, Francesco; Conti, Paolo; Pazzaglia, Gabriele

2008-11-01

95

Evolutionary combinatorial chemistry: application of genetic algorithms  

Microsoft Academic Search

Evolutionary chemistry combines the evaluation of molecular properties and synthesis of novel compounds in a feedback loop to arrive at molecules with the desired properties. Inspired by natural evolutionary processes, combinatorial chemistry in combination with mathematical optimization methods and biological testing provides new approaches to drug discovery. Genetic algorithms have been applied with success in the design and automated synthesis

Lutz Weber

1998-01-01

96

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

97

Reverse engineering the genotype-phenotype map with natural genetic variation  

Microsoft Academic Search

The genetic variation that occurs naturally in a population is a powerful resource for studying how genotype affects phenotype. Each allele is a perturbation of the biological system, and genetic crosses, through the processes of recombination and segregation, randomize the distribution of these alleles among the progeny of a cross. The randomized genetic perturbations affect traits directly and indirectly, and

Matthew V. Rockman

2008-01-01

98

Time-reversal imaging of seismic sources and application to the great Sumatra earthquake  

NASA Astrophysics Data System (ADS)

The increasing power of computers and numerical methods (like spectral element methods) allows continuously improving modelization of the propagation of seismic waves in heterogeneous media and the development of new applications in particular time reversal in the three-dimensional Earth. The concept of time-reversal (hereafter referred to as TR) was previously successfully applied for acoustic waves in many fields like medical imaging, underwater acoustics and non destructive testing. We present here the first application at the global scale of TR with associated reverse movies of seismic waves propagation by sending back long period time-reversed seismograms. We show that seismic wave energy is refocused at the right location and the right time of the earthquake. When TR is applied to the Sumatra-Andaman earthquake (26 Dec. 2004), the migration of the rupture from the south towards the north is retrieved. Therefore, TR is potentially interesting for constraining the spatio-temporal history of complex earthquakes.

Larmat, Carene; Montagner, Jean-Paul; Fink, Mathias; Capdeville, Yann; Tourin, Arnaud; Clévédé, Eric

2006-10-01

99

Time-reversal optical focusing for biophotonics applications  

NASA Astrophysics Data System (ADS)

I will discuss our recent work on the use of digital optical phase conjugation and ultrasound tagging to accomplish timereversal deep tissue optical focusing for fluorescence imaging and other applications.

Yang, Changhuei

2014-03-01

100

A strategy for the identification of new abiotic stress determinants in Arabidopsis using web-based data mining and reverse genetics.  

PubMed

Since the sequencing of the Arabidopsis thaliana genome in 2000, plant researchers have faced the complex challenge of assigning function to thousands of genes. Functional discovery by in silico prediction or homology search resolved a significant number of genes, but only a minor part has been experimentally validated. Arabidopsis entry into the post-genomic era signified a massive increase in high-throughput approaches to functional discovery, which have since become available through publicly-available web-based resources. The present work focuses on an easy and straightforward strategy that couples data-mining to reverse genetics principles, to allow for the identification of new abiotic stress determinant genes. The strategy explores systematic microarray-based transcriptomics experiments, involving Arabidopsis abiotic stress responses. An overview of the most significant resources and databases for functional discovery in Arabidopsis is presented. The successful application of the outlined strategy is illustrated by the identification of a new abiotic stress determinant gene, HRR, which displays a heat-stress-related phenotype after a loss-of-function reverse genetics approach. PMID:22136640

Azevedo, Herlânder; Silva-Correia, Joana; Oliveira, Juliana; Laranjeira, Sara; Barbeta, Cátia; Amorim-Silva, Vitor; Botella, Miguel A; Lino-Neto, Teresa; Tavares, Rui M

2011-12-01

101

Clinical applications of schizophrenia genetics: genetic diagnosis, risk, and counseling in the molecular era  

PubMed Central

Schizophrenia is a complex neuropsychiatric disease with documented clinical and genetic heterogeneity, and evidence for neurodevelopmental origins. Driven by new genetic technologies and advances in molecular medicine, there has recently been concrete progress in understanding some of the specific genetic causes of this serious psychiatric illness. In particular, several large rare structural variants have been convincingly associated with schizophrenia, in targeted studies over two decades with respect to 22q11.2 microdeletions, and more recently in large-scale, genome-wide case-control studies. These advances promise to help many families afflicted with this disease. In this review, we critically appraise recent developments in the field of schizophrenia genetics through the lens of immediate clinical applicability. Much work remains in translating the recent surge of genetic research discoveries into the clinic. The epidemiology and basic genetic parameters (such as penetrance and expression) of most genomic disorders associated with schizophrenia are not yet well characterized. To date, 22q11.2 deletion syndrome is the only established genetic subtype of schizophrenia of proven clinical relevance. We use this well-established association as a model to chart the pathway for translating emerging genetic discoveries into clinical practice. We also propose new directions for research involving general genetic risk prediction and counseling in schizophrenia.

Costain, Gregory; Bassett, Anne S

2012-01-01

102

GENETIC PROGRAMMING: AN INTRODUCTION AND SURVEY OF APPLICATIONS  

Microsoft Academic Search

The aim of this paper is to provide an introduction to the rapidly developing field of genetic programming (GP). Particular emphasis is placed on the application of GP to engineering problem solving. First, the basic methodology is introduced. This is followed by a review of applications in the areas of systems modelling, control, optimisation and scheduling, design and signal processing.

M. J. Willis; H. G Hiden; P. Marenbach; B. McKay; G. A. Montague

103

GENETIC ANALYSIS OF GEOTAXIS IN DROSOPHILA MELANOGASTER: COMPLEMENTATION BETWEEN FORWARD AND REVERSE SELECTION LINES  

Microsoft Academic Search

THE RESPONSE TO ARTIFICIAL SELECTION FOR GEOTACTIC BEHAVIOR IN 4 LINES OF DROSOPHILA MELANOGASTER WAS MEASURED. THE NEGATIVE FORWARD LINE SHOWED CONTINUED RESPONSE TO SELECTION BEYOND GENERATION 65; THE POSITIVE FORWARD LINE DID NOT. THE REVERSE SELECTION LINES OBTAINED NEARLY THE SAME SCORES AS DID THE FORWARD LINES BY GENERATION 56 OF REVERSE SELECTION. RESULTS OF A COMPLEMENTATION TEST BETWEEN

ROY C. HOSTETTER; JERRY HIRSCH

1967-01-01

104

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.

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

2012-01-01

105

Environmental Optimization: Applications of Genetic Algorithms  

Microsoft Academic Search

The genetic algorithm (GA) has found wide acceptance in many fields, ranging from economics through engineering. In the environmental\\u000a sciences, some disciplines are using GAs regularly as a tool to solve typical problems; while in other areas, they have hardly\\u000a been assessed for use in research projects. The key to using GAs in environmental sciences is to pose the problem

Sue Ellen Haupt

106

Intermediate-Type Vancomycin Resistance (VISA) in Genetically-Distinct Staphylococcus aureus Isolates Is Linked to Specific, Reversible Metabolic Alterations  

PubMed Central

Intermediate (VISA-type) vancomycin resistance in Staphylococcus aureus has been associated with a range of physiologic and genetic alterations. Previous work described the emergence of VISA-type resistance in two clonally-distinct series of isolates. In both series (the first belonging to MRSA clone ST8-USA300, and the second to ST5-USA100), resistance was conferred by a single mutation in yvqF (a negative regulator of the vraSR two-component system associated with vancomycin resistance). In the USA300 series, resistance was reversed by a secondary mutation in vraSR. In this study, we combined systems-level metabolomic profiling with statistical modeling techniques to discover specific, reversible metabolic alterations associated with the VISA phenotype.

Alexander, Elizabeth L.; Gardete, Susana; Bar, Haim Y.; Wells, Martin T.; Tomasz, Alexander; Rhee, Kyu Y.

2014-01-01

107

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

108

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

109

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

110

Genetically engineered antibody molecules and their application.  

PubMed

Immunoglobulin genes can be efficiently expressed following transfection into myeloma cells. Using protoplast fusion, transfection frequencies greater than 10(-3) can be achieved. Compatible plasmids containing two different selectible markers are used to simultaneously deliver heavy and light chain genes to the same cell. To produce molecules with differing specificities the rearranged and expressed variable regions can be cloned from the appropriate hybridoma. In some cases, variable regions from cDNAs can be inserted into the expression vectors. It is possible to manipulate the immunoglobulin genes and produce novel antibody molecules. Antibodies have been produced in which the variable regions from mouse antibodies have been joined to human constant regions. In addition, antibodies with altered constant regions have been produced. These genetically engineered antibodies provide a unique set of reagents to study structure-function relationships within the molecule. They also can potentially be used in the diagnosis and therapy of human disease. PMID:3327412

Morrison, S L; Wims, L; Wallick, S; Tan, L; Oi, V T

1987-01-01

111

Genetic Patterns as a Function of Landscape Process: Applications of Neutral Genetic Markers for Predictive Modeling in Landscape Ecology  

Microsoft Academic Search

\\u000a Integrating landscape ecology and population genetics (Manel et al. 2003), landscape genetics1 aims to link observed patterns of genetic variation to underlying landscape process(es) (Storfer et al. 2007). Landscape\\u000a genetics is a useful, emerging approach with the potential to develop new understanding of ecological theory and improve management\\u000a decisions (Balkenhol et al. 2009). Current applications that incorporate both genetic data

Melanie A. Murphy; Jeffrey S. Evans

112

Current concepts and clinical applications of stroke genetics.  

PubMed

Driven by innovative technologies, novel analytical methods, and collaborations unimaginable not long ago, our understanding of the role of genetic variation in stroke has advanced substantially in recent years. However, a vast amount of data have accumulated quickly, and increasingly complex methodologies used in studies make keeping up to date on relevant findings difficult. In addition to well known, highly penetrant rare mutations that cause mendelian disorders related to stroke, several common genetic variants have been associated with common stroke subtypes, some of which also affect disease severity and clinical outcome. Furthermore, common genetic variations in biological pathways that have an important role in the pathophysiology of cerebrovascular diseases-such as blood pressure and oxidative phosphorylation-have been implicated in stroke. Clinical and translational applications of these and future discoveries in stroke genetics include identification of novel targets for treatment and development of personalised approaches to stroke prevention and management. PMID:24646874

Falcone, Guido J; Malik, Rainer; Dichgans, Martin; Rosand, Jonathan

2014-04-01

113

Application of Genetic Algorithms in Seismic Tomography  

Microsoft Academic Search

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

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

2010-01-01

114

Genetic algorithm application in optimization of wireless sensor networks.  

PubMed

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

115

Combining Formal Methods and Functional Strategies Regarding the Reverse Engineering of Interactive Applications  

Microsoft Academic Search

Graphical user interfaces (GUIs) make software easy to use by providing the user with visual controls. Therefore, correctness of GUI's code is essential to the correct execution of the overall software. Models can help in the evaluation of interactive applications by allow- ing designers to concentrate on its more important aspects. This paper describes our approach to reverse engineer an

J. C. Silva; José Creissac Campos; João Saraiva

2006-01-01

116

Automated Reverse Engineering of UML Sequence Diagrams for Dynamic Web Applications  

Microsoft Academic Search

This paper presents an approach and tool to automatically instrument dynamic Web applications using source transformation technology, and to reverse engineer a UML 2.1 sequence diagram from the execution traces generated by the resulting instrumentation. The result can be directly imported and visualized in a UML toolset such as rational software architect. Our approach dynamically filters traces to reduce redundant

Manar H. Alalfi; James R. Cordy; Thomas R. Dean

2009-01-01

117

Genetic engineering applications to biotechnology in the genus Bacillus  

SciTech Connect

This review presents a global picture of current applications and capabilities of genetic engineering to biotechnology in Bacillus, particularly B. subtilis, so that the academic biotechnologist, the industrial microbiologist, and the manager may turn to one source to study this subject. 236 references.

Workman, W.E.; McLinden, J.H.; Dean, D.H.

1986-06-09

118

Applications of Genetic Methods to NASA Design and Operations Problems  

NASA Technical Reports Server (NTRS)

We review four recent NASA-funded applications in which evolutionary/genetic methods are important. In the process we survey: the kinds of problems being solved today with these methods; techniques and tools used; problems encountered; and areas where research is needed. The presentation slides are annotated briefly at the top of each page.

Laird, Philip D.

1996-01-01

119

Application of genetic algorithms to hypersonic flight control  

Microsoft Academic Search

The paper presents an application of genetic algorithms to the design of a longitudinal flight controller for a hypersonic accelerator vehicle which is to be used to launch small satellites. A feature of hypersonic air-breathing flight vehicles is the high level of engine integration with the airframe. As a result, maintenance of vehicle attitude is not simply an issue of

K. J. Austin; P. A. Jacobs

2001-01-01

120

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

121

New applications of the H-reversal trajectory using solar sails  

NASA Astrophysics Data System (ADS)

Advanced solar sailing has been an increasingly attractive propulsion system for highly non-Keplerian orbits. Three new applications of the orbital angular momentum reversal (H-reversal) trajectories using solar sails are presented: space observation, heliocentric orbit transfer and collision orbits with asteroids. A theoretical proof for the existence of double H-reversal trajectories (referred to as ‘H2RTs’) is given, and the characteristics of the H2RTs are introduced before a discussion of the mission applications. A new family of H2RTs was obtained using a 3D dynamic model of the two-body frame. In a time-optimal control model, the minimum period H2RTs both inside and outside the ecliptic plane were examined using an ideal solar sail. Due to the quasi-heliostationary property at its two symmetrical aphelia, the H2RTs were deemed suitable for space observation. For the second application, the heliocentric transfer orbit was able to function as the time-optimal H-reversal trajectory, since its perihelion velocity is a circular or elliptic velocity. Such a transfer orbit can place the sailcraft into a clockwise orbit in the ecliptic plane, with a high inclination or displacement above or below the Sun. The third application of the H-reversal trajectory was simulated impacting an asteroid passing near Earth in a head-on collision. The collision point can be designed through selecting different perihelia or different launch windows. Sample orbits of each application were presented through numerical simulation. The results can serve as a reference for theoretical research and engineering design.

Zeng, Xiang-Yuan; Baoyin, Hexi; Li, Jun-Feng; Gong, Sheng-Ping

2011-07-01

122

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

Microsoft Academic Search

Due to the phenomenon of male pregnancy, the ¢ sh family Syngnathidae (seahorses and pipe¢ shes) 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

Adam G. Jones; DeEtte Walker; John C. Avise

2001-01-01

123

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

124

Genetic evidence for a contribution of EphA:ephrinA reverse signaling to motor axon guidance.  

PubMed

Repulsive Eph forward signaling from limb-derived ephrins guides the axons of lateral motor column (LMC) motor neurons. LMC axons also express ephrinAs, while their EphA receptors are expressed in the limb mesenchyme. In vitro studies have suggested that reverse signaling from limb-derived EphA4 to axonal ephrinAs might result in attraction of LMC axons. However, genetic evidence for this function is lacking. Here we use the Dunn chamber turning assay to show that EphA proteins are chemoattractants and elicit fast turning responses in LMC neurons in vitro. Moreover, ectopic expression of EphA4 in chick hindlimb changes the limb trajectory of LMC axons. Nervous system-specific deletion of EphA4 in mice resulted in fewer LMC axon projection errors than the ubiquitous deletion of EphA4. Additionally, a signaling-incompetent EphA4 mutant partially rescued guidance errors in the hindlimb, suggesting that limb-derived EphA4 contributes to the establishment of LMC projections. In summary, we provide evidence for a role of EphA:ephrinA attractive reverse signaling in motor axon guidance and in vivo evidence of in-parallel forward Eph and reverse ephrin signaling function in the same neuronal population. PMID:22496566

Dudanova, Irina; Kao, Tzu-Jen; Herrmann, Julia E; Zheng, Binhai; Kania, Artur; Klein, Rüdiger

2012-04-11

125

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

126

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.

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

2014-01-01

127

Time-Reversal Imaging of seismic sources and application to recent large Earthquakes  

NASA Astrophysics Data System (ADS)

The occurrence of the disastrous Sumatra-Andaman earthquake on dec. 26, 2004 makes it necessary to develop innovative techniques for studying the complex spatio-temporal characteristics of rupture. The concept of time-reversal (hereafter referred to as TR) was previously successfully applied for acoustic waves in many fields such as medical imaging, underwater acoustics and non destructive testing. The increasing power of computers and numerical methods (such as spectral element methods) enables one to simulate more and more accurately the propagation of seismic waves in heterogeneous media and to develop new applications, in particular time reversal in the three-dimensional Earth. We present here the first applications at the global scale of TR with associated reverse movies of seismic waves propagation by sending back time--reversed seismograms. We show that seismic wave energy is refocused at the right location and the right time of the earthquake. When TR is applied to the Sumatra-- Andaman earthquake (26 dec. 2004), the migration of the rupture from the south towards the north is retrieved. All corresponding movies can be downloaded at the following webpage: http://www.gps.caltech.edu/~carene Other applications to recent smaller earthquakes will be also shown. Therefore, the technique of TR is potentially interesting for automatically locating earthquakes in space and time and for constraining the spatio-temporal history of complex earthquakes .

Montagner, J.; Larmat, C.; Fink, M.; Capdeville, Y.; Tourin, A.

2006-12-01

128

Surfactin: biosynthesis, genetics and potential applications.  

PubMed

Even after forty years of its discovery by Arima et al, surfactin, a potent lipopeptide biosurfactant, still attracts attention and fancy of the applied microbiologists and biotechnologists worldwide, mainly due to its versatile bioactive properties and potential industrial implications. Starting from its first invented characteristic as an inhibitor of fibrin clot formation coupled with its significant ability to reduce surface tension of water, it has been credited with antifungal, antiviral, antitumor, insecticidal and antimycoplasma activities. These properties of therapeutic and commercial importance and its recent use as an enhanced oil recovery and a bioremediation agent make it a truly versatile biomolecule, the commercial potential of which could not be fully realized, particularly as a therapeutic agent, mainly because of its hemolytic property. This chapter thus addresses the issues related to the versatile nature of the most studied microbial surfactant, surfactin and its potential commercial and health-care applications. PMID:20545293

Sen, Ramkrishna

2010-01-01

129

XX sex reversal, palmoplantar keratoderma, and predisposition to squamous cell carcinoma: genetic analysis in one family.  

PubMed

We describe a large inbred Sicilian family that includes four 46, XX (SRY-) brothers. Palmoplantar hyperkeratosis (PPK) and an associated predisposition to squamous cell carcinoma (SCC) of the skin, segregates as a recessive trait within the family. Interestingly, all the PPK-affected members of the family are phenotypic males (46,XY or 46,XX) while seven XX sibs are healthy phenotypic females with no signs of PPK. We propose that homozygosity for a single mutational event, possibly including contiguous genes, may cause PPK/SCC in both XY or XX individuals and sex reversal in XX individuals. The family is informative for linkage analysis for the PPK trait and allows linkage exclusion for the sex reversal trait. Here we show that 15 loci involved in PPK etiology, skin differentiation, function or malignancy, and nine loci involved in sex determination/differentiation are not implicated in the phenotype of this family. PMID:16158431

Radi, Orietta; Parma, Pietro; Imbeaud, Sandrine; Nasca, Maria Rita; Uccellatore, Filippo; Maraschio, Paola; Tiepolo, Luciano; Micali, Giuseppe; Camerino, Giovanna

2005-10-15

130

Expanding applications of chemical genetics in signal transduction  

PubMed Central

Chemical genetics represents an expanding collection of techniques applied to a variety of signaling processes. These techniques use a combination of chemical reporters and protein engineering to identify targets of a signaling enzyme in a global and non-directed manner without resorting to hypothesis-driven candidate approaches. In the last year, chemical genetics has been applied to a variety of kinases, revealing a much broader spectrum of substrates than had been appreciated. Here, we discuss recent developments in chemical genetics, including insights from our own proteomic screen for substrates of the kinase ERK2. These studies have revealed that many kinases have overlapping substrate specificity, and they often target several proteins in any particular downstream pathway. It remains to be determined whether this configuration exists to provide redundant control, or whether each target contributes a fraction of the total regulatory effect. From a general perspective, chemical genetics is applicable in principle to a broad range of posttranslational modifications (PTMs), most notably methylation and acetylation, although many challenges remain in implementing this approach. Recent developments in chemical reporters and protein engineering suggest that chemical genetics will soon be a powerful tool for mapping signal transduction through these and other PTMs.

Carlson, Scott M.; White, Forest M.

2012-01-01

131

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.

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

132

Reverse genetics approach towards understanding pathogenesis of H5N1 Hong Kong influenza A virus infection.  

PubMed Central

In 1990, Palese and colleagues established a method (reverse genetics) that allowed one to generate influenza virus containing a gene segment derived from cloned cDNA. Although this method contributed tremendously to our understanding of influenza pathogenesis, the requirement of helper viruses limited its use in many experimental settings. Recently, we and others established systems for the generation of influenza viruses entirely from cloned cDNAs. These systems require only DNA cloning and transfection techniques, and can therefore be easily implemented by laboratories working in the fields of molecular biology and virology. Thus, for the first time, a system is now available that allows highly efficient generation of influenza virus without technical limitations. Using this technology, we generated the same strain of H5N1 influenza viruses that caused an outbreak in Hong Kong in 1997, killing six people.

Hatta, M; Neumann, G; Kawaoka, Y

2001-01-01

133

Development of a reverse genetics system for the aG strain of rabies virus in China.  

PubMed

The aG rabies virus strain has been attenuated through multiple passages in cells and is now used as a vaccine strain in China. We attempted to develop a reverse genetics system using the aG strain. Recombinant full-length genomic cDNA was flanked by a hammerhead ribozyme and the hepatitis delta virus ribozyme. Three helper plasmids encoding the nucleoprotein, the phosphoprotein, and the large protein were produced and introduced together with a plasmid containing the full-length aG viral genome into BHK-21 cells by transfection. Recombinant virus was successfully recovered from the cloned cDNA under the control of a CMV promoter driven by RNA polymerase II. The recombinant virus was confirmed by RT-PCR, and the titer of the recombinant virus was 6.2 log LD50. PMID:24272786

Wenqiang, Jiao; Yin, Xiangping; Lan, Xi; Li, Xuerui; Liu, Jixing

2014-05-01

134

Elimination of transistor’s switching losses by diode reverse recovery in dedicated application  

Microsoft Academic Search

This paper deals with reverse recovery effect of various diodespsila structures and its elimination in dedicated applications. In principle it deals with the commutation process between transistorpsilas turn-on and diodepsilas turn-off in DC\\/DC converters. Quantification of received data was based on experimental measurements and consequently was converted into continuous form for graphic interpretation in dependence on switching frequency, supply voltage

M. Frivaldsky; R. Sul

2008-01-01

135

Reversible symptoms and clearance of mutant prion protein in an inducible model of a genetic prion disease in Drosophila melanogaster.  

PubMed

Prion diseases are progressive disorders that affect the central nervous system leading to memory loss, personality changes, ataxia and neurodegeneration. In humans, these disorders include Creutzfeldt-Jakob disease, kuru and Gerstmann-Straüssler-Scheinker (GSS) syndrome, the latter being a dominantly inherited prion disease associated with missense mutations in the gene that codes for the prion protein. The exact mechanism by which mutant prion proteins affect the central nervous system and cause neurological disease is not well understood. We have generated an inducible model of GSS disease in Drosophila melanogaster by temporally expressing a misfolded form of the murine prion protein in cholinergic neurons. Flies accumulating this mutant protein develop motor abnormalities which are associated with electrophysiological defects in cholinergic neurons. We find that, upon blocking the expression of the mutant protein, both behavioral and electrophysiological defects can be reversed. This represents the first case of reversibility reported in a model of genetic prion disease. Additionally, we observe that endogenous mechanisms exist within Drosophila that are capable of clearing the accumulated prion protein. PMID:24686303

Murali, A; Maue, R A; Dolph, P J

2014-07-01

136

Genetic engineering of cytokinins and their application to agriculture.  

PubMed

Cytokinins are master regulators of plant growth and development. They are involved in the regulation of many important physiological and metabolic processes. Recent progress in cytokinin research at the molecular level, including identification of related genes and cytokinin receptors, plus elucidation of signal transduction, has greatly increased our understanding of cytokinin actions. Although still in its infant stage, molecular breeding of crops with altered cytokinin metabolism, when combined with the transgenic approach, has shown very promising potential for application to agriculture. In this review we briefly introduce recent progress in cytokinin molecular biology, discuss applications of cytokinin genetic engineering to agriculture, and present implications and future research directions. PMID:18855152

Ma, Qing-Hu

2008-01-01

137

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

138

The molecular genetics of sex determination and sex reversal in mammals.  

PubMed

The process of sex determination in mammals normally unfolds in three distinct stages: (1) establishment of chromosomal sex at fertilization (XX or XY); (2) commitment to the appropriate pathway of gonadal differentiation with respect to chromosomal sex, through the action (or absence) of the Y chromosome gene SRY; and (3) correct development of secondary sexual characteristics, including internal and external genitalia, in accordance with gonadal sex. At any of these three steps, the process of sex determination can go awry, leading to disorders of sexual development. In this article, we review the typical mechanism and process of mammalian sex determination, with an emphasis on the well-characterized mouse and human models. We also consider aberrant mammalian sex determination, focusing on examples of sex reversal stemming from gene defects. PMID:23044871

Quinn, Alexander; Koopman, Peter

2012-10-01

139

Application of Iterative Time-Reversal for Electromagnetic Wave Focusing in a Wave Chaotic System  

NASA Astrophysics Data System (ADS)

Time-reversal mirrors exploit the time-reversal invariance of the wave equation to achieve spatial and temporal focusing, and they have been shown to be very effective sensors of perturbations to wave chaotic systems. The sensing technique is based on a classical analogue of the Loschmidt echo [1]. However, dissipation results in an imperfect focusing, hence we created a sensing technique employing exponential amplification to overcome this limitation [1,2]. We now apply the technique of iterative time-reversal, which had been demonstrated in a dissipative acoustic system, to an electromagnetic time-reversal mirror, and experimentally demonstrate improved temporal focusing. We also use a numerical model of a network of transmission lines to demonstrate improved focusing by the iterative technique for various degrees and statistical distributions of loss in the system. The application of the iterative technique to improve the performance and practicality of our sensor is explored.[4pt] [1] B. T. Taddese, et al., Appl. Phys. Lett. 95, 114103 (2009).[0pt] [2] B. T. Taddese, et al., J. Appl. Phys. 108, (2010) in press; arXiv:1008.2409.

Taddese, Biniyam; Antonsen, Thomas; Ott, Edward; Anlage, Steven

2011-03-01

140

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

PubMed

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

141

Broadening the application of evolutionarily based genetic pest management.  

PubMed

Insect- and tick-vectored diseases such as malaria, dengue fever, and Lyme disease cause human suffering, and current approaches for prevention are not adequate. Invasive plants and animals such as Scotch broom, zebra mussels, and gypsy moths continue to cause environmental damage and economic losses in agriculture and forestry. Rodents transmit diseases and cause major pre- and postharvest losses, especially in less affluent countries. Each of these problems might benefit from the developing field of Genetic Pest Management that is conceptually based on principles of evolutionary biology. This article briefly describes the history of this field, new molecular tools in this field, and potential applications of those tools. There will be a need for evolutionary biologists to interact with researchers and practitioners in a variety of other fields to determine the most appropriate targets for genetic pest management, the most appropriate methods for specific targets, and the potential of natural selection to diminish the effectiveness of genetic pest management. In addition to producing environmentally sustainable pest management solutions, research efforts in this area could lead to new insights about the evolution of selfish genetic elements in natural systems and will provide students with the opportunity to develop a more sophisticated understanding of the role of evolutionary biology in solving societal problems. PMID:17999722

Gould, Fred

2008-02-01

142

Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase persists in macaques despite antiretroviral therapy.  

PubMed

The impact of antiretroviral therapy (ART) on the genetics of simian immunodeficiency virus (SIV) or human immunodeficiency virus (HIV) populations has been incompletely characterized. We analyzed SIV genetic variation before, during, and after ART in a macaque model. Six pigtail macaques were infected with an SIV/HIV chimeric virus, RT-SHIV(mne), in which SIV reverse transcriptase (RT) was replaced by HIV-1 RT. Three animals received a short course of efavirenz (EFV) monotherapy before combination ART was started. All macaques received 20 weeks of tenofovir, emtricitabine, and EFV. Plasma virus populations were analyzed by single-genome sequencing. Population diversity was measured by average pairwise difference, and changes in viral genetics were assessed by phylogenetic and panmixia analyses. After 20 weeks of ART, viral diversity was not different from pretherapy viral diversity despite more than 10,000-fold declines in viremia, indicating that, within this range, there is no relationship between diversity and plasma viremia. In two animals with consistent SIV RNA suppression to <15 copies/ml during ART, there was no evidence of viral evolution. In contrast, in the four macaques with viremias >15 copies/ml during therapy, there was divergence between pre- and during-ART virus populations. Drug resistance mutations emerged in two of these four animals, resulting in virologic failure in the animal with the highest level of pretherapy viremia. Taken together, these findings indicate that viral diversity does not decrease with suppressive ART, that ongoing replication occurs with viremias >15 copies/ml, and that in this macaque model of ART drug resistance likely emerges as a result of incomplete suppression and preexisting drug resistance mutations. PMID:21084490

Kearney, Mary; Spindler, Jon; Shao, Wei; Maldarelli, Frank; Palmer, Sarah; Hu, Shiu-Lok; Lifson, Jeffrey D; KewalRamani, Vineet N; Mellors, John W; Coffin, John M; Ambrose, Zandrea

2011-01-01

143

Genetic selection of intragenic suppressor mutations that reverse the effect of common p53 cancer mutations.  

PubMed Central

Several lines of evidence suggest that the presence of the wild-type tumor suppressor gene p53 in human cancers correlates well with successful anti-cancer therapy. Restoration of wild-type p53 function to cancer cells that have lost it might therefore improve treatment outcomes. Using a systematic yeast genetic approach, we selected second-site suppressor mutations that can overcome the deleterious effects of common p53 cancer mutations in human cells. We identified several suppressor mutations for the V143A, G245S and R249S cancer mutations. The beneficial effects of these suppressor mutations were demonstrated using mammalian reporter gene and apoptosis assays. Further experiments showed that these suppressor mutations could override additional p53 cancer mutations. The mechanisms of such suppressor mutations can be elucidated by structural studies, ultimately leading to a framework for the discovery of small molecules able to stabilize p53 mutants.

Brachmann, R K; Yu, K; Eby, Y; Pavletich, N P; Boeke, J D

1998-01-01

144

The application of genetic algorithm based on matlab in function optimization  

Microsoft Academic Search

This paper introduces the theory of genetic algorithm. The specific operation flow of genetic algorithm is described. The application of genetic algorithm in function optimization has been achieved by the using of matlab programming language. The process of programming shows that it is very easy, flexible and efficient to optimize and compute with matlab language, and the effectiveness of genetic

Guangya Liu; Jingli Chen

2011-01-01

145

Negative-strand RNA viruses: genetic engineering and applications.  

PubMed Central

The negative-strand RNA viruses are a broad group of animal viruses that comprise several important human pathogens, including influenza, measles, mumps, rabies, respiratory syncytial, Ebola, and hantaviruses. The development of new strategies to genetically manipulate the genomes of negative-strand RNA viruses has provided us with new tools to study the structure-function relationships of the viral components and their contributions to the pathogenicity of these viruses. It is also now possible to envision rational approaches--based on genetic engineering techniques--to design live attenuated vaccines against some of these viral agents. In addition, the use of different negative-strand RNA viruses as vectors to efficiently express foreign polypeptides has also become feasible, and these novel vectors have potential applications in disease prevention as well as in gene therapy. Images Fig. 1

Palese, P; Zheng, H; Engelhardt, O G; Pleschka, S; Garcia-Sastre, A

1996-01-01

146

Exposure to diethylstilbestrol during embryonic and larval stages of medaka fish (Oryzias latipes) leads to sex reversal in genetic males and reduced gonad weight in genetic females.  

PubMed

Molecular and cellular mechanisms involved in artificially induced ovarian differentiation were analyzed by exposing embryos of medaka (Oryzias latipes) to a potent nonsteroidal estrogen, diethylstilbestrol (DES). Embryos were exposed for short-exposure (SE) [from 0 to 8 d postfertilization (dpf)] and long-exposure (LE) periods (from 0 to 18/28 dpf) to 1 ng/ml of DES, and status of sexual differentiation in somatic and germ cells of these gonads was analyzed at 8, 18, and 28 dpf by histology, cell proliferation assays, TUNEL assay, and in situ hybridization using sex-specific somatic and germ cell markers. Additionally, gonads of exposed fry were examined after withdrawal of DES to see whether effects of DES in exposed fish were reversible or not. DES induced germ cell proliferation and meiosis in XY fry of SE and LE groups. However, SE induced only a partial reduction in expression of gonadal soma-derived factor, the male-dominant somatic cell marker, and was not sufficient to induce ovarian development after withdrawal of DES. On the contrary, LE resulted in complete loss of such male-specific gene expression in somatic cells of XY gonads, and these gonads underwent sustained ovarian development even after withdrawal of DES. Importantly, LE to DES affected germ cell proliferation in XX gonads adversely during early stages of sexual differentiation, leading to reduced gonad weight in adulthood. Interestingly, apoptosis was not the cause for reduction in germ cell number. Taken together, these results indicated that DES exposure has long-lasting effects on the gonadal development in genetic males (sex reversal) and females (reduced gonad weight) of medaka. PMID:21239430

Paul-Prasanth, Bindhu; Shibata, Yasushi; Horiguchi, Ryo; Nagahama, Yoshitaka

2011-02-01

147

Reverse Genetics in Candida albicans Predicts ARF Cycling Is Essential for Drug Resistance and Virulence  

PubMed Central

Candida albicans, the major fungal pathogen of humans, causes life-threatening infections in immunocompromised individuals. Due to limited available therapy options, this can frequently lead to therapy failure and emergence of drug resistance. To improve current treatment strategies, we have combined comprehensive chemical-genomic screening in Saccharomyces cerevisiae and validation in C. albicans with the goal of identifying compounds that can couple with the fungistatic drug fluconazole to make it fungicidal. Among the genes identified in the yeast screen, we found that only AGE3, which codes for an ADP-ribosylation factor GTPase activating effector protein, abrogates fluconazole tolerance in C. albicans. The age3 mutant was more sensitive to other sterols and cell wall inhibitors, including caspofungin. The deletion of AGE3 in drug resistant clinical isolates and in constitutively active calcineurin signaling mutants restored fluconazole sensitivity. We confirmed chemically the AGE3-dependent drug sensitivity by showing a potent fungicidal synergy between fluconazole and brefeldin A (an inhibitor of the guanine nucleotide exchange factor for ADP ribosylation factors) in wild type C. albicans as well as in drug resistant clinical isolates. Addition of calcineurin inhibitors to the fluconazole/brefeldin A combination only initially improved pathogen killing. Brefeldin A synergized with different drugs in non-albicans Candida species as well as Aspergillus fumigatus. Microarray studies showed that core transcriptional responses to two different drug classes are not significantly altered in age3 mutants. The therapeutic potential of inhibiting ARF activities was demonstrated by in vivo studies that showed age3 mutants are avirulent in wild type mice, attenuated in virulence in immunocompromised mice and that fluconazole treatment was significantly more efficacious when ARF signaling was genetically compromised. This work describes a new, widely conserved, broad-spectrum mechanism involved in fungal drug resistance and virulence and offers a potential route for single or improved combination therapies.

Epp, Elias; Vanier, Ghyslaine; Harcus, Doreen; Lee, Anna Y.; Jansen, Gregor; Hallett, Michael; Sheppard, Don C.; Thomas, David Y.; Munro, Carol A.; Mullick, Alaka; Whiteway, Malcolm

2010-01-01

148

High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics.  

PubMed

A library of 29,482 T-DNA enhancer trap lines has been generated in rice cv. Nipponbare. The regions flanking the T-DNA left border from the first 12,707 primary transformants were systematically isolated by adapter anchor PCR and sequenced. A survey of the 7480 genomic sequences larger than 30 bp (average length 250 bp), representing 56.4% of the total readable sequences and matching the rice bacterial artificial chromosome/phage artificial chromosome (BAC/PAC) sequences assembled in pseudomolecules allowed the assigning of 6645 (88.8%) T-DNA insertion sites to at least one position in the rice genome of cv. Nipponbare. T-DNA insertions appear to be rather randomly distributed over the 12 rice chromosomes, with a slightly higher insertion frequency in chromosomes 1, 2, 3 and 6. The distribution of 723 independent T-DNA insertions along the chromosome 1 pseudomolecule did not differ significantly from that of the predicted coding sequences in exhibiting a lower insertion density around the centromere region and a higher density in the subtelomeric regions where the gene density is higher. Further establishment of density graphs of T-DNA inserts along the recently released 12 rice pseudomolecules confirmed this non-uniform chromosome distribution. T-DNA appeared less prone to hot spots and cold spots of integration when compared with those revealed by a concurrent assignment of the Tos17 retrotransposon flanking sequences deposited in the National Center for Biotechnology Information (NCBI). T-DNA inserts rarely integrated into repetitive sequences. Based on the predicted gene annotation of chromosome 1, preferential insertion within the first 250 bp from the putative ATG start codon has been observed. Using 4 kb of sequences surrounding the insertion points, 62% of the sequences showed significant similarity to gene encoding known proteins (E-value < 1.00 e(-05)). To illustrate the in silico reverse genetic approach, identification of 83 T-DNA insertions within genes coding for transcription factors (TF) is presented. Based both on the estimated number of members of several large TF gene families (e.g. Myb, WRKY, HD-ZIP, Zinc-finger) and on the frequency of insertions in chromosome 1 predicted genes, we could extrapolate that 7-10% of the rice gene complement is already tagged by T-DNA insertion in the 6116 independent transformant population. This large resource is of high significance while assisting studies unravelling gene function in rice and cereals, notably through in silico reverse genetics. PMID:15255873

Sallaud, Christophe; Gay, Céline; Larmande, Pierre; Bès, Martine; Piffanelli, Pietro; Piégu, Benoit; Droc, Gaétan; Regad, Farid; Bourgeois, Emmanuelle; Meynard, Donaldo; Périn, Christophe; Sabau, Xavier; Ghesquière, Alain; Glaszmann, Jean Christophe; Delseny, Michel; Guiderdoni, Emmanuel

2004-08-01

149

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.

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

2009-01-01

150

Characterization of influenza virus NS1 protein by using a novel helper-virus-free reverse genetic system.  

PubMed

We have developed a novel helper-virus-free reverse genetic system to genetically manipulate influenza A viruses. The RNPs, which were purified from the influenza A/WSN/33 (WSN) virus, were treated with RNase H in the presence of NS (nonstructural) cDNA fragments. This specifically digested the NS RNP. The NS-digested RNPs thus obtained were transfected into cells together with the in vitro-reconstituted NS RNP. The NS-digested RNPs alone did not rescue viruses; however, cotransfection with the NS RNP did. This protocol was also used to rescue the NP transfectant. We obtained two NS1 mutants, dl12 and N110, using this protocol. The dl12 NS gene contains a deletion of 12 amino acids at positions 66 to 77 near the N terminus. This virus was temperature sensitive in Madin-Darby bovine kidney (MDBK) cells as well as in Vero cells. The translation of all viral proteins as well as cellular proteins was significantly disrupted during a later time of infection at the nonpermissive temperature of 39 degrees C. The N110 mutant consists of 110 amino acids which are the N-terminal 48% of the WSN virus NS1 protein. Growth of this virus was significantly reduced at any temperature. In the virus-infected cells, translation of the M1 protein was reduced to 10 to 20% of that of the wild-type virus; however, the translation of neither the nucleoprotein nor NS1 was significantly interfered with, indicating the important role of NS1 in translational stimulation of the M1 protein. PMID:10823862

Enami, M; Enami, K

2000-06-01

151

Characterization of Influenza Virus NS1 Protein by Using a Novel Helper-Virus-Free Reverse Genetic System  

PubMed Central

We have developed a novel helper-virus-free reverse genetic system to genetically manipulate influenza A viruses. The RNPs, which were purified from the influenza A/WSN/33 (WSN) virus, were treated with RNase H in the presence of NS (nonstructural) cDNA fragments. This specifically digested the NS RNP. The NS-digested RNPs thus obtained were transfected into cells together with the in vitro-reconstituted NS RNP. The NS-digested RNPs alone did not rescue viruses; however, cotransfection with the NS RNP did. This protocol was also used to rescue the NP transfectant. We obtained two NS1 mutants, dl12 and N110, using this protocol. The dl12 NS gene contains a deletion of 12 amino acids at positions 66 to 77 near the N terminus. This virus was temperature sensitive in Madin-Darby bovine kidney (MDBK) cells as well as in Vero cells. The translation of all viral proteins as well as cellular proteins was significantly disrupted during a later time of infection at the nonpermissive temperature of 39°C. The N110 mutant consists of 110 amino acids which are the N-terminal 48% of the WSN virus NS1 protein. Growth of this virus was significantly reduced at any temperature. In the virus-infected cells, translation of the M1 protein was reduced to 10 to 20% of that of the wild-type virus; however, the translation of neither the nucleoprotein nor NS1 was significantly interfered with, indicating the important role of NS1 in translational stimulation of the M1 protein.

Enami, Masayoshi; Enami, Kazue

2000-01-01

152

Genotyping technologies: application to biotransformation enzyme genetic polymorphism screening.  

PubMed

Pharmacogenomics encompasses several major areas: the study of polymorphic variations to drug response and disease susceptibility, identification of the effects of drugs/xenobiotics at the genomic level, and genotype/phenotype associations. The most common type of human genetic variations is single-nucleotide polymorphisms (SNPs). Several novel approaches to detection of SNPs are currently available. The range of new methods includes modifications of several conventional techniques such as PCR, mass spectrometry, and sequencing as well as more innovative technologies such as fluorescence resonance energy transfer and microarrays. The application of each of these techniques is largely dependent on the number of SNPs to be screened and sample size. The current chapter presents an overview of the general concepts of a variety of genotyping technologies with an emphasis on the recently developed methodologies, including a comparison of the advantages, applicability, cost efficiency, and limitations of these methods. PMID:24623222

Romkes, Marjorie; Buch, Shama C

2014-01-01

153

High-throughput, luciferase-based reverse genetics systems for identifying inhibitors of Marburg and Ebola viruses.  

PubMed

Marburg virus (MARV) and Ebola virus (EBOV), members of the family Filoviridae, represent a significant challenge to global public health. Currently, no licensed therapies exist to treat filovirus infections, which cause up to 90% mortality in human cases. To facilitate development of antivirals against these viruses, we established two distinct screening platforms based on MARV and EBOV reverse genetics systems that express secreted Gaussia luciferase (gLuc). The first platform is a mini-genome replicon to screen viral replication inhibitors using gLuc quantification in a BSL-2 setting. The second platform is complementary to the first and expresses gLuc as a reporter gene product encoded in recombinant infectious MARV and EBOV, thereby allowing for rapid quantification of viral growth during treatment with antiviral compounds. We characterized these viruses by comparing luciferase activity to virus production, and validated luciferase activity as an authentic real-time measure of viral growth. As proof of concept, we adapt both mini-genome and infectious virus platforms to high-throughput formats, and demonstrate efficacy of several antiviral compounds. We anticipate that both approaches will prove highly useful in the development of anti-filovirus therapies, as well as in basic research on the filovirus life cycle. PMID:24713118

Uebelhoer, Luke S; Albariño, César G; McMullan, Laura K; Chakrabarti, Ayan K; Vincent, Joel P; Nichol, Stuart T; Towner, Jonathan S

2014-06-01

154

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

155

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

156

Understand Corporate Rationales for Engaging in Reverse Stock Splits - A Data Mining Application  

Microsoft Academic Search

There has been much written on the individual topics of bankruptcy prediction, corporate performance, and reverse stock splits. However, there is little research into the relationship between reverse stock splits and corporate performance as well as bankruptcies. The purpose of this study is to provide and empirically support rationales for reverse splits by classifying reverse splitting firms into two groups,

Melody Y. Kiang; Dorothy M. Fisher; Steve A. Fisher; Robert T. H. Chi

2005-01-01

157

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.

158

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

159

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

160

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

161

A Reverse Genetics System for the Great Lakes Strain of Viral Hemorrhagic Septicemia Virus: the NV Gene is Required for Pathogenicity  

Microsoft Academic Search

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\\u000a IVb, has invaded the Great Lakes in North America, causing large-scale epidemics in wild fish. An efficient reverse genetics\\u000a system was developed to generate a recombinant VHSV

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

162

Xanthan gum biosynthesis and application: a biochemical/genetic perspective.  

PubMed

Xanthan gum is a complex exopolysaccharide produced by the plant-pathogenic bacterium Xanthomonas campestris pv. campestris. It consists of D-glucosyl, D-mannosyl, and D-glucuronyl acid residues in a molar ratio of 2:2:1 and variable proportions of O-acetyl and pyruvyl residues. Because of its physical properties, it is widely used as a thickener or viscosifier in both food and non-food industries. Xanthan gum is also used as a stabilizer for a wide variety of suspensions, emulsions, and foams. This article outlines aspects of the biochemical assembly and genetic loci involved in its biosynthesis, including the synthesis of the sugar nucleotide substrates, the building and decoration of the pentasaccharide subunit, and the polymerization and secretion of the polymer. An overview of the applications and industrial production of xanthan is also covered. PMID:9763683

Becker, A; Katzen, F; Pühler, A; Ielpi, L

1998-08-01

163

Application of chromosomal microdissection, polymerase chain reaction (PCR), and reverse chromosome painting in prenatal diagnosis  

SciTech Connect

De novo marker chromosomes have been found in about 0.04% of amniotic fluid cultures. The origin of these marker chromosomes is difficult to identify by routine chromosome banding analysis. In the present study, we applied microdissection, PCR, and reverse chromosome painting to two amniotic fluid cases with a karyotype of 47,XX,+mar, and 47,XX,+?i(9p), respectively. Fluorescence in situ hybridization of the biotin-labeled DNA probe generated from 5 copies of the dissected marker chromosomes was applied to the normal metaphase spreads and revealed that the marker originated from the p arm of chromosomes 14 and 22, while the ?i(9p) was actually i(4p). Reverse painting of the same probe to the metaphase spreads of the patients completely painted the marker chromosomes in question, which confirms the accuracy of the analysis. Our study provides an example of the application of chromosome microdissection and molecular cytogenetics in prenatal diagnosis for the identification of marker chromosomes unidentifiable by routine analysis.

Wang, N.; Xu, J.; Cedrone, E. [Univ. of Rochester School of Medicine, Rochester, NY (United States)

1994-09-01

164

Topology reconstruction for B-Rep modeling from 3D mesh in reverse engineering applications  

NASA Astrophysics Data System (ADS)

Nowadays, most of the manufactured objects are designed using CAD (Computer-Aided Design) software. Nevertheless, for visualization, data exchange or manufacturing applications, the geometric model has to be discretized into a 3D mesh composed of a finite number of vertices and edges. But, in some cases, the initial model may be lost or unavailable. In other cases, the 3D discrete representation may be modified, for example after a numerical simulation, and does not correspond anymore to the initial model. A reverse engineering method is then required to reconstruct a 3D continuous representation from the discrete one. In previous work, we have presented a new approach for 3D geometric primitive extraction. In this paper, to complete our automatic and comprehensive reverse engineering process, we propose a method to construct the topology of the retrieved object. To reconstruct a B-Rep model, a new formalism is now introduced to define the adjacency relations. Then a new process is used to construct the boundaries of the object. The whole process is tested on 3D industrial meshes and bring a solution to recover B-Rep models.

Bénière, Roseline; Subsol, Gérard; Gesquière, Gilles; Le Breton, François; Puech, William

2012-02-01

165

Application of iTRAQ Reagents to Relatively Quantify the Reversible Redox State of Cysteine Residues  

PubMed Central

Cysteines are one of the most rarely used amino acids, but when conserved in proteins they often play critical roles in structure, function, or regulation. Reversible cysteine modifications allow for potential redox regulation of proteins. Traditional measurement of the relative absolute quantity of a protein between two samples is not always necessarily proportional to the activity of the protein. We propose application of iTRAQ reagents in combination with a previous thiol selection method to relatively quantify the redox state of cysteines both within and between samples in a single analysis. Our method allows for the identification of the proteins, identification of redox-sensitive cysteines within proteins, and quantification of the redox status of individual cysteine-containing peptides. As a proof of principle, we applied this technique to yeast alcohol dehydrogenase-1 exposed in vitro to H2O2 and also in vivo to the complex proteome of the Gram-negative bacterium Bacillus subtilis.

McDonagh, Brian; Martinez-Acedo, Pablo; Vazquez, Jesus; Padilla, C. Alicia; Sheehan, David; Barcena, Jose Antonio

2012-01-01

166

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

167

Refining a neural network credit application vetting system with a genetic algorithm  

Microsoft Academic Search

This paper describes how a simulated genetic process is used to automate the configuration and training of a back propagation trained multi-layer perceptron network used for credit application vetting. The network is trained on past loan case data, and is then used to classify the suitability of issuing credit on new loan applications. A prototype scheme for using a genetic

A. G. Williamson

1995-01-01

168

Exact and Approximation Algorithms for Sorting by Reversals, with Application to Genome Rearrangement  

Microsoft Academic Search

Motivated by the problem in computational biology of reconstructingthe series of chromosome inversions by which one organism evolved from another,we consider the problem of computing the shortest series of reversals that transformone permutation to another. The permutations describe the order of geneson corresponding chromosomes, and a reversal takes an arbitrary substring ofelements and reverses their order.For this problem we develop

John D. Kececioglu; David Sankoff

1995-01-01

169

Genetics  

MedlinePLUS

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

170

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

171

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

2006-09-01

172

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.

2014-01-01

173

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

PubMed

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

Enyeart, Peter J; Mohr, Georg; Ellington, Andrew D; Lambowitz, Alan M

2014-01-01

174

Interdependence of Hemagglutinin Glycosylation and Neuraminidase as Regulators of Influenza Virus Growth: a Study by Reverse Genetics  

PubMed Central

The hemagglutinin (HA) of fowl plague virus A/FPV/Rostock/34 (H7N1) carries two N-linked oligosaccharides attached to Asn123 and Asn149 in close vicinity to the receptor-binding pocket. In previous studies in which HA mutants lacking either one (mutants G1 and G2) or both (mutant G1,2) glycosylation sites had been expressed from a simian virus 40 vector, we showed that these glycans regulate receptor binding affinity (M. Ohuchi, R. Ohuchi, A. Feldmann, and H. D. Klenk, J. Virol. 71:8377–8384, 1997). We have now investigated the effect of these mutations on virus growth using recombinant viruses generated by an RNA polymerase I-based reverse genetics system. Two reassortants of influenza virus strain A/WSN/33 were used as helper viruses to obtain two series of HA mutant viruses differing only in the neuraminidase (NA). Studies using N1 NA viruses revealed that loss of the oligosaccharide from Asn149 (mutant G2) or loss of both oligosaccharides (mutant G1,2) has a pronounced effect on virus growth in MDCK cells. Growth of virus lacking both oligosaccharides from infected cells was retarded, and virus yields in the medium were decreased about 20-fold. Likewise, there was a reduction in plaque size that was distinct with G1,2 and less pronounced with G2. These effects could be attributed to a highly impaired release of mutant progeny viruses from host cells. In contrast, with recombinant viruses containing N2 NA, these restrictions were much less apparent. N1 recombinants showed lower neuraminidase activity than N2 recombinants, indicating that N2 NA is able to partly overrule the high-affinity binding of mutant HA to the receptor. These results demonstrate that N-glycans flanking the receptor-binding site of the HA molecule are potent regulators of influenza virus growth, with the glycan at Asn149 being dominant and that at Asn123 being less effective. In addition, we show here that HA and NA activities need to be highly balanced in order to allow productive influenza virus infection.

Wagner, Ralf; Wolff, Thorsten; Herwig, Astrid; Pleschka, Stephan; Klenk, Hans-Dieter

2000-01-01

175

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

176

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

177

Genetic Algorithms And Its Application To Economic Load Dispatch  

Microsoft Academic Search

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

Kavita Borana

2010-01-01

178

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

179

Second-law analysis and optimization of reverse brayton cycles of different configurations for cryogenic applications  

NASA Astrophysics Data System (ADS)

Second-law of thermodynamics (2nd law) and exergy analyses and optimization offour Reverse Brayton Refrigeration (RBR) cryogenic cycle configurations: Conventional 1-stage compression cycle; Conventional 2-stage compression cycle; 1-stage compressionModified cycle with intermediate cooling of the recuperator using an auxiliary cooler; andan Integrated 2-stage expansion RBR cycle are performed. The conventional RBR cyclesare analyzed for low and high pressure ratio applications using multistage compressorswith intercooling. Analytical solutions for the conventional cycles are developed includingthermal and fluid flow irreversibilities of the recuperators and all heat exchangers inaddition to the compression and expansion processes. Analytical solutions are used to findthe thermodynamic bounds for the performance of the cycles. Exergy irreversibilitydiagrams of the cycles are developed and the effects of important system parameters onRBR cycle performance are investigated. 2nd law/exergy analyses, and optimization of thecycles with intermediate cooling of the recuperator, considering the cooling temperatureand the recuperator effectiveness and pressure drop, are included. The effect of the 2ndlaw/exergy efficiency of the auxiliary cooler on the total system efficiencies is presented.

Streit, James Ryder; Razani, Arsalan

2012-06-01

180

Investigations on the Suitability of Coated Steel Piping System for High Pressure Seawater Reverse Osmosis Application  

NASA Astrophysics Data System (ADS)

This study deals with the investigations concerning with the suitability of coated steel piping system as an economically viable alternative to costly stainless steel piping for high pressure seawater reverse osmosis (SWRO) application. The piping system selected for investigation is a carbon steel piping coated internally and externally with thermoplastic coating (coating powder Plascoat PPA 571). The performance of thermoplastic coating was investigated by conducting SWRO pilot plant test, salt spray test, mechanical tests and testing of the coating under crevices (both in pilot plant and laboratory), and for leachable organics and inorganics (both in laboratory and pilot plant test). The testing of coating in the pilot plant resulted in the formation of some blisters on the internal surface of the pipes. The blisters were broken causing the corrosion of underneath steel. The coating showed a poor resistance to salt fog test. In general, the coating performed satisfactorily under the crevices but showed blistering on either side of the test panels. The adhesive strength of the coating was found to be poor; however, it showed good flexibility. The results of chemical analysis did not show the leaching of organic or inorganic pollutants from the coating.

Mobin, Mohammad

2010-03-01

181

Application of statistical design for the optimization of amino acid separation by reverse-phase HPLC.  

PubMed

Modified resolution and overall separation factors used to quantify the separation of complex chromatography systems are described. These factors were proven to be applicable to the optimization of amino acid resolution in reverse-phase (RP) HPLC chromatograms. To optimize precolumn derivatization with phenylisothiocyanate, a 2(5-1) fractional factorial design in triplicate was employed. The five independent variables for optimizing the overall separation factor were triethylamine content of the aqueous buffer, pH of the aqueous buffer, separation temperature, methanol/acetonitrile concentration ratio in the organic eluant, and mobile phase flow rate. Of these, triethylamine concentration and methanol/acetonitrile concentration ratio were the most important. The methodology captured the interaction between variables. Temperature appeared in the interaction terms; consequently, it was included in the hierarchic model. The preliminary model based on the factorial experiments was not able to explain the response curvature in the design space; therefore, a central composite design was used to provide a quadratic model. Constrained nonlinear programming was used for optimization purposes. The quadratic model predicted the optimal levels of the variables. In this study, the best levels of the five independent variables that provide the maximum modified resolution for each pair of consecutive amino acids appearing in the chromatograph were determined. These results are of utmost importance for accurate analysis of a subset of amino acids. PMID:18722994

Gheshlaghi, R; Scharer, J M; Moo-Young, M; Douglas, P L

2008-12-01

182

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

183

The application of genetic algorithm in model identification  

Microsoft Academic Search

A kind of improved genetic algorithm for identifying transfer function of thermal process in power plant is introduced. In the algorithm, floating-point coding, rank-based selection, elitist reservation and grouping method are used, the premature convergence is restrained, the global and local searching ability is improved. The genetic algorithm-based model identification MATLAB program is designed, the transfer functions of thermal process

Liu Changliang; Liu Jizhen; Niu Yuguang; Yao Wanye

2002-01-01

184

Detection of measles virus genome directly from clinical samples by reverse transcriptase-polymerase chain reaction and genetic variability  

Microsoft Academic Search

A simple and sensitive method for the detection of measles virus genome was developed, amplifying the regions encoding the nucleocapsid (N) protein and hemagglutinin (H) protein of measles virus by reverse transcriptase-polymerase chain reaction (RT-PCR). We examined a variety of measles patients: 28 patients with natural infection, 4 with measles encephalitis and 1 with subacute sclerosing panencephalitis (SSPE). In 28

Tetsuo Nakayama; Takayuki Mori; Shinya Yamaguchi; Satomi Sonoda; Sinnji Asamura; Ryoko Yamashita; Yoshinao Takeuchi; Takashi Urano

1995-01-01

185

nMOS reversible energy recovery logic for ultra-low-energy applications  

Microsoft Academic Search

We propose a new fully reversible adiabatic logic,nMOS reversible energy recovery logic (nRERL), which usesnMOS transistors only and a simpler 6-phase clocked power. Itsarea overhead and energy consumption are smaller, comparedwith the other fully adiabatic logics. We employed bootstrappednMOS switches to simplify the nRERL circuits. With the simulationresults for a full adder, we confirmed that the nRERL circuitconsumed substantially less

Joonho Lim; Dong-Gyu Kim; Soo-Ik Chae

2000-01-01

186

Application of perfluoropolyether reverse micelles in supercritical CO 2 to dyeing process  

Microsoft Academic Search

Dyeing of wool fabrics with conventional acid dyes in a supercritical CO2 has been investigated using a reverse micellar system. A reverse micelle composed of perfluoro 2,5,8,11-tetramethyl-3,6,9,12-tetraoxapentadecanoic acid ammonium salt\\/CO2\\/water had a high potential to solubilize conventional acid dyes and to dye wool fabrics in this system. It has found that dyeability of the acid dye on wool in this

J. H Jun; K Sawada; M Ueda

2004-01-01

187

Reverse traceroute  

Microsoft Academic Search

Traceroute is the most widely used Internet diagnos- tic tool today. Network operators use it to help identify routing failures, poor performance, and router misconfig- urations. Researchers use it to map the Internet, predict performance, geolocate routers, and classify the perfor- mance of ISPs. However, traceroute has a fundamental limitation that affects all these applications: it does not provide reverse

Ethan Katz-Bassett; Harsha V. Madhyastha; Colin Scott

188

Reverse traceroute  

Microsoft Academic Search

Traceroute is the most widely used Internet diagnostic tool today. Network operators use it to help identify routing fail- ures, pathinflation, androutermisconfigurations. Researchers use it to map the Internet, predict performance, geolocate routers, and classify the performance of ISPs. However, traceroute has long had a fundamental limitation that affects all these applications: it does not provide reverse path infor- mation.

Ethan Katz-Bassett; Harsha V. Madhyastha; Vijay Kumar Adhikari; Colin Scott; Justine Sherry; Peter van Wesep; Thomas E. Anderson; Arvind Krishnamurthy

2010-01-01

189

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

190

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.

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

2014-01-01

191

Genetics  

NSDL National Science Digital Library

This Genetics activity helps students to understand the basic principles of genetics, including concepts of recessive and dominant alleles, relationships of phenotype to genotype, Punnett squares, and pedigree analysis. The introductory section on inheritance of albinism demonstrates how understanding meiosis and fertilization provides the basis for understanding inheritance and Punnett squares. The next two sections, Coin Toss Genetics and analysis of class data on the sex makeup of sibships, help students understand the probabilistic nature of Punnett square predictions. The final activities analyze the genetics of sickle cell anemia and pedigrees for families with albinism and achondroplasia.

Doherty, Jennifer; Waldron, Ingrid; Poethig, Scott

192

Genetic System for Reversible Integration of DNA Constructs and lacZ Gene Fusions into the Escherichia coli Chromosome  

Microsoft Academic Search

A plasmid system for site-specific integration into and excision and recovery of gene constructs and lacZ gene fusions from the Escherichia coli chromosome was developed. Plasmid suicide vectors utilizing the origin of replication of R6K plasmids and containing the attP sequence of bacteriophage ?, multiple cloning site, and antibiotic resistance markers facilitate reversible integration into the E. coli chromosome by

Ratree Platt; Christopher Drescher; Sei-Kyoung Park; Gregory J. Phillips

2000-01-01

193

Mitochondrial and mitochondia-related nuclear genetic function in rabbit urinary bladder following reversal of outlet obstruction  

Microsoft Academic Search

Partial outlet obstruction of the rabbit urinary bladder causes increased tissue hypertrophy and decreased contractility of that organ; we showed that, in an experimental rabbit model, both correlate closely with alterations in the status and expression of mitochondrial (mt), and mt-related nuclear, genetic parameters in bladder smooth muscle. Here we investigate the rate and overall level of recovery of mt

Christina A. Nevel-McGarvey; Dorothea Rohrmann; Robert M. Levin; Alan P. Hudson

1999-01-01

194

Asymmetry in Family History Implicates Nonstandard Genetic Mechanisms: Application to the Genetics of Breast Cancer  

PubMed Central

Genome-wide association studies typically target inherited autosomal variants, but less studied genetic mechanisms can play a role in complex disease. Sex-linked variants aside, three genetic phenomena can induce differential risk in maternal versus paternal lineages of affected individuals: 1. maternal effects, reflecting the maternal genome's influence on prenatal development; 2. mitochondrial variants, which are inherited maternally; 3. autosomal genes, whose effects depend on parent of origin. We algebraically show that small asymmetries in family histories of affected individuals may reflect much larger genetic risks acting via those mechanisms. We apply these ideas to a study of sisters of women with breast cancer. Among 5,091 distinct families of women reporting that exactly one grandmother had breast cancer, risk was skewed toward maternal grandmothers (p<0.0001), especially if the granddaughter was diagnosed between age 45 and 54. Maternal genetic effects, mitochondrial variants, or variant genes with parent-of-origin effects may influence risk of perimenopausal breast cancer.

Weinberg, Clarice R.; Shi, Min; DeRoo, Lisa A.; Taylor, Jack A.; Sandler, Dale P.; Umbach, David M.

2014-01-01

195

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

196

Application of a genetic algorithm to wind turbine design  

Microsoft Academic Search

This paper presents an optimization method for stall-regulated horizontal-axis wind turbines. A hybrid approach is used that combines the advantages of a genetic algorithm with an inverse design method. This method is used to determine the optimum blade pitch and blade chord and twist distributions that maximize the annual energy production. To illustrate the method, a family of 25 wind

M. S. Selig; V. L. Coverstone-Carroll

1996-01-01

197

Application of Genetic/Genomic Approaches to Allergic Disorders  

PubMed Central

Completion of the human genome project and rapid progress in genetics and bioinformatics have enabled the development of large public databases, which include genetic and genomic data linked to clinical health data. With the massive amount of information available, clinicians and researchers have the unique opportunity to complement and integrate their daily practice with the existing resources to clarify the underlying etiology of complex phenotypes such as allergic diseases. The genome itself is now often utilized as a starting point for many studies and multiple innovative approaches have emerged applying genetic/genomic strategies to key questions in the field of allergy and immunology. There have been several successes, which have uncovered new insights into the biologic underpinnings of allergic disorders. Herein, we will provide an in depth review of genomic approaches to identifying genes and biologic networks involved in allergic diseases. We will discuss genetic and phenotypic variation, statistical approaches for gene discovery, public databases, functional genomics, clinical implications, and the challenges that remain.

Baye, Tesfaye M.; Martin, Lisa J.; Khurana Hershey, Gurjit K.

2010-01-01

198

Genetic Principles and Applications to the Genus Hemerocallis1  

Microsoft Academic Search

This paper is a review paper for the subsequent document on the Genus Hemerocallis. This paper establishes the baseline facts as are currently experimentally know and which are at the heart of understanding the genetics of the Genus Hemerocallis. This paper develops models which will be used elsewhere in the analysis and synthesis of color and patterning of the various

Terrence P. McGarty

199

Reverse micelle mediated synthesis, processing, mechanical and biological characterization of hydroxyapatite nanopowders for bone graft application  

NASA Astrophysics Data System (ADS)

Hydroxyapatite (HA) is the most widely used bioceramic material in bone graft applications because of its compositional similarity with natural bone. However, synthetic HA does not show similar mechanical and biological properties to the inorganic component of bone. Properties of ceramic material depend on starting materials, processing techniques, densification and microstructure of the final product. The objective of this research was to process HA whisker reinforced HA composite using HA nanopowders and whiskers. HA nanopowders with different length scale and morphology were synthesized by reverse micelle system using NP5 and NP12 as surfactants and cyclohexane as organic solvent. The lowest average aspect ratio was 1.357+/-0.39 with average particle size of 66 nm and the highest average aspect ratio was 7.277+/-3.227 with average length of 150 nm and width of 20 nm, were synthesized. Micron sized HA whiskers with aspect ratio between 20 and 50, average particle length of 15 mum and width of 400 nm was synthesized using urea as a precipitating agent. Desired microstructure was obtained after sintering with spherical HA nanopowder and whiskers along with dopants. Addition of whiskers decreased density of the sintered compacts. However, at 10 wt% whisker content sample showed microhardness and fracture toughness of 3.6 GPa and 1.5 MPa.m1/2, respectively, and a compressive strength of 80 MPa was obtained. Mineralization study in simulated body fluid (SBF) showed formation of apatite layer on the dense HA compacts indicating a good tendency of bond formation with natural bone. Cytotoxicity results showed excellent cell attachment on the HA surface. In the Appendices, 3 journal articles have been attached which describe synthesis, processing and characterization of undoped and doped PZT nanopowders. Free standing and agglomerated PZT nanopowders were synthesized by the sucrose templated method and the citrate nitrate autocombustion method. Particle size in the range of 50 to 90 nm was obtained. The effect of dopants on sintering and dielectric properties was studied by varying the amount of ZnO, SrO and La2O3 addition in PZT nanopowders. Sintering temperature of the bulk PZT was reduced to 900°C compared to the conventional sintering temperature of 1285°C and the highest dielectric constant of about 2100 was obtained.

Banerjee, Ashis

200

Application of the time reversal of electromagnetic fields to locate lightning discharges  

NASA Astrophysics Data System (ADS)

In this paper, we propose a new method for locating lightning discharges. The proposed method is based on the time reversal technique introduced for acoustics in the early 1990s. By analogy to the derivations in acoustics, equations for the focusing of electromagnetic fields back to the source by time reversal are derived. We show that the wavefronts generated by back-propagating the time-reversed fields will add up in phase at the lightning strike location. Based on this observation, we present an algorithm to locate lightning discharges which requires at least three field sensors. The algorithm is illustrated and shown to be very efficient using numerically-generated fields for different cases and considering different numbers of sensors.

Mora, N.; Rachidi, F.; Rubinstein, M.

2012-11-01

201

Solar cell reverse bias testing to meet new cell technology and satellite applications demands  

SciTech Connect

This paper examines the capabilities of specific silicon solar cell types to withstand reverse bias stresses resulting from or intensified by changes in cell technology and to withstand more severe shadowing conditions inherent in current satellite designs. Sample groups of cells were tested using voltages suggested by recent satellite mission requirements. The sample groups of cells had the following characteristics: shallow junctions (less than or equal to0.2 ..mu..m), back surface fields and reflectors, laser-scribed edges, and welded interconnects. Test results show high variability and leakiness among the reverse bias characteristics. Cell failures caused by reverse bias stresses under simulated mission conditions may become a significant consideration at -40 volts or less.

Williams, R.D.; Goodelle, G.S.; Mardesich, N.

1984-05-01

202

Solar cell reverse bias testing to meet new cell technology and satellite applications demands  

NASA Astrophysics Data System (ADS)

This paper examines the capabilities of specific silicon solar cell types to withstand reverse-bias stresses resulting from or intensified by changes in cell technology, and to withstand the more severe shadowing conditions inherent in current satellite designs. Sample groups of cells were tested using voltages suggested by recent satellite mission requirements. The sample groups of cells had the following characteristics: shallow junctions (less than 200 nm), back surface fields and reflectors, laser-scribed edges, and welded interconnects. Test results show high variability and leakiness among the reverse-bias characteristics. Cell failures caused by reverse-bias stresses under simulated mission conditions may become a significant consideration at -40 volts or less.

Williams, R. D.; Goodelle, G. S.; Mardesich, N.

203

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

204

Application of reverse transcription-PCR and real-time PCR in nanotoxicity research.  

PubMed

Reverse transcription-polymerase chain reaction (RT-PCR) is a relatively simple and inexpensive technique to determine the expression level of target genes and is widely used in biomedical science research including nanotoxicology studies for semiquantitative analysis. Real-time PCR allows for the detection of PCR amplification in the exponential growth phase of the reaction and is much more quantitative than traditional RT-PCR. Although a number of kits and reagents for RT-PCR and real-time PCR are commercially available, the basic principles are the same. Here, we describe the procedures for total RNA isolation by using TRI Reagent, for reverse transcription (RT) by M-MLV reverse transcriptase, and for PCR by GoTaq(®) DNA Polymerase. And real-time PCR will be performed on an iQ5 multicolor real-time PCR detection system by using iQ™ SYBR Green Supermix. PMID:22975959

Mo, Yiqun; Wan, Rong; Zhang, Qunwei

2012-01-01

205

[ISSR markers and their applications in plant genetics].  

PubMed

Recently, inter-simple sequence repeat (ISSR) markers have emerged as an alternative system with reliability and advantages of microsatellites (SSR). The technique involves amplification of genomic segments flanked by inversely oriented and closely spaced microsatellite sequences by a single primer or a pair of primers based on SSRs anchored 5' or 3' with 1-4 purine or pyramidine residues. The sequences of repeats and anchor nucleates are arbitrarily selected. Coupled with the separation of amplification products on a polyacrylamide or agarose gels,ISSR amplification can reveal a much larger number of fragments per primer than RAPD. It is concluded that ISSR technique provides a quick, reliable and highly informative system for DNA fingerprinting.ISSR markers are inherited in Mendelin mode and segregated as dominant markers. This technique has been widely used in the studies of cultivar identification, genetic mapping, gene tagging,genetic diversity, evolution and molecular ecology. PMID:16135460

Wang, Jian-bo

2002-09-01

206

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.

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

2012-01-01

207

Exploitation of genetically modified inoculants for industrial ecology applications  

Microsoft Academic Search

The major growth seen in the biotechnology industry in recent decades has largely been driven by the exploitation of genetic\\u000a engineering techniques. The initial benefits have been predominantly in the biomedical area, with products such as vaccines\\u000a and hormones that have received broad public approval. In the environmental biotechnology and industrial ecology sectors,\\u000a biotechnology has the potential to make significant

John P. Morrissey; Ultan F. Walsh; Anne O'Donnell; Yvan Moënne-Loccoz; Fergal O'Gara

2002-01-01

208

Hairy Root and Its Application in Plant Genetic Engineering  

Microsoft Academic Search

Abstract Agrobacterium rhizogenesConn. causes hairy root disease in plants. Hairy root-infected A. rhizogenesis char- acterized by a high growth,rate and genetic stability. Hairy root cultures have been proven,to be an efficient means,of producing secondary,metabolites that are normally biosynthesized in roots of differentiated plants. Furthermore, a transgenic root system offers tremendous potential for introducing additional genes along with the Ri plasmid,

Zhi-bi Huand; Min Du

2006-01-01

209

Temperature sensitive mutants of influenza A virus generated by reverse genetics and clustered charged to alanine mutagenesis.  

PubMed

Temperature sensitive (ts) mutants of influenza A virus have the potential to serve as live attenuated (att) virus vaccines. Previously, ts mutants were isolated by chemical mutagenesis or arose spontaneously, and most likely contained point mutations in one or more genes. While sufficiently attenuated, even the most genetically stable of these viruses was found to revert to a more virulent form in a seronegative vaccinee. Recently developed technology, however, allows the introduction of engineered mutations into the genome of influenza A and B viruses, permitting the rational design of attenuated mutants with the potential for increased genetic stability. To accomplish this goal, we have introduced ts mutations into the PB2 gene of A/Los Angeles/2/87 (H3N2) and rescued the mutated genes into infectious viruses. We have used clustered charged to alanine mutagenesis (substitution of alanine for charged amino acid residues which are present in clusters) of the PB2 gene to generate novel ts mutants. Viruses containing such ts PB2 genes were attenuated in mice and ferrets. This approach has thus yielded several vaccine candidates with ts and attenuated characteristics in animal models. Combination of these mutations with each other or with other ts mutations may lead to a high level of genetic stability. PMID:9029775

Parkin, N T; Chiu, P; Coelingh, K L

1996-12-01

210

DNA marker applications to molecular genetics and genomics in tomato.  

PubMed

Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding. PMID:23641178

Shirasawa, Kenta; Hirakawa, Hideki

2013-03-01

211

Fabrication of multiple electrodes by reverse EDM and their application in micro ECM  

Microsoft Academic Search

Micro electrodes of various shapes were fabricated by reverse electrical discharge machining (REDM). The machining characteristics of REDM were investigated under varying capacitances and applied voltages, and optimal conditions for stable machining were suggested. Multiple-tipped micro electrodes fabricated by REDM were then introduced for micro electrochemical machining in order to increase productivity over single micro electrodes. By using various multiple

Bo Hyun Kim; Byung Jin Park; Chong Nam Chu

2006-01-01

212

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

213

An invariance principle for reversible Markov processes. Applications to random motions in random environments  

Microsoft Academic Search

We present an invariance principle for antisymmetric functions of a reversible Markov process which immediately implies convergence to Brownian motion for a wide class of random motions in random environments. We apply it to establish convergence to Brownian motion (i) for a walker moving in the infinite cluster of the two-dimensional bond percolation model, (ii) for ad-dimensional walker moving in

A. De Masi; P. A. Ferrari; S. Goldstein; W. D. Wick

1989-01-01

214

Solar cell reverse bias testing to meet new cell technology and satellite applications demands  

Microsoft Academic Search

This paper examines the capabilities of specific silicon solar cell types to withstand reverse-bias stresses resulting from or intensified by changes in cell technology, and to withstand the more severe shadowing conditions inherent in current satellite designs. Sample groups of cells were tested using voltages suggested by recent satellite mission requirements. The sample groups of cells had the following characteristics:

R. D. Williams; G. S. Goodelle; N. Mardesich

1984-01-01

215

GLOBAL OPTIMIZATION OF REVERSE-FLOW GAS CYCLONES: APPLICATION TO SMALL-SCALE CYCLONE DESIGN  

Microsoft Academic Search

This paper addresses the optimum design of reverse-flow gas cyclones through the solution of 2 numerical nonlinear optimization problems that respectively maximize cyclone collection and an efficiency\\/cost ratio. The simulation model was based on the predictive properties of the 1998 finite diffusivity model of Mothes and Löffler, in which the particle turbulent dispersion coefficient is estimated through an empirical correlation

R. L. R. Salcedo; M. G. Cândido

2001-01-01

216

Application of double hot-wire anemometer for the detection of the flow reversal  

Microsoft Academic Search

In this paper the rational description of the sensor constructed to detect the flow reversal has been presented. The sensor consists of two parallel heated wires the distance between them is appointed in such a manner that the thermal interaction of wires may be observed. In the sensor the wires are connected in series, and they are supplied by one

Jan Kielbasa

2001-01-01

217

Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution  

Microsoft Academic Search

In comparative genomics, algorithms that sort permutations by reversals are often used to propose evolutionary scenarios of large-scale genomic mutations between species. One of the main problems of such methods is that they give one solution while the number of optimal solutions is huge, with no criteria to discriminate among them. Bergeron et al. started to give some structure to

Marília D. V. Braga; Marie-france Sagot; Celine Scornavacca; Eric Tannier

2008-01-01

218

Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution  

Microsoft Academic Search

In comparative genomics, algorithms that sort permutations by reversals are often used to propose evolutionary scenarios of rearrangements between species. One of the main problems of such methods is that they give one solution while the number of optimal solutions is huge, with no criteria to discriminate among them. Bergeron et al. started to give some structure to the set

Marília D. V. Braga; Marie-France Sagot; Celine Scornavacca; Eric Tannier

2008-01-01

219

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

220

Application and optimization in chromium-contaminated wastewater treatment of the reverse osmosis technology  

Microsoft Academic Search

Background: Chromium (Cr) is essential element used to plate other metals. Electroplating industry’s effluents are the most important sources of chromium pollution in the environment. This paper describes a study conducted to determine the efficiency of reverse-osmosis (RO) as a membrane filtration technique for removal of Cr from synthetic wastewater samples prepared similar to electroplating effluents. Methods: The RO unit

H. Mohammadi; Mitra Gholami; M. Rahimi

2009-01-01

221

Production of novel ebola virus-like particles from cDNAs: an alternative to ebola virus generation by reverse genetics.  

PubMed

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 10(3) 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

222

Genetic algorithms and genetic programming for multiscale modeling: Applications in materials science and chemistry and advances in scalability  

NASA Astrophysics Data System (ADS)

Effective and efficient rnultiscale modeling is essential to advance both the science and synthesis in a, wide array of fields such as physics, chemistry, materials science; biology, biotechnology and pharmacology. This study investigates the efficacy and potential of rising genetic algorithms for rnultiscale materials modeling and addresses some of the challenges involved in designing competent algorithms that solve hard problems quickly, reliably and accurately. In particular, this thesis demonstrates the use of genetic algorithms (GAs) and genetic programming (GP) in multiscale modeling with the help of two non-trivial case studies in materials science and chemistry. The first case study explores the utility of genetic programming (GP) in multi-timescaling alloy kinetics simulations. In essence, GP is used to bridge molecular dynamics and kinetic Monte Carlo methods to span orders-of-magnitude in simulation time. Specifically, GP is used to regress symbolically an inline barrier function from a limited set of molecular dynamics simulations to enable kinetic Monte Carlo that simulate seconds of real time. Results on a non-trivial example of vacancy-assisted migration on a surface of a face-centered cubic (fcc) Copper-Cobalt (CuxCo 1-x) alloy show that GP predicts all barriers with 0.1% error from calculations for less than 3% of active configurations, independent of type of potentials used to obtain the learning set of barriers via molecular dynamics. The resulting method enables 2--9 orders-of-magnitude increase in real-time dynamics simulations taking 4--7 orders-of-magnitude less CPU time. The second case study presents the application of multiobjective genetic algorithms (MOGAs) in multiscaling quantum chemistry simulations. Specifically, MOGAs are used to bridge high-level quantum chemistry and semiempirical methods to provide accurate representation of complex molecular excited-state and ground-state behavior. Results on ethylene and benzene---two common building blocks in organic chemistry---indicate that MOGAs produce High-quality semiempirical methods that (1) are stable to small perturbations, (2) yield accurate configuration energies on untested and critical excited states, and (3) yield ab initio quality excited-state dynamics. The proposed method enables simulations of more complex systems to realistic, multi-picosecond timescales, well beyond previous attempts or expectation of human experts, and 2--3 orders-of-magnitude reduction in computational cost. While the two applications use simple evolutionary operators, in order to tackle more complex systems, their scalability and limitations have to be investigated. The second part of the thesis addresses some of the challenges involved with a successful design of genetic algorithms and genetic programming for multiscale modeling. The first issue addressed is the scalability of genetic programming, where facetwise models are built to assess the population size required by GP to ensure adequate supply of raw building blocks and also to ensure accurate decision-making between competing building blocks. This study also presents a design of competent genetic programming, where traditional fixed recombination operators are replaced by building and sampling probabilistic models of promising candidate programs. The proposed scalable GP, called extended compact GP (eCGP), combines the ideas from extended compact genetic algorithm (eCGA) and probabilistic incremental program evolution (PIPE) and adaptively identifies, propagates and exchanges important subsolutions of a search problem. Results show that eCGP scales cubically with problem size on both GP-easy and GP-hard problems. Finally, facetwise models are developed to explore limitations of scalability of MOGAs, where the scalability of multiobjective algorithms in reliably maintaining Pareto-optimal solutions is addressed. The results show that even when the building blocks are accurately identified, massive multimodality of the search problems can easily overwhelm the nicher (diversity preserving operator) and l

Sastry, Kumara Narasimha

223

Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources  

PubMed Central

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively.

van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, Maria A.; Van Damme, Patrick; Garcia, Willman; Tapia, Cesar; Romero, Jose; Siguenas, Manuel; Hormaza, Jose I.

2012-01-01

224

[Initiative of introducing the applications of genetics for public health purposes in Poland].  

PubMed

An integration of scientific associations involved in public health and genetics to apply genetics achievements might create new perspectives of public health and health promotion in Poland and allow to apply genomic applications that are currently in transition from research to public health practice. Activities might enable to undertake preventive actions as population screening programs based on genome-based knowledge and technologies as targeted preventive interventions. The achievements in the field of public health genetics or genomics have been taking place in several countries and have begun to have an impact on population health status. PMID:22708309

Luty?ska, Anna; Krzysztof, Kuszewski; Wysocki, Miros?aw J

2012-01-01

225

Application of coevolutionary genetic algorithms for multiobjective optimization  

NASA Astrophysics Data System (ADS)

Multiobjective optimization is clearly one of the most important classes of problems in science and engineering. The solution of real problem involved in multiobjective optimization must satisfy all optimization objectives simultaneously, and in general the solution is a set of indeterminacy points. The task of multiobjective optimization is to estimate the distribution of this solution set, then to find the satisfying solution in it. Many methods solving multiobjective optimization using genetic algorithm have been proposed in recent twenty years. But these approaches tend to work negatively, causing that the population converges to small number of solutions due to the random genetic drift. To avoid this phenomenon, a multiobjective coevolutionary genetic algorithm (MoCGA) for multiobjective optimization is proposed. The primary design goal of the proposed approach is to produce a reasonably good approximation of the true Pareto front of a problem. In the algorithms, each objective corresponds to a population. At each generation, these populations compete among themselves. An ecological population density competition equation is used for reference to describe the relation between multiple objectives and to direct the adjustment over the relation at individual and population levels. The proposed approach store the Pareto optimal point obtained along the evolutionary process into external set. The proposed approach is validated using Schaffer's test function f2 and it is compared with the Niched Pareto GA (nPGA). Simulation experiments prove that the algorithm has a better performance in finding the Pareto solutions, and the MoCGA can have advantages over the other algorithms under consideration in convergence to the Pareto-optimal front.

Liu, Jian-guo; Li, Zu-shu; Wu, Wei-ping

2007-12-01

226

[Application of genetic polymorphisms in blood to forensic anthropology].  

PubMed

1. The Ainu subjects and, as controls, Wajin subjects obtained in the District of Hokkaido, were studied for blood groups, serum groups and red cell enzyme groups. The high n gene and r" gene frequencies seem to be characteristic in the distribution of the Ainu. In considering the high frequencies of Fya and Agx genes, low incidence K gene and Rh negative type, and existence of Di (a+) type, it is conceivable that the distribution of these blood group in the Ainu are closer to those in Mongoloid than to those in Caucasoid. The results of genetic distance analysis were in full agreement with the genetic affinity of the Ainu to the Mongoloid racial stock. According to the phylogenetic tree constructed on the basis of 16 polymorphic loci, it may be concluded that the Ainu are derived from the common stock of Mongoloids, which in turn has common ancestry with American Indians. The Negritos which are thought to be oldest living aborigines of southeast Asia and the western pacific. We investigated for grouping some genetic polymorphic traits from Negrito blood samples collected in the Philippines. A total of more than 500 samples were examined for 20 genetic traits. The most outstanding features of Negritos were as follows: Di (a+) type was found and all individuals were Lu (a-b +) and K-k+ types. Mia, Wra and Jsa genes were absent and all samples were U+ type. The existence of Dia gene and absence of both Lua and K genes are thought to suggest that the distribution of Negritos is quite close to that of Mongoloid populations. Fy (a-b-) and Js (a+) types are not found in our study. These results do not suggest similarity between Negritos and African. 2. The tandem repeat of a 28-base-pair (bp) sequence downstream of the human c-Ha-ras-1 oncogene was studied as a probe for DNA fingerprinting. Multiple hypervariable patterns were observed by Southern hybridization at low stringency. The patterns were specific to individuals, indicating the availability of the 28-bp repeat as a probe for DNA fingerprinting. Moreover, we cloned the tandem repeat of a 33-bp sequence, which cross-hybridized with the 28-bp repeat. This 33-bp repeat detected another set of hypervariable restriction fragments by Southern hybridization at the same stringency. These results suggest that "probe walking" can be employed to develop novel probes that provide different DNA fingerprints.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:1766142

Misawa, S

1991-08-01

227

Application of genetic algorithms in nonlinear heat conduction problems.  

PubMed

Genetic algorithms are employed to optimize dimensionless temperature in nonlinear heat conduction problems. Three common geometries are selected for the analysis and the concept of minimum entropy generation is used to determine the optimum temperatures under the same constraints. The thermal conductivity is assumed to vary linearly with temperature while internal heat generation is assumed to be uniform. The dimensionless governing equations are obtained for each selected geometry and the dimensionless temperature distributions are obtained using MATLAB. It is observed that GA gives the minimum dimensionless temperature in each selected geometry. PMID:24695517

Kadri, Muhammad Bilal; Khan, Waqar A

2014-01-01

228

Development and application of a reverse Monte Carlo radiative transfer code for rocket plume base heating  

NASA Technical Reports Server (NTRS)

A reverse Monte Carlo radiative transfer code to predict rocket plume base heating is presented. In this technique rays representing the radiation propagation are traced backwards in time from the receiving surface to the point of emission in the plume. This increases the computational efficiency relative to the forward Monte Carlo technique when calculating the radiation reaching a specific point, as only the rays that strike the receiving point are considered.

Everson, John; Nelson, H. F.

1993-01-01

229

Application of magnetized coaxial plasma gun for external control of field-reversed configuration  

Microsoft Academic Search

Magnetized coaxial plasma gun (MCPG) has been utilized to generate spheromak plasma. In this work, we propose to employ a MCPG as tools for pre-ionization, fueling and biasing of field- reversed configuration (FRC) plasma. Start-up experiments with a MCPG pre-ionization have been performed and a FRC has been formed successfully. In the case with a MCPG, the initial plasma density

Tomohiro Kiguchi; Taisuke Nishida; Naoki Yamamoto; Tomohiko Asai; Tsutomu Takahashi; Yasuyuki Nogi; Toshiki Takahashi

2006-01-01

230

Antisymmetric interface characteristics of reversible dual actions and its application to system design  

Microsoft Academic Search

This paper tries to characterize cognitive interface of interactions with the systems that do not divide people into users and non-users. From anti-symmetric characteristics of mobile phone and intenet\\/PC telecommunication, this paper draws a dynamic cognitive model based on reversible dual interactions, open and closed, with anti-symmetric interface characteristics. Closed (Open) interactions cause stronger (weaker) adaptations and telecommunication traffic biases,

Shinsuke Shimogawa

2005-01-01

231

Fabrication of multiple electrodes by reverse EDM and their application in micro ECM  

NASA Astrophysics Data System (ADS)

Micro electrodes of various shapes were fabricated by reverse electrical discharge machining (REDM). The machining characteristics of REDM were investigated under varying capacitances and applied voltages, and optimal conditions for stable machining were suggested. Multiple-tipped micro electrodes fabricated by REDM were then introduced for micro electrochemical machining in order to increase productivity over single micro electrodes. By using various multiple electrodes, micro hole arrays, grooves and channels were machined on stainless steel.

Kim, Bo Hyun; Park, Byung Jin; Chu, Chong Nam

2006-04-01

232

The application of matched filter and 'reversed' filter in coherent-on-receive system  

NASA Astrophysics Data System (ADS)

The problem of achieving the coherent-on-receive property using a matched filter and a 'reversed' filter is examined. Using this approach, the random initial pulse, the frequency jitter, the intrapulse frequency modulation, and the amplitude fluctuation of magnetron transmitted pulses can be compensated. Using high-speed digital signal processing and a highly stabilized receiver, an improvement factor of about 50 dB can be obtained for a magnetron radar.

Zhang, Peng; Sun, Zhong Kang

233

The application of matched filter and 'reversed' filter in coherent-on-receive system  

Microsoft Academic Search

The problem of achieving the coherent-on-receive property using a matched filter and a 'reversed' filter is examined. Using this approach, the random initial pulse, the frequency jitter, the intrapulse frequency modulation, and the amplitude fluctuation of magnetron transmitted pulses can be compensated. Using high-speed digital signal processing and a highly stabilized receiver, an improvement factor of about 50 dB can

Peng Zhang; Zhong Kang Sun

1986-01-01

234

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

235

Reversal of sterilization due to application of quinacrine by means of transcervical tubal catheterization.  

PubMed

The cornual and intramural scarring associated with quinacrine-induced female sterilization has been presumed to make this method irreversible. However, this article presents the cases of two women from Calcutta, India, with successful reversal achieved through transcervical catheterization with recanalization under fluoroscopic guidance. The first woman, age 28 years, had been sterilized five years earlier by three treatments with 252 mg of quinacrine; the second, age 22 years, had been sterilized two years before reversal request with two quinacrine doses. Recanalization of the proximal right tube was achieved in both cases through use of two or three catheterization systems in sequential order; attempts to repair the left tube resulted only in venous intravasation. The gritty sensation during guide-wire recanalization was consistent with fibrosis in the intramural portion of the fallopian tube. The availability of this technique may increase the acceptability of quinacrine sterilization, especially in countries such as Egypt and Indonesia where national family planning programs require that sterilization techniques are reversible. PMID:7703582

Thurmond, A S; Jones, M K; Mullick, B; Kessel, E

1995-01-01

236

Application of genetic algorithm to hexagon-based motion estimation.  

PubMed

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

Kung, Chih-Ming; Cheng, Wan-Shu; Jeng, Jyh-Horng

2014-01-01

237

Reverse pharmacognosy: application of selnergy, a new tool for lead discovery. The example of epsilon-viniferin.  

PubMed

The aim of reverse pharmacognosy is to find new biological targets for natural compounds by virtual or real screening and identify natural resources that contain the active molecules. To demonstrate the applicability of this concept, we report here a study on epsilon-viniferin, an active ingredient for cosmetic development. Nevertheless, this natural substance is weakly defined in terms of biological properties. SELNERGY, an inverse docking computer software, was used to identify putative binding biological targets for epsilon-viniferin. Among the 400 screened proteins two targets were retained. For cosmetic application, cyclic nucleotide phosphodiesterase 4 (PDE4) was the most interesting candidate. Moreover, other PDE subtypes (1, 2, 3, 5 and 6) were not retained, indicating a selectivity for PDE4. The experimental binding tests on the 6 subtypes of PDE revealed a significant selectivity of epsilon-viniferin for the PDE4 subtype. This selectivity was confirmed by evaluation of epsilon-viniferin on the secretion of TNF-alpha and Interleukin-8. Our data demonstrated that epsilon-viniferin possesses anti-inflammatory properties by inhibiting PDE4 subtype. In conclusion, reverse pharmacognosy and its inverse docking component cannot only be integrated into a program for new lead discovery but is also a useful approach to find new applications for identified compounds. PMID:16472225

Do, Quoc-Tuan; Renimel, Isabelle; Andre, Patrice; Lugnier, Claire; Muller, Christian D; Bernard, Philippe

2005-09-01

238

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

239

Detection by Reverse Transcription-PCR and Genetic Characterization of Field Isolates of Swine Hepatitis E Virus from Pigs in Different Geographic Regions of the United States  

PubMed Central

Hepatitis E virus (HEV) is an important public health concern in many developing countries. HEV is also endemic in some industrialized counties, including the United States. With our recent discovery of swine HEV in pigs that is genetically closely related to human HEV, hepatitis E is now considered a zoonotic disease. Human strains of HEV are genetically heterogenic. So far in the United States, only one strain of swine HEV has been identified and characterized from a pig. To determine the extent of genetic variations and the nature of swine HEV infections in U.S. pigs, we developed a universal reverse transcription-PCR (RT-PCR) assay that is capable of detecting genetically divergent strains of HEV. By using this universal RT-PCR assay, we tested fecal and serum samples of pigs of 2 to 4 months of age from 37 different U.S. swine farms for the presence of swine HEV RNA. Thirty-four of the 96 pigs (35%) and 20 of the 37 swine herds (54%) tested were positive for swine HEV RNA. The sequences of a 348-bp region within the ORF2 gene of 27 swine HEV isolates from different geographic regions were determined. Sequence analyses revealed that the 27 U.S. swine HEV isolates shared 88 to 100% nucleotide sequence identities with each other and 89 to 98% identities with the prototype U.S. strain of swine HEV. These U.S. swine HEV isolates are only distantly related to the Taiwanese strains of swine HEV, with about 74 to 78% nucleotide sequence identities; to most known human strains of HEV worldwide, with <79% sequence identities; and to avian HEV, with 54 to 56% sequence identities. Phylogenetic analysis showed that all the U.S. swine HEV isolates identified in this study clustered in the same genotype with the prototype U.S. swine HEV and the two U.S. strains of human HEV. The data from this study indicated that swine HEV is widespread and enzoonotic in U.S. swine herds and that, as is with human HEV, swine HEV isolates from different geographic regions of the world are also genetically heterogenic. These data further raise potential concerns for zoonosis, xenozoonosis, and food safety.

Huang, F. F.; Haqshenas, G.; Guenette, D. K.; Halbur, P. G.; Schommer, S. K.; Pierson, F. W.; Toth, T.E.; Meng, X. J.

2002-01-01

240

Application of Carbonate Reservoir using waveform inversion and reverse-time migration methods  

NASA Astrophysics Data System (ADS)

Recent exploration targets of oil and gas resources are deeper and more complicated subsurface structures, and carbonate reservoirs have become one of the attractive and challenging targets in seismic exploration. To increase the rate of success in oil and gas exploration, it is required to delineate detailed subsurface structures. Accordingly, migration method is more important factor in seismic data processing for the delineation. Seismic migration method has a long history, and there have been developed lots of migration techniques. Among them, reverse-time migration is promising, because it can provide reliable images for the complicated model even in the case of significant velocity contrasts in the model. The reliability of seismic migration images is dependent on the subsurface velocity models, which can be extracted in several ways. These days, geophysicists try to obtain velocity models through seismic full waveform inversion. Since Lailly (1983) and Tarantola (1984) proposed that the adjoint state of wave equations can be used in waveform inversion, the back-propagation techniques used in reverse-time migration have been used in waveform inversion, which accelerated the development of waveform inversion. In this study, we applied acoustic waveform inversion and reverse-time migration methods to carbonate reservoir models with various reservoir thicknesses to examine the feasibility of the methods in delineating carbonate reservoir models. We first extracted subsurface material properties from acoustic waveform inversion, and then applied reverse-time migration using the inverted velocities as a background model. The waveform inversion in this study used back-propagation technique, and conjugate gradient method was used in optimization. The inversion was performed using the frequency-selection strategy. Finally waveform inversion results showed that carbonate reservoir models are clearly inverted by waveform inversion and migration images based on the inversion results are quite reliable. Different thicknesses of reservoir models were also described and the results revealed that the lower boundary of the reservoir was not delineated because of energy loss. From these results, it was noted that carbonate reservoirs can be properly imaged and interpreted by waveform inversion and reverse-time migration methods. This work was supported by the Energy Resources R&D program of the Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Korea government Ministry of Knowledge Economy (No. 2009201030001A, No. 2010T100200133) and the Brain Korea 21 project of Energy System Engineering.

Kim, W.; Kim, H.; Min, D.; Keehm, Y.

2011-12-01

241

A graph-based genetic algorithm and its application to the multiobjective evolution of median molecules.  

PubMed

In this paper we propose a novel graph-based genetic algorithm for the evolution of novel molecular graphs from a predefined set of elements or molecular fragments with an external objective function. A brief overview of existing genetic algorithm approaches in molecular design is provided followed by a description of our approach. The paper continues to suggest a novel application of this program to the multiobjective evolution of median molecules that are structurally representative of a set of objective molecules. We conclude with a summary of our initial results along with a discussion of a variety of improvements and applications of our approach. PMID:15154776

Brown, Nathan; McKay, Ben; Gilardoni, François; Gasteiger, Johann

2004-01-01

242

Reverse Transcriptase.  

National Technical Information Service (NTIS)

Contents: Purification and properties of reverse transcriptase; Biosynthesis of reverse transcriptase; Differentiation of cellular DNA polymerases from reverse transcriptase; Characterization of reverse transcriptase complexes in vivo and in vitro; Revers...

1982-01-01

243

[Genetic anomalies of pancreatic carcinoma and clinical applications].  

PubMed

Pancreatic cancer is a dismal disease. The 5-years overall survival ranges from 1% to 5%. Surgery is the only curative treatment available. Survival of selected patients with small lesion (< 2 cm) confined to the pancreas is improved to 19-41%. Presently the major effort is on studies of the cancer development phenomena to improve detection of patients with early lesions. The analysis of oncogene and tumor-suppressor gene activation may enable us to better define and cure this disease. Molecular genetic new tecnquiques performed on pancreatic juice, duodenal juice and stool, probably are the most promising new approach for early diagnosis of pancreatic cancer. This could be the right path to diagnose pancreatic malignant lesions at a curable stage, and to discriminate patients with a more favourable prognosis candidates to be submitted to adjuvant therapy with a curative intent, and also to discriminate real pancreatic cancer from patients with chronic pancreatitis. PMID:11692539

Pantalone, D; Pelo, E; Minuti, B; Mazza, E; Nesi, G; Falchini, M; Ragionieri, I; Pantalone, F; Torricelli, F

2001-01-01

244

Application of genetic algorithms to lubrication pump stacking design  

NASA Astrophysics Data System (ADS)

Sizing a pump stacking used in an aircraft lubrication system is a challenging task. The combination of several pumps, in parallel and in a single casing, must deliver specified oil flow rates, on a variable number of circuits, and under given flight conditions. Furthermore, the optimal assembly has to minimize overall dimensions, weight and cost. This optimization problem involves a large space search, continuous and discrete variables and multi-objectives. Genetic Algorithms (GA)--stochastic search methods that mimic the metaphor of natural biological evolution--seem well suited to solve that kind of problems. A new GA is proposed. The efficiency of this GA is first demonstrated in solving various mathematical test-cases and then applied to the industrial problem.

Kelner, V.; Leonard, O.

2004-07-01

245

Development and Characterization of a Reverse Genetic System for Studying Dengue Virus Serotype 3 Strain Variation and Neutralization  

PubMed Central

Dengue viruses (DENV) are enveloped single-stranded positive-sense RNA viruses transmitted by Aedes spp. mosquitoes. There are four genetically distinct serotypes designated DENV-1 through DENV-4, each further subdivided into distinct genotypes. The dengue scientific community has long contended that infection with one serotype confers lifelong protection against subsequent infection with the same serotype, irrespective of virus genotype. However this hypothesis is under increased scrutiny and the role of DENV genotypic variation in protection from repeated infection is less certain. As dengue vaccine trials move increasingly into field-testing, there is an urgent need to develop tools to better define the role of genotypic variation in DENV infection and immunity. To better understand genotypic variation in DENV-3 neutralization and protection, we designed and constructed a panel of isogenic, recombinant DENV-3 infectious clones, each expressing an envelope glycoprotein from a different DENV-3 genotype; Philippines 1982 (genotype I), Thailand 1995 (genotype II), Sri Lanka 1989 and Cuba 2002 (genotype III) and Puerto Rico 1977 (genotype IV). We used the panel to explore how natural envelope variation influences DENV-polyclonal serum interactions. When the recombinant viruses were tested in neutralization assays using immune sera from primary DENV infections, neutralization titers varied by as much as ?19-fold, depending on the expressed envelope glycoprotein. The observed variability in neutralization titers suggests that relatively few residue changes in the E glycoprotein may have significant effects on DENV specific humoral immunity and influence antibody mediated protection or disease enhancement in the setting of both natural infection and vaccination. These genotypic differences are also likely to be important in temporal and spatial microevolution of DENV-3 in the background of heterotypic neutralization. The recombinant and synthetic tools described here are valuable for testing hypotheses on genetic determinants of DENV-3 immunopathogenesis.

Messer, William B.; Yount, Boyd; Hacker, Kari E.; Donaldson, Eric F.; Huynh, Jeremy P.; de Silva, Aravinda M.; Baric, Ralph S.

2012-01-01

246

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.

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

2011-01-01

247

Comparison of some reversible watermarking methods in application to medical images.  

PubMed

Several reversible watermarking schemes have been proposed for images of sensitive content, like medical imaging, for which any modification may affect their interpretation. In this work, we distinguish these methods according to the way watermark insertion is conducted: additive and substitutive. Some of these approaches have been tested on different sets of medical images issued from three distinct modalities: Magnetic Resonance Images, Positron Emission Tomography and Ultrasound Imaging. Comparison analysis has been conducted with respect to several aspects including data hiding capacity and image quality preservation. Experimental results show different limitations which depend on the watermark approach but also on image modality specificities. PMID:19963538

Pan, W; Coatrieux, G; Montagner, J; Cuppens, N; Cuppens, F; Roux, Ch

2009-01-01

248

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

249

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.

250

genetics  

NSDL National Science Digital Library

learning about our genetic make up We've been learning about DNA. Go to each web site, read and follow the instructions of the activities provided. On a piece of paper write your answers to the following questions and submit your work. Put the site for each of the questions you are answering. The first site is, ...

Curran, Carolyn

2011-12-05

251

An application of time-reversed acoustics to the imaging of a salt-dome flank  

NASA Astrophysics Data System (ADS)

We present results of applying the concept of time-reversed acoustics (TRA) to the imaging of a salt-dome flank in a v(z) medium. A simulated multi-level walk-away VSP survey with sources at the surface and receivers in the borehole can be sorted into an equivalent reverse VSP (RVSP) with effective downhole sources and surface receivers. We apply the TRA process to the RVSP traces and create a zero offset seismic section as if it had been collected from collocated downhole sources and receivers. This procedure effectively redatums the wavefield from the surface to the borehole, eliminating the need for any complicated processing. The redatummed traces are created by summing the autocorrelations of the traces in the RVSP common shot gather. Theory says that each shot gather should be from receivers which completely surround the source. From practical considerations, we only have available the RVSP common receivers on the earth's surface, so we obtain an approximate zero offset section. Even with this restriction, our example shows that the results are encouraging. The image of the salt dome flank is created from the redatummed traces using a standard post-stack depth migration algorithm. This image compares favorably with the salt dome flank model.

Willis, M. E.; Lu, R.; Campman, X.; Toksöz, N.; Zhang, Y.; de Hoop, M. V.

2005-12-01

252

Topological properties of the time-reversal-symmetric Kitaev chain and applications to organic superconductors  

NASA Astrophysics Data System (ADS)

We show that the pair of Majorana modes at each end of a 1D spin triplet superconductor with ???=-???=p?0 (two time reversed copies of the Kitaev p-wave chain) are topologically robust to perturbations such as mixing by the Sz=0 component of the order parameter (???=???), transverse hopping, nonagnetic disorder, and also, importantly, to time-reversal (TR) breaking perturbations such as applied Zeeman fields/magnetic impurities and the mixing by the Sy=0 component of the order parameter (???=???). We show that the robustness to TR-breaking results from a hidden chiral symmetry, which places the system in the BDI class in the presence of the generic TR-breaking perturbations (the TR-invariant system is both DIII and BDI). Our work has important implications for the quasi-1D organic superconductors (TMTSF)2X (X =PF6,CIO4) (Bechgaard salts) and Li0.9Mo6O17, which have been proposed as triplet superconductors with equal spin pairing (???,????0,???=0) in the presence of magnetic fields.

Dumitrescu, E.; Tewari, Sumanta

2013-12-01

253

[Application of Tm-shift genotyping method in genetic studies].  

PubMed

Melting Temperature shift (Tm-shift) is a new genotyping method. With two GC-rich tails of unequal length combined to 5'-terminal of allele-specific primers, genotypes can be determined by the distinct Tms of the PCR products with inspection of a melting curve on the real-time PCR machine. In this study, 29 SNPs were genotyped with 2 048 samples by using Tm-shift genotyping method, and the results were assessed by success rate, consistent rate, and accuracy. The results indicated that among 29 SNPs, 27 SNPs could be genotyped by Tm-shift. In other words, the success rate was 93.1%. The accuracy confirmed by direct sequencing was 100%. The consistency was 100% with 3 control samples, and 97% from a replication study in 100 samples. Thus, Tm-shift is a genotyping method with advantages including low cost, high accuracy, stability, reliability, flexible throughput, and easy operation, which can be applied to genetic studies widely. PMID:23208146

Yuan, Fang; Xu, Jin; Ji, Lin-Dan; Fei, Li-Juan; Liu, Pan-Pan; Zhang, Li-Na

2012-11-01

254

A Java collaborative interface for genetic programming applications: image analysis for scientific inquiry  

Microsoft Academic Search

Discusses several key issues involved in designing and using a Java collaborative interface for genetic programming applications over the World Wide Web. We present our implementation that has been used in a new system that assists scientists in classifying and extracting novel features in remotely sensed satellite imagery. This paper also identifies issues in developing a class library that facilitates

Tommaso F. Bersano-Begey; Jason M. Daida; John F. Vesecky; Frank L. Ludwig

1997-01-01

255

Green fluorescent protein-based reporter systems for genetic analysis of bacteria including monocopy applications  

Microsoft Academic Search

The green fluorescent protein (GFP) gene, gfp, was used to develop versatile reporter systems for genetic analysis in, and monitoring of bacteria. This reporter system is available on a plasmid and on a mini-transposon located in a suicide delivery plasmid for generation of chromosomal fusions. To achieve sensitivity levels necessary for use in monocopy applications and for detection of single

Antonio Suarez; Andrea Güttler; Michael Strätz; Lothar H Staendner; Kenneth N Timmis; Carlos A Guzmán

1997-01-01

256

An Application of a Plastic Optical Fiber Sensor and Genetic Algorithm for Structural Health Monitoring  

Microsoft Academic Search

This article demonstrates the potential of a new extrinsic plastic optical fiber (POF) sensor for vibration-based structural health monitoring (SHM) applications. A simple genetic algorithm (GA) is used in conjunction with the POF sensor. The construction and principle of operation of the intensity-based POF sensor used in the study is described, highlighting the advantages of the present sensor over previous

K. S. C. Kuang; M. Maalej; S. T. Quek

2006-01-01

257

Genetic machine learning approach for data fusion applications in dense Wireless Sensor Networks  

Microsoft Academic Search

Wireless sensor networks (WSN) are being targeted for use in applications like security, resources monitoring and factory automation. However, the reduced available resources raise a lot of technical challenges. Self-organization in WSN is a desirable characteristic that can be achieved by means of data fusion techniques when delivering reliable data to users. In this paper it is proposed a genetic

Alex R. Pinto; Benedito Bitencort; Mario A. R. Dantas; Carlos B. Montez; Francisco Vasques

2008-01-01

258

Application of Genetic Algorithm for the Reduction of Reactive Power Losses in Radial Distribution System  

Microsoft Academic Search

Power losses in distribution system have become the most concerned issue in power losses analysis in any power system. In the effort of reducing power losses within distribution system, reactive power compensation has become increasingly important as it affects the operational, economical and quality of service for electric power systems. This paper presents the application of genetic algorithm approach for

Perumal Nallagownden; L. T. Thin; N. C. Guan; C. M. H. Mahmud

2006-01-01

259

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

260

A homozygous mutant embryonic stem cell bank applicable for phenotype-driven genetic screening  

Microsoft Academic Search

Genome-wide mutagenesis in mouse embryonic stem cells (ESCs) is a powerful tool, but the diploid nature of the mammalian genome hampers its application for recessive genetic screening. We have previously reported a method to induce homozygous mutant ESCs from heterozygous mutants by tetracycline-dependent transient disruption of the Bloom's syndrome gene. However, we could not purify homozygous mutants from a large

Chikara Kokubu; Junko Yoshida; Keiko Akagi; Ayako Isotani; Akiko Oshitani; Kosuke Yusa; Ryuji Ikeda; Yue Huang; Allan Bradley; Kyoji Horie; Junji Takeda

2011-01-01

261

Parallelized genetic optimization of spatial light modulator addressing for diffractive applications.  

PubMed

We describe a new technique for optimizing the addressing of spatial light modulators in dynamic holographic applications. The method utilizes 200 times parallelization using imaging of subholograms in combination with genetic optimization. Compared to a fixed linear addressing curve for all different gratings, the diffraction efficiency can be improved by up to 25% for a Holoeye Pluto LCoS modulator. PMID:24663371

Haist, Tobias; Lingel, Christian; Adler, Rodolfo; Osten, Wolfgang

2014-03-01

262

Traffic Engineering for Hard Real Time Multicast Applications Using Genetic Algorithm  

Microsoft Academic Search

In this paper, the problem of finding a near-optimal routing solution for a set of real time applications with multicast traffic flows in a meshed core network is stud- ied. Such kind of network is typically a core network of automobile, airplane, or industry control networks. We will introduce our routing planning methodology based on a genetic algorithm, and will

Shu Zhang; Lothar Kreft; Ulrich Killat

263

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

264

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

265

Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus  

PubMed Central

Severe acute respiratory syndrome with high mortality rates (?50%) is associated with a novel group 2c betacoronavirus designated Middle East respiratory syndrome coronavirus (MERS-CoV). We synthesized a panel of contiguous cDNAs that spanned the entire genome. Following contig assembly into genome-length cDNA, transfected full-length transcripts recovered several recombinant viruses (rMERS-CoV) that contained the expected marker mutations inserted into the component clones. Because the wild-type MERS-CoV contains a tissue culture-adapted T1015N mutation in the S glycoprotein, rMERS-CoV replicated ?0.5 log less efficiently than wild-type virus. In addition, we ablated expression of the accessory protein ORF5 (rMERS•ORF5) and replaced it with tomato red fluorescent protein (rMERS-RFP) or deleted the entire ORF3, 4, and 5 accessory cluster (rMERS-?ORF3–5). Recombinant rMERS-CoV, rMERS-CoV•ORF5, and MERS-CoV-RFP replicated to high titers, whereas MERS-?ORF3–5 showed 1–1.5 logs reduced titer compared with rMERS-CoV. Northern blot analyses confirmed the associated molecular changes in the recombinant viruses, and sequence analysis demonstrated that RFP was expressed from the appropriate consensus sequence AACGAA. We further show dipeptidyl peptidase 4 expression, MERS-CoV replication, and RNA and protein synthesis in human airway epithelial cell cultures, primary lung fibroblasts, primary lung microvascular endothelial cells, and primary alveolar type II pneumocytes, demonstrating a much broader tissue tropism than severe acute respiratory syndrome coronavirus. The availability of a MERS-CoV molecular clone, as well as recombinant viruses expressing indicator proteins, will allow for high-throughput testing of therapeutic compounds and provide a genetic platform for studying gene function and the rational design of live virus vaccines.

Scobey, Trevor; Yount, Boyd L.; Sims, Amy C.; Donaldson, Eric F.; Agnihothram, Sudhakar S.; Menachery, Vineet D.; Graham, Rachel L.; Swanstrom, Jesica; Bove, Peter F.; Kim, Jeeho D.; Grego, Sonia; Randell, Scott H.; Baric, Ralph S.

2013-01-01

266

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

267

Modified high-accuracy 3D shape data conversion system for reverse engineering applications  

NASA Astrophysics Data System (ADS)

In the paper the sequential steps of reverse engineering based on the data gathered by full-field optical system are discussed. The compete conversion process of a cloud of point coordinates to CAD/CAM is presented. The triangulation algorithm, which automatically creates the triangle mesh from the input cloud of points is described. Each block of this algorithm is explained din details with special attention paid to the parameters controlling the quality of the data conversion process. The adaptive process of reducing the number of the triangles on the base of second derivative of local curvature of objects' surface is explained. The error analysis is discussed at each step of the cloud data processing in dependency of the algorithm initial parameters.

Sitnik, Robert; Kujawinska, Malgorzata

2001-10-01

268

A low distorsion and reversible watermark: application to angiographic images of the retina.  

PubMed

Medical image security can be enhanced using watermarking, which allows embedding the protection information as a digital signature, by modifying the pixel gray levels of the image. In this paper we propose a reversible watermarking scheme which guarantees that once the embedded message is read, alterations introduced during the insertion process can be removed from the image. Thereafter, original pixel gray levels of the image are restored. The proposed approach relies on estimation of image signal that is invariant to the insertion process, and permits to introduce a very slight watermark within the image. In fact, the insertion process adds or subtracts at least one gray level to the pixels of the original image. Depending on the image to be watermarked, in our case angiographic images of the retina, it is expected that such image alteration will not have any impact on the diagnosis quality, and consequently that the watermark can be kept within the image while this one is interpreted. PMID:17282674

Coatrieux, G; Puentes, J; Roux, C; Lamard, M; Daccache, W

2005-01-01

269

Genetic programme of cardiogenesis: implications for therapeutic application  

PubMed Central

It has become accepted that new cardiomyocytes can be derived from stem cells. Although the potential for therapeutic application is evident, the reported efficiency of differentiation varies greatly from 0.02 to 54%. To obtain clinically relevant numbers of newly differentiated cardiac cells, stem cell differentiation should be as efficient as possible. A plausible way to increase the efficiency of differentiation of stem cells into cardiomyocytes is through the introduction of cardiac specific regulatory genes in the stem cells. This review summarises the role of several key transcription factors in cardiogenesis.

van Tuyn, J.; de Vries, A.A.F.; van der Laarse, A.; Schalij, M.J.; van der Wall, E.E.; Atsma, D.E.

2004-01-01

270

Genetic variants in telomerase reverse transcriptase (TERT) and telomerase-associated protein 1 (TEP1) and the risk of male infertility.  

PubMed

Telomeres are critical in maintaining genomic stability and integrity, and telomerase expression in spermatogonial stem cells is responsible for the maintenance of telomere length in the human male germline. Genetic variants in telomere-associated pathway genes might affect telomere length and chromosomal stability, and subsequently disease susceptibility. Thus, we hypothesize that single nucleotide polymorphisms (SNPs) in this pathway could contribute to male infertility risk. In a case-control study of 580 male infertility cases and 580 matched controls, 8 common SNPs in telomerase reverse transcriptase (TERT) and telomerase-associated protein 1 (TEP1) were genotyped. Overall, we found that TERT rs2736100 was inversely associated with male infertility risk (adjusted odds ratio (OR)=0.66, 95% confidence interval (CI): 0.47-0.92; Ptrend=0.011), whereas TEP1 rs1713449 was positively associated with risk of male infertility (adjusted OR=1.39, 95% CI: 1.20-1.62; Ptrend<0.001). In addition, subjects carrying risk genotypes of these both loci had a two-fold (95% CI: 1.34-3.15) increase in the risk of male infertility, indicating a significant gene-gene interaction between these two loci (P for multiplicative interaction=0.009). Moreover, linear regression analysis showed that individuals carrying the TEP1 rs1713419 variants have significantly higher levels of sperm DNA fragmentation (?=2.243, P=0.016). In conclusion, our results give the first evidence that genetic variations of TERT rs2736100 and TEP1 rs1713449 were associated with susceptibility to male infertility. PMID:24269974

Yan, Lifeng; Wu, Shengmin; Zhang, Shenghu; Ji, Guixiang; Gu, Aihua

2014-01-25

271

ODS2: a multiplatform software application for creating integrated physical and genetic maps.  

PubMed Central

A contig map is a physical map that shows the native order of a library of overlapping genomic clones. One common method for creating such maps involves using hybridization to detect clone overlaps. False- positive and false-negative hybridization errors, the presence of chimeric clones, and gaps in library coverage lead to ambiguity and error in the clone order. Genomes with good genetic maps, such as Neurospora crassa, provide a means for reducing ambiguities and errors when constructing contig maps if clones can be anchored with genetic markers to the genetic map. A software application called ODS2 for creating contig maps based on clone-clone hybridization data is presented. This application is also designed to exploit partial ordering information provided by anchorage of clones to a genetic map. This information, along with clone-clone hybridization data, is used by a clone ordering algorithm and is represented graphically, allowing users to interactively align physical and genetic maps. ODS2 has a graphical user interface and is implemented entirely in Java, so it runs on multiple platforms. Other features include the flexibility of storing data in a local file or relational database and the ability to create full or minimum tiling contig maps.

Hall, D; Bhandarkar, S M; Wang, J

2001-01-01

272

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

273

Genetic algorithms  

NASA Technical Reports Server (NTRS)

Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

Wang, Lui; Bayer, Steven E.

1991-01-01

274

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

275

A "Reverse-Schur" Approach to Optimization With Linear PDE Constraints: Application to Biomolecule Analysis and Design  

PubMed Central

We present a partial-differential-equation (PDE)-constrained approach for optimizing a molecule’s electrostatic interactions with a target molecule. The approach, which we call reverse-Schur co-optimization, can be more than two orders of magnitude faster than the traditional approach to electrostatic optimization. The efficiency of the co-optimization approach may enhance the value of electrostatic optimization for ligand-design efforts–in such projects, it is often desirable to screen many candidate ligands for their viability, and the optimization of electrostatic interactions can improve ligand binding affinity and specificity. The theoretical basis for electrostatic optimization derives from linear-response theory, most commonly continuum models, and simple assumptions about molecular binding processes. Although the theory has been used successfully to study a wide variety of molecular binding events, its implications have not yet been fully explored, in part due to the computational expense associated with the optimization. The co-optimization algorithm achieves improved performance by solving the optimization and electrostatic simulation problems simultaneously, and is applicable to both unconstrained and constrained optimization problems. Reverse-Schur co-optimization resembles other well-known techniques for solving optimization problems with PDE constraints. Model problems as well as realistic examples validate the reverse-Schur method, and demonstrate that our technique and alternative PDE-constrained methods scale very favorably compared to the standard approach. Regularization, which ordinarily requires an explicit representation of the objective function, can be included using an approximate Hessian calculated using the new BIBEE/P (boundary-integral-based electrostatics estimation by preconditioning) method.

Bardhan, Jaydeep P.; Altman, Michael D.

2009-01-01

276

BAGGING OPTIMAL ROC CURVE METHOD FOR PREDICTIVE GENETIC TESTS, WITH AN APPLICATION FOR RHEUMATOID ARTHRITIS  

PubMed Central

Translation studies have been initiated to assess the combined effect of genetic loci from recently accomplished genome-wide association studies and the existing risk factors for early disease prediction. We propose a bagging optimal receiver operating characteristic (ROC) curve method to facilitate this research. Through simulation and real data application, we compared the new method with the commonly used allele counting method and logistic regression, and found that the new method yields a better performance. The new method was applied on the Wellcome Trust data set to form a predictive genetic test for rheumatoid arthritis. The formed test reached an area under the curve (AUC) value of 0.7.

Lu, Qing; Cui, Yuehua; Ye, Chengyin; Wei, Changshuai; Elston, Robert C.

2013-01-01

277

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.

Newman, Robert H.; Zhang, Jin

2014-01-01

278

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.

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

279

Molecular identification and genetic analysis of Norovirus genogroups I and II in water environments: comparative analysis of different reverse transcription-PCR assays.  

PubMed

Noroviruses have received increased attention in recent years because their role as etiologic agents in acute gastroenteritis outbreaks is now clearly established. Our inability to grow them in cell culture and the lack of an animal model hinder the characterization of these viruses. More recently, molecular approaches have been used to study the genetic relationships that exist among them. In the present study, environmental samples from seawater, estuarine water, and effluents of sewage treatment plants were analyzed in order to evaluate the role of environmental surface contamination as a possible vehicle for transmission of norovirus genogroups I and II. Novel broad-range reverse transcription-PCR/nested assays targeting the region coding for the RNA-dependent RNA polymerase were developed, amplifying fragments of 516 bp and 687 bp in the nested reactions for genogroups II and I, respectively. The assays were evaluated and compared against widely used published assays. The newly designed assays provide long regions for high-confidence BLAST searches in public databases and therefore are useful diagnostic tools for molecular diagnosis and typing of human noroviruses in clinical and environmental samples, as well as for the study of molecular epidemiology and the evolution of these viruses. PMID:17483265

La Rosa, G; Fontana, S; Di Grazia, A; Iaconelli, M; Pourshaban, M; Muscillo, M

2007-07-01

280

Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network  

PubMed Central

Gene expression profiles are an increasingly common data source that can yield insights into the functions of cells at a system-wide level. The present work considers the limitations in information content of gene expression data for reverse engineering regulatory networks. An in silico genetic regulatory network was constructed for this purpose. Using the in silico network, a formal identifiability analysis was performed that considered the accuracy with which the parameters in the network could be estimated using gene expression data and prior structural knowledge (which transcription factors regulate which genes) as a function of the input perturbation and stochastic gene expression. The analysis yielded experimentally relevant results. It was observed that, in addition to prior structural knowledge, prior knowledge of kinetic parameters, particularly mRNA degradation rate constants, was necessary for the network to be identifiable. Also, with the exception of cases where the noise due to stochastic gene expression was high, complex perturbations were more favorable for identifying the network than simple ones. Although the results may be specific to the network considered, the present study provides a framework for posing similar questions in other systems.

Zak, Daniel E.; Gonye, Gregory E.; Schwaber, James S.; Doyle, Francis J.

2003-01-01

281

[Reversible injection occlusion of vas deferens: animal experimentation and clinical application].  

PubMed

Liquid polyether-type polyurethane elastomer was injected vas deferens for contraception. It solidified at body temperature and became a thrombus plug which obstructed the duct and thus prevented spermatozoa from passing through. Preliminary studies in rabbits showed that the optimal volume of injected material should be 7.5 times the volume of 1 cm vas segment; the effective rate was 100%. Pathological sections of the obstructed segment of vas revealed no inflammation, adhesion, granulation, or scar tissue. This method was applied clinically in 1040 cases. 0.09-0.19 ml of the elastomer was injected into each vas percutaneously according to the caliber. Semen became free of spermatozoa in 98% of the cases 15-30 days after injection and the contraception rate was 100% effective. Complications occurred in 15 cases (1.44%), including 13 local infections and 2 hemaomas. Plugs were taken out quite easily in 5 cases and the sperm count indicated that in all cases, recanalization had taken place. This method of contraception is simple, effective, and reversible. (author's modified) PMID:12267912

Zhao, S C

1986-02-01

282

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

283

Equilibrium paradigm for field-reversed configurations and application to experiments  

NASA Astrophysics Data System (ADS)

Fresh insights on field-reversed configurations (FRCs) are incorporated in a new paradigm for equilibria. In particular four new or unappreciated properties are accounted for: an empirically based scrape-off layer thickness; a new, more accurate axial force balance relation; viscous force regularity at the O-point; and the broken-surface effect. The new paradigm corrects glaring defects of previous models (rigid rotor, Hill's vortex). Further, the new paradigm is simple enough to be easily used as an interpretive tool despite the limited data suite in most experiments. It is applied to the newly enhanced FRC data compendium, a database of 69 records from 15 facilities. Several important observations and corrections on the previous understanding of FRCs follow, three of which stand out. (1) The traditional axial force balance (``average-?'' relation) gives an inaccurate scaling with the separatrix-to-wall radius ratio. (2) The improved equilibrium paradigm yields separatrix particle transport rates of 3-5 m2/s for ``best confinement'' examples; this is a factor of three lower than crude ``bulk'' estimates commonly used. (3) The transport compared to the Bohm rate shows a great deal of scatter (40% scatter/mean ratio), i.e., ``Bohm'' is not a useful representation for transport scaling.

Steinhauer, Loren C.; Intrator, T. P.

2009-07-01

284

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

285

Performance and cost of energy transport and storage systems for dish applications using reversible chemical reactions  

NASA Technical Reports Server (NTRS)

The use of reversible chemical reactions for energy transport and storage for parabolic dish networks is considered. Performance and cost characteristics are estimated for systems using three reactions (sulfur-trioxide decomposition, steam reforming of methane, and carbon-dioxide reforming of methane). Systems are considered with and without storage, and in several energy-delivery configurations that give different profiles of energy delivered versus temperature. Cost estimates are derived assuming the use of metal components and of advanced ceramics. (The latter reduces the costs by three- to five-fold). The process that led to the selection of the three reactions is described, and the effects of varying temperatures, pressures, and heat exchanger sizes are addressed. A state-of-the-art survey was performed as part of this study. As a result of this survey, it appears that formidable technical risks exist for any attempt to implement the systems analyzed in this study, especially in the area of reactor design and performance. The behavior of all components and complete systems under thermal energy transients is very poorly understood. This study indicates that thermochemical storage systems that store reactants as liquids have efficiencies below 60%, which is in agreement with the findings of earlier investigators.

Schredder, J. M.; Fujita, T.

1984-01-01

286

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

NASA Astrophysics Data System (ADS)

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 Rossler 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, Kevin Andrew

287

[Application of genetically engineered mice model in the research of gastrointestinal tumor].  

PubMed

The gene knockout is based on the DNA homologous recombination and embryonic stem cell technology. It is an experimental method for modification of specific gene loci, which is one of the most direct means to clarifying gene functions. The similarity of genomes between mouse and human is as high as up to 95%. The life cycle of mice is relatively short, and easy to breed with stronger reproductive capacity. Therefore, the knockout mice are suitable for observing the whole process of disease pathogenesis. With genetic manipulation technology, researchers can produce the simulations of phenotypic effect by human genetic variation. This article focuses on genetically engineered mice models and their application in gastrointestinal cancer. PMID:24760653

Jiang, Yannan; Yu, Yingyan

2014-04-25

288

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

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

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

291

Genetics and alcoholism: how close are we to potential clinical applications?  

PubMed

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 and individual genes that likely contribute to the development of this condition. Most of these genes are related to neurotransmitter systems and to alcohol metabolizing enzymes. We briefly review the evidence for this before discussing intermediate phenotypes of alcoholism under genetic control, pharmacogenetic aspects of alcoholism treatment, and the possibility of future clinical applications based on these areas. PMID:16838828

Quickfall, Jeremy; el-Guebaly, Nady

2006-06-01

292

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.

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

2012-01-01

293

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.

294

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

295

Reversibility and Stability of ZnO-Sb2Te3 Nanocomposite Films for Phase Change Memory Applications.  

PubMed

(ZnO)x(Sb2Te3)1-x materials with different ZnO contents have been systemically studied with an aim of finding the most suitable composition for phase change memory applications. It was found that ZnO-doping could improve thermal stability and electrical behavior of Sb2Te3 film. Sb2Te3-rich nanocrystals, surrounded by ZnO-rich amorphous phases, were observed in annealed ZnO-doped Sb2Te3 composite films, and the segregated domains exhibited a relatively uniform distribution. The ZnO-doped Sb2Te3 composite films, especially with 5.2 at% ZnO concentration were found to have higher crystallization temperature, higher crystalline resistance, and faster crystallization speed in comparison with Ge2Sb2Te5. A reversible repetitive optical switching behavior can be observed in (ZnO)5.2(Sb2Te3)94.8, confirming that the ZnO doping is responsible for a fast switching and the compound is stable with cycling. Therefore, it is promising for the applications in phase change memory devices. PMID:24802948

Wang, Guoxiang; Chen, Yimin; Shen, Xiang; Li, Junjian; Wang, Rongping; Lu, Yegang; Dai, Shixun; Xu, Tiefeng; Nie, Qiuhua

2014-06-11

296

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

297

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

NASA Astrophysics Data System (ADS)

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.

1980-08-01

298

Nested Quantization Index Modulation for Reversible Watermarking and Its Application to Healthcare Information Management Systems  

PubMed Central

Digital watermarking has attracted lots of researches to healthcare information management systems for access control, patients' data protection, and information retrieval. The well-known quantization index modulation-(QIM-) based watermarking has its limitations as the host image will be destroyed; however, the recovery of medical images is essential to avoid misdiagnosis. In this paper, we propose the nested QIM-based watermarking, which is preferable to the QIM-based watermarking for the medical image applications. As the host image can be exactly reconstructed by the nested QIM-based watermarking. The capacity of the embedded watermark can be increased by taking advantage of the proposed nest structure. The algorithm and mathematical model of the nested QIM-based watermarking including forward and inverse model is presented. Due to algorithms and architectures of forward and inverse nested QIM, the concurrent programs and special processors for the nested QIM-based watermarking are easily implemented.

Ko, Lu-Ting; Chen, Jwu-E.; Shieh, Yaw-Shih; Hsin, Hsi-Chin; Sung, Tze-Yun

2012-01-01

299

Experimental Pathways towards Developing a Rotavirus Reverse Genetics System: Synthetic Full Length Rotavirus ssRNAs Are Neither Infectious nor Translated in Permissive Cells  

PubMed Central

At present the ability to create rationally engineered mutant rotaviruses is limited because of the lack of a tractable helper virus-free reverse genetics system. Using the cell culture adapted bovine RV RF strain (G6P6 [1]), we have attempted to recover infectious RV by co-transfecting in vitro transcribed ssRNAs which are identical in sequence to the positive sense strand of each of the 11 dsRNA genomic segments of the RF strain. The RNAs were produced either from cDNAs cloned by a target sequence-independent procedure, or from purified double layered RV particles (DLPs). We have validated their translational function by in vitro synthesis of 35S-labelled proteins in rabbit reticulocyte lysates; all 11 proteins encoded by the RV genome were expressed. Transfection experiments with DLP- or cDNA-derived ssRNAs suggested that the RNAs do not act independently as mRNAs for protein synthesis, once delivered into various mammalian cell lines, and exhibit cytotoxicity. Transfected RNAs were not infectious since a viral cytopathic effect was not observed after infection of MA104 cells with lysates from transfected cells. By contrast, an engineered mRNA encoding eGFP was expressed when transfected under identical conditions into the same cell lines. Co-expression of plasmids encoding NSP2 and NSP5 using a fowlpox T7 polymerase recombinant virus revealed viroplasm-like structure formation, but this did not enable the translation of transfected RV ssRNAs. Attempts to recover RV from ssRNAs transcribed intracellularly from transfected cDNAs were also unsuccessful and suggested that these RNAs were also not translated, in contrast to successful translation from a transfected cDNA encoding an eGFP mRNA.

Richards, James E.; Desselberger, Ulrich; Lever, Andrew M.

2013-01-01

300

Reverse Genetics Screen in Zebrafish Identifies a Role of miR-142a-3p in Vascular Development and Integrity  

PubMed Central

MicroRNAs are a well-studied class of non-coding RNA and are known to regulate developmental processes in eukaryotes. Their role in key biological processes such as vasculature development has attracted interest. However, a comprehensive understanding of molecular regulation of angiogenesis and vascular integrity during development remains less explored. Here we identified miRNAs involved in the development and maintenance of vasculature in zebrafish embryos using a reverse genetics approach. Using a combination of bioinformatics predictions and literature based evidences we mined over 701 Human and 329 Zebrafish miRNAs to derive a list of 29 miRNAs targeting vascular specific genes in zebrafish. We shortlisted eight miRNAs and investigated their potential role in regulating vascular development in zebrafish transgenic model. In this screen we identified three miRNAs, namely miR-1, miR-144 and miR-142a-3p that have the potential to influence vascular development in zebrafish. We show that miR-142a-3p mediates vascular integrity and developmental angiogenesis in vivo. Overexpression of miR-142a-3p results in loss of vascular integrity, hemorrhage and vascular remodeling during zebrafish embryonic development, while loss of function of miR-142a-3p causes abnormal vascular remodeling. MiR-142a-3p functions in part by directly repressing cdh5 (VE-cadherin). The vascular abnormalities that results from modulation of miR-142a-3p are reminiscent of cdh5 perturbation in zebrafish embryos. We also demonstrate that the action of miR-142a on cdh5 is potentially regulated by Lmo2, an important transcription factor, known for its role in vasculature development. The miR142a-3p mediated control of cdh5 constitutes an additional layer of regulation for maintaining vascular integrity and developmental angiogenesis. These findings have implications in development, wound repair and tumor growth.

Lalwani, Mukesh Kumar; Sharma, Meenakshi; Singh, Angom Ramcharan; Chauhan, Rajendra Kumar; Patowary, Ashok; Singh, Naresh; Scaria, Vinod; Sivasubbu, Sridhar

2012-01-01

301

Reverse-genetic approach to verify physiological roles of rice phytoalexins: characterization of a knockdown mutant of OsCPS4 phytoalexin biosynthetic gene in rice.  

PubMed

A variety of labdane-related diterpenoids, including phytocassanes, oryzalexins and momilactones, were identified as phytoalexins in rice (Oryza sativa L.). Momilactone B was also isolated as an allelochemical exuded from rice roots. The biosynthetic genes of these phytoalexins have been identified, including six labdane-related diterpene cyclase genes such as OsCPS2, OsCPS4, OsKSL4, OsKSL7, OsKSL8 and OsKSL10. Here we identified an OsCPS4 knockdown mutant, cps4-tos, by screening Tos17 mutant lines using polymerase chain reaction. OsCPS4 encodes a syn-copalyl diphosphate synthase responsible for momilactones and oryzalexin S biosynthesis. Because Tos17 was inserted into the third intron of OsCPS4, the mature OsCPS4 mRNA was detected in the cps4-tos mutant as well as the wild type. Nevertheless, mature OsCPS4 transcript levels in the cps4-tos mutant were about one sixth those in the wild type. The cps4-tos mutant was more susceptible to rice blast fungus than the wild type, possibly due to lower levels of momilactones and oryzalexin S in the mutant. Moreover, co-cultivation experiments suggested that the allelopathic effect of cps4-tos against some kinds of lowland weeds was significantly lower than that of the wild type, probably because of lower momilactone content exuded from cps4-tos roots. A reverse-genetic strategy using the cps4-tos mutant showed the possible roles of momilactones not only as phytoalexins but also as allelopathic substances. PMID:23621683

Toyomasu, Tomonobu; Usui, Masami; Sugawara, Chizu; Otomo, Kazuko; Hirose, Yuko; Miyao, Akio; Hirochika, Hirohiko; Okada, Kazunori; Shimizu, Takafumi; Koga, Jinichiro; Hasegawa, Morifumi; Chuba, Masaru; Kawana, Yoshiaki; Kuroda, Masaharu; Minami, Eiichi; Mitsuhashi, Wataru; Yamane, Hisakazu

2014-01-01

302

Reverse Algols  

NASA Technical Reports Server (NTRS)

Reverse Algols, binary systems with a semidetached configuration in which the more massive component is in contact with the critical equipotential surface, are examined. Observational evidence for reverse Algols is presented and the parameters of seven reverse Algols are listed. The evolution of Algols and reverse Algols is discussed. It is suggested that, because reverse Algols represent the premass-reversal semidetached phase of close binary evolution, the evolutionary time scale between regular and reverse Algols is the ratio of the number of confirmed systems of these two Algol types.

Leung, K. C.

1989-01-01

303

Reversible switches of DNA nanostructures between ``Closed'' and ``Open'' states and their biosensing applications  

NASA Astrophysics Data System (ADS)

A novel and versatile biosensing platform based on the structural conversion of 3D DNA nanostructures from ETDNA (Equilateral Triangle) to TPFDNA (Triangular Pyramid Frustum) was proposed for the first time. The inputs of aptamers and their relative targets made the DNA structure change from the ``Open'' to the ``Closed'' state, leading to the faradaic impedance changes as the output signals. The specific properties of excellent stability and specific rigid structure of 3D DNA nanostructures made the biosensor function as a regenerable, reusable and intelligent platform. The sensor exhibited excellent selectivity for IFN-? detection with a wide linear range of 1.0 × 10-9 to 2.0 × 10-6 M and a low detection limit of 5.2 × 10-10 M. The distinctive features of DNA nanostructures make them potentially advantageous for a broad range of biosensing, bionanoelectronics, and therapeutic applications.A novel and versatile biosensing platform based on the structural conversion of 3D DNA nanostructures from ETDNA (Equilateral Triangle) to TPFDNA (Triangular Pyramid Frustum) was proposed for the first time. The inputs of aptamers and their relative targets made the DNA structure change from the ``Open'' to the ``Closed'' state, leading to the faradaic impedance changes as the output signals. The specific properties of excellent stability and specific rigid structure of 3D DNA nanostructures made the biosensor function as a regenerable, reusable and intelligent platform. The sensor exhibited excellent selectivity for IFN-? detection with a wide linear range of 1.0 × 10-9 to 2.0 × 10-6 M and a low detection limit of 5.2 × 10-10 M. The distinctive features of DNA nanostructures make them potentially advantageous for a broad range of biosensing, bionanoelectronics, and therapeutic applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr01576a

Sheng, Qing-Lin; Liu, Rui-Xiao; Zheng, Jian-Bin; Zhu, Jun-Jie

2013-07-01

304

An updated definition of genet applicable to clonal seaweeds, bryophytes, and vascular plants  

Microsoft Academic Search

The genet of clonal plants is currently defined as the genetic individual that develops from the zy- gote and that produces ramets vegetatively. Genetic individuality refers to the fact that it is consid- ered to be a genetically uniform plant. However, somatic mutations may give rise to genetic mosaics within the genet, invalidating the assumption of its genetic uniformity. On

Ricardo Scrosati

2002-01-01

305

Prions: pathogenesis and reverse genetics.  

PubMed

Spongiform encephalopathies are a group of infectious neurodegenerative diseases. The infectious agent that causes transmissible spongiform encephalopathies was termed prion by Stanley Prusiner. The prion hypothesis states that the partially protease-resistant and detergent-insoluble prion protein (PrPsc) is identical with the infectious agent, and lacks any detectable nucleic acids. Since the latter discovery, transgenic mice have contributed many important insights into the field of prion biology. The prion protein (PrPc) is encoded by the Prnp gene, and disruption of Prnp leads to resistance to infection by prions. Introduction of mutant PrPc genes into PrPc-deficient mice was used to investigate structure-activity relationships of the PrPc gene with regard to scrapie susceptibility. Ectopic expression of PrPc in PrPc knockout mice proved a useful tool for the identification of host cells competent for prion replication. Finally, the availability of PrPc knockout and transgenic mice overexpressing PrPc allowed selective reconstitution experiments aimed at expressing PrPc in neurografts or in specific populations of hemato- and lymphopoietic cells. The latter studies helped in elucidating some of the mechanisms of prion spread and disease pathogenesis. PMID:11193143

Aguzzi, A; Klein, M A; Montrasio, F; Pekarik, V; Brandner, S; Furukawa, H; Käser, P; Röckl, C; Glatzel, M

2000-01-01

306

Applications of single-strand conformation polymorphism (SSCP) to taxonomy, diagnosis, population genetics and molecular evolution of parasitic nematodes  

Microsoft Academic Search

The analysis of genetic variation in parasitic nematodes has important implications for studying aspects of taxonomy, diagnosis, population genetics, drug resistance and molecular evolution. This article highlights some applications of PCR-based single-strand conformation polymorphism (SSCP) for the analysis of sequence variation in individual parasites (and their populations) to address some of these areas. It also describes the principles and advantages

Robin B. Gasser; Neil B. Chilton

2001-01-01

307

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

308

New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background  

PubMed Central

Background Few genetic factors predisposing to the sporadic form of amyotrophic lateral sclerosis (ALS) have been identified, but the pathology itself seems to be a true multifactorial disease in which complex interactions between environmental and genetic susceptibility factors take place. The purpose of this study was to approach genetic data with an innovative statistical method such as artificial neural networks to identify a possible genetic background predisposing to the disease. A DNA multiarray panel was applied to genotype more than 60 polymorphisms within 35 genes selected from pathways of lipid and homocysteine metabolism, regulation of blood pressure, coagulation, inflammation, cellular adhesion and matrix integrity, in 54 sporadic ALS patients and 208 controls. Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis Results Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis. An unexpected discovery of a strong genetic background in sporadic ALS using a DNA multiarray panel and analytical processing of the data with advanced artificial neural networks was found. The predictive accuracy obtained with Linear Discriminant Analysis and Standard Artificial Neural Networks ranged from 70% to 79% (average 75.31%) and from 69.1 to 86.2% (average 76.6%) respectively. The corresponding value obtained with Advanced Intelligent Systems reached an average of 96.0% (range 94.4 to 97.6%). This latter approach allowed the identification of seven genetic variants essential to differentiate cases from controls: apolipoprotein E arg158cys; hepatic lipase -480 C/T; endothelial nitric oxide synthase 690 C/T and glu298asp; vitamin K-dependent coagulation factor seven arg353glu, glycoprotein Ia/IIa 873 G/A and E-selectin ser128arg. Conclusion This study provides an alternative and reliable method to approach complex diseases. Indeed, the application of a novel artificial intelligence-based method offers a new insight into genetic markers of sporadic ALS pointing out the existence of a strong genetic background.

Penco, Silvana; Buscema, Massimo; Patrosso, Maria Cristina; Marocchi, Alessandro; Grossi, Enzo

2008-01-01

309

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.

2014-01-01

310

Solid-Phase Extraction and Reverse-Phase HPLC: Application to Study the Urinary Excretion Pattern of Benzophenone-3 and its Metabolite 2,4-Dihydroxybenzophenone in Human Urine  

PubMed Central

Background: Benzophenone-3 (BZ-3) is a common ultraviolet (UV) absorbing compound in sunscreens. It is the most bioavailable species of all UV-absorbing compounds after topical application and can be found in plasma and urine. Objectives: The aim of this study was to develop a reverse-phase high performance liquid chromatography (HPLC) method for determining the amounts BZ-3 and its metabolite 2,4-dihydroxybenzophenone (DHB) in human urine. The method had to be suitable for handling a large number of samples. It also had to be rapid and simple, but still sensitive, accurate and reproducible. The assay was applied to study the urinary excretion pattern after repeated whole-body applications of a commercial sunscreen, containing 4% BZ-3, to 25 healthy volunteers. Methods: Each sample was analyzed with regard to both conjugated/non-conjugated BZ-3 and conjugated/non-conjugated DHB, since both BZ-3 and DHB are extensively conjugated in the body. Solid-phase extraction (SPE) with C8 columns was followed by reverse-phase HPLC. For separation a Genesis C18 column was used with an acethonitrile-water mobile phase and the UV-detector was set at 287 nm. Results: The assay was linear r2 > 0.99, with detection limits for BZ-3 and DHB of 0.01 ?mol L?1 and 0.16 ?mol L?1 respectively. Relative standard deviation (RSD) was less than 10% for BZ-3 and less than 13% for DHB. The excretion pattern varied among the human volunteers; we discerned different patterns among the individuals. Conclusions: The reverse-phase HPLC assay and extraction procedures developed are suitable for use when a large number of samples need to be analyzed and the method fulfilled our objectives. The differences in excretion pattern may be due to differences in enzyme activity but further studies, especially about genetic polymorphism, need to be performed to verify this finding.

Gonzalez, Helena; Jacobson, Carl-Eric; Wennberg, Ann-Marie; Larko, Olle; Farbrot, Anne

2008-01-01

311

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.

Abdul-Muneer, P. M.

2014-01-01

312

[The application of xMAP technology in genetic typing of measles virus].  

PubMed

The genetic typing of measles virus in clinical samples using xMAP technology was applied. The study provided the calculation and application of specific oligonucleotide probes of genotypes D4, D6 and D7 of measles virus. The strain HobO96 genotype A of measles virus as a check sample was used. The technical approaches to the optimization of preparatory work organization and to the process of identification of measles virus genotypes are described. The presence of genotypes D4, D6 and D7 in clinical samples is proved by the sequence analysis. The genetic typing effectiveness of technique of DNA hybridization using xMAP technology on the instrumental base BioPlex (BioRad, USA) is demonstrated. PMID:22164419

Maksimov, N L; Agafonov, A P; Drozdov, I G

2011-08-01

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.

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

2010-01-01

314

Reversal of acute complex regional pain syndrome using the practical application of neurodiagnostic evaluation process: a case study.  

PubMed

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

315

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.

2008-09-22

316

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

317

Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: application to noninvasive sampling.  

PubMed

Species identification through noninvasive sampling is increasingly used in animal conservation genetics, given that it obviates the need to handle free-living individuals. Noninvasive sampling is particularly valuable for elusive and small species such as rodents. Although rodents are not usually assumed to be the most obvious target for conservation, of the 21 species or near-species present in Iberia, three are considered endangered and declining, while several others are poorly studied. Here, we develop a genetic tool for identifying all rodent species in Iberia by noninvasive genetic sampling. To achieve this purpose, we selected one mitochondrial gene [cytochrome b (cyt-b)] and one nuclear gene [interphotoreceptor retinoid-binding protein (IRBP)], which we first sequenced using tissue samples. Both genes allow for the phylogenetic distinction of all species except the sibling species Microtus lusitanicus and Microtus duodecimcostatus. Overall, cyt-b showed higher resolution than IRBP, revealing a clear barcoding gap. To allow these markers to be applied to noninvasive samples, we selected a short highly diagnostic fragment from each gene, which we used to obtain sequences from faeces and bones from owl pellets. Amplification success for the cyt-b and IRBP fragment was 85% and 43% in faecal and 88% and 64% in owl-pellet DNA extractions, respectively. The method allows the unambiguous identification of the great majority of Iberian rodent species from noninvasive samples, with application in studies of distribution, spatial ecology and population dynamics, and for conservation. PMID:23095787

Barbosa, S; Pauperio, J; Searle, J B; Alves, P C

2013-01-01

318

Neuro-Genetic Optimization of the Diffuser Elements for Applications in a Valveless Diaphragm Micropumps System  

PubMed Central

In this study, a hybridized neuro-genetic optimization methodology realized by embedding numerical simulations trained artificial neural networks (ANN) into a genetic algorithm (GA) is used to optimize the flow rectification efficiency of the diffuser element for a valveless diaphragm micropump application. A higher efficiency ratio of the diffuser element consequently yields a higher flow rate for the micropump. For that purpose, optimization of the diffuser element is essential to determine the maximum pumping rate that the micropump is able to generate. Numerical simulations are initially carried out using CoventorWare® to analyze the effects of varying parameters such as diffuser angle, Reynolds number and aspect ratio on the volumetric flow rate of the micropump. A limited range of simulation results will then be used to train the neural network via back-propagation algorithm and optimization process commence subsequently by embedding the trained ANN results as a fitness function into GA. The objective of the optimization is to maximize the efficiency ratio of the diffuser element for the range of parameters investigated. The optimized efficiency ratio obtained from the neuro-genetic optimization is 1.38, which is higher than any of the maximum efficiency ratio attained from the overall parametric studies, establishing the superiority of the optimization method.

Lee, Hing Wah; Azid, Ishak Hj Abdul

2009-01-01

319

Candida guilliermondii: biotechnological applications, perspectives for biological control, emerging clinical importance and recent advances in genetics.  

PubMed

Candida guilliermondii (teleomorph Meyerozyma guilliermondii) is an ascomycetous species belonging to the Saccharomycotina CTG clade which has been studied over the last 40 years due to its biotechnological interest, biological control potential and clinical importance. Such a wide range of applications in various areas of fundamental and applied scientific research has progressively made C. guilliermondii an attractive model for exploring the potential of yeast metabolic engineering as well as for elucidating new molecular events supporting pathogenicity and antifungal resistance. All these research fields now take advantage of the establishment of a useful molecular toolbox specifically dedicated to C. guilliermondii genetics including the construction of recipient strains, the development of selectable markers and reporter genes and optimization of transformation protocols. This area of study is further supported by the availability of the complete genome sequence of the reference strain ATCC 6260 and the creation of numerous databases dedicated to gene ontology annotation (metabolic pathways, virulence, and morphogenesis). These genetic tools and genomic resources represent essential prerequisites for further successful development of C. guilliermondii research in medical mycology and in biological control by facilitating the identification of the multiple factors that contribute to its pathogenic potential. These genetic and genomic advances should also expedite future practical uses of C. guilliermondii strains of biotechnological interest by opening a window into a better understanding of the biosynthetic pathways of valuable metabolites. PMID:23616192

Papon, Nicolas; Savini, Vincenzo; Lanoue, Arnaud; Simkin, Andrew J; Crèche, Joël; Giglioli-Guivarc'h, Nathalie; Clastre, Marc; Courdavault, Vincent; Sibirny, Andriy A

2013-08-01

320

Classification of rare missense substitutions, using risk surfaces, with genetic- and molecular-epidemiology applications.  

PubMed

Many individually rare missense substitutions are encountered during deep resequencing of candidate susceptibility genes and clinical mutation screening of known susceptibility genes. BRCA1 and BRCA2 are among the most resequenced of all genes, and clinical mutation screening of these genes provides an extensive data set for analysis of rare missense substitutions. Align-GVGD is a mathematically simple missense substitution analysis algorithm, based on the Grantham difference, which has already contributed to classification of missense substitutions in BRCA1, BRCA2, and CHEK2. However, the distribution of genetic risk as a function of Align-GVGD's output variables Grantham variation (GV) and Grantham deviation (GD) has not been well characterized. Here, we used data from the Myriad Genetic Laboratories database of nearly 70,000 full-sequence tests plus two risk estimates, one approximating the odds ratio and the other reflecting strength of selection, to display the distribution of risk in the GV-GD plane as a series of surfaces. We abstracted contours from the surfaces and used the contours to define a sequence of missense substitution grades ordered from greatest risk to least risk. The grades were validated internally using a third, personal and family history-based, measure of risk. The Align-GVGD grades defined here are applicable to both the genetic epidemiology problem of classifying rare missense substitutions observed in known susceptibility genes and the molecular epidemiology problem of analyzing rare missense substitutions observed during case-control mutation screening studies of candidate susceptibility genes. PMID:18951461

Tavtigian, Sean V; Byrnes, Graham B; Goldgar, David E; Thomas, Alun

2008-11-01

321

Classification of Rare Missense Substitutions, Using Risk Surfaces, With Genetic- and Molecular-Epidemiology Applications  

PubMed Central

Many individually rare missense substitutions are encountered during deep resequencing of candidate susceptibility genes and clinical mutation screening of known susceptibility genes. BRCA1 and BRCA2 are among the most resequenced of all genes, and clinical mutation screening of these genes provides an extensive data set for analysis of rare missense substitutions. Align-GVGD is a mathematically simple missense substitution analysis algorithm, based on the Grantham difference, which has already contributed to classification of missense substitutions in BRCA1, BRCA2, and CHEK2. However, the distribution of genetic risk as a function of Align-GVGD's output variables Grantham variation (GV) and Grantham deviation (GD) has not been well characterized. Here, we used data from the Myriad Genetic Laboratories database of nearly 70,000 full-sequence tests plus two risk estimates, one approximating the odds ratio and the other reflecting strength of selection, to display the distribution of risk in the GV-GD plane as a series of surfaces. We abstracted contours from the surfaces and used the contours to define a sequence of missense substitution grades ordered from greatest risk to least risk. The grades were validated internally using a third, personal and family history-based, measure of risk. The Align-GVGD grades defined here are applicable to both the genetic epidemiology problem of classifying rare missense substitutions observed in known susceptibility genes and the molecular epidemiology problem of analyzing rare missense substitutions observed during case-control mutation screening studies of candidate susceptibility genes.

Tavtigian, Sean V.; Byrnes, Graham B.; Goldgar, David E.; Thomas, Alun

2014-01-01

322

Defect Band Luminescence Intensity Reversal as Related to Application of Anti-Reflection Coating on mc-Si PV Cells: Preprint  

SciTech Connect

Photoluminescence (PL) imaging is widely used to identify defective regions within mc-Si PV cells. Recent PL imaging investigations of defect band luminescence (DBL) in mc-Si have revealed a perplexing phenomenon. Namely, the reversal of the DBL intensity in various regions of mc-Si PV material upon the application of a SiNx:H anti-reflective coating (ARC). Regions with low DBL intensity before ARC application often exhibit high DBL intensity afterwards, and the converse is also true. PL imaging alone cannot explain this effect. We have used high resolution cathodoluminescence (CL) spectroscopy and electron beam induced current (EBIC) techniques to elucidate the origin of the DBL intensity reversal. Multiple sub-bandgap energy levels were identified that change in peak position and intensity upon the application of the ARC. Using this data, in addition to EBIC contrast information, we provide an explanation for the DBL intensity reversal based on the interaction of the detected energy levels with the SiNx:H ARC application. Multiple investigations have suggested that this is a global problem for mc-Si PV cells. Our results have the potential to provide mc-Si PV producers a pathway to increased efficiencies through defect mitigation strategies.

Guthrey, H.; Johnston, S.; Yan, F.; Gorman, B.; Al-Jassim, M.

2012-06-01

323

Genetic model for longitudinal studies of aging, health, and longevity and its potential application to incomplete data.  

PubMed

Many longitudinal studies of aging collect genetic information only for a sub-sample of participants of the study. These data also do not include recent findings, new ideas and methodological concepts developed by distinct groups of researchers. The formal statistical analyses of genetic data ignore this additional information and therefore cannot utilize the entire research potential of the data. In this paper, we present a stochastic model for studying such longitudinal data in joint analyses of genetic and non-genetic sub-samples. The model incorporates several major concepts of aging known to date and usually studied independently. These include age-specific physiological norms, allostasis and allostatic load, stochasticity, and decline in stress resistance and adaptive capacity with age. The approach allows for studying all these concepts in their mutual connection, even if respective mechanisms are not directly measured in data (which is typical for longitudinal data available to date). The model takes into account dependence of longitudinal indices and hazard rates on genetic markers and permits evaluation of all these characteristics for carriers of different alleles (genotypes) to address questions concerning genetic influence on aging-related characteristics. The method is based on extracting genetic information from the entire sample of longitudinal data consisting of genetic and non-genetic sub-samples. Thus it results in a substantial increase in the accuracy of statistical estimates of genetic parameters compared to methods that use only information from a genetic sub-sample. Such an increase is achieved without collecting additional genetic data. Simulation studies illustrate the increase in the accuracy in different scenarios for datasets structurally similar to the Framingham Heart Study. Possible applications of the model and its further generalizations are discussed. PMID:19490866

Arbeev, Konstantin G; Akushevich, Igor; Kulminski, Alexander M; Arbeeva, Liubov S; Akushevich, Lucy; Ukraintseva, Svetlana V; Culminskaya, Irina V; Yashin, Anatoli I

2009-05-01

324

Linear score tests for variance components in linear mixed models and applications to genetic association studies.  

PubMed

Following the rapid development of genome-scale genotyping technologies, genetic association mapping has become a popular tool to detect genomic regions responsible for certain (disease) phenotypes, especially in early-phase pharmacogenomic studies with limited sample size. In response to such applications, a good association test needs to be (1) applicable to a wide range of possible genetic models, including, but not limited to, the presence of gene-by-environment or gene-by-gene interactions and non-linearity of a group of marker effects, (2) accurate in small samples, fast to compute on the genomic scale, and amenable to large scale multiple testing corrections, and (3) reasonably powerful to locate causal genomic regions. The kernel machine method represented in linear mixed models provides a viable solution by transforming the problem into testing the nullity of variance components. In this study, we consider score-based tests by choosing a statistic linear in the score function. When the model under the null hypothesis has only one error variance parameter, our test is exact in finite samples. When the null model has more than one variance parameter, we develop a new moment-based approximation that performs well in simulations. Through simulations and analysis of real data, we demonstrate that the new test possesses most of the aforementioned characteristics, especially when compared to existing quadratic score tests or restricted likelihood ratio tests. PMID:24328714

Qu, Long; Guennel, Tobias; Marshall, Scott L

2013-12-01

325

Application of a magnetized coaxial plasma gun for formation of a high-beta field-reversed configuration  

Microsoft Academic Search

We have tested a field-reversed configuration (FRC) formation with a spheromak injection for the first time. In this method, initial pre-ionized plasma is injected as a magnetized spheromak-like plasmoid into the discharge chamber prior to main field reversal. The FRC plasma with an electron density of 1.3×1021m?3, a separatrix radius of 0.04m and a plasma length of 0.8m was produced

T. Nishida; T. Kiguchi; T. Asai; T. Takahashi; Y. Matsuzawa; T. Okano; Y. Nogi

2006-01-01

326

Improvement of pixel electrode circuit for active-matrix OLED by application of reversed-biased voltage  

Microsoft Academic Search

In this paper, an improved ac pixel electrode circuit for active-matrix organic light-emitting display (AMOLED) has been proposed by adding a thin-film transistor. This circuit can provide an ac driving mode for AMOLED and makes the OLED in a reversed-biased voltage during the reverse cycle. And a circuit design for understanding ac driving mode was presented. The circuit simulation results

Yujuan Si; Liuqi Lang; Yi Zhao; Xinfa Chen; Shiyong Liu

2005-01-01

327

KI effects on the reversible electrodeposition of silver on poly(ethylene oxide) for application in electrochromic devices  

Microsoft Academic Search

A new approach to electrochromics, based on the reversible coating-dissolution of an oxide from an inorganic electrochromic electrolyte consisting of a silver–amine complex in a polymer electrolyte (PEO), has proven successful. The reversible electrodeposition of silver onto indium–tin oxide coated glass (ITO) was investigated and the influence of HClO4 and KI was evaluated.Several characteristics of the electrolyte Ag-PEO make it

M. R. S. Oliveira; D. A. A. Mello; E. A. Ponzio; S. C. de Oliveira

2010-01-01

328

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.

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

2014-01-01

329

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

330

Update: Biochemistry of Genetic Manipulation.  

ERIC Educational Resources Information Center

Various topics on the biochemistry of genetic manipulation are discussed. These include genetic transformation and DNA; genetic expression; DNA replication, repair, and mutation; technology of genetic manipulation; and applications of genetic manipulation. Other techniques employed are also considered. (JN)

Barker, G. R.

1983-01-01

331

Reverse Logistics  

Microsoft Academic Search

Environmental concerns and rapid development of e-commerce bring a new focused field in reverse logistics. In order to avoid return losses and add customerspsila value, there is a need for companies to find proper ways to reduce wastes and recover the value from used products for further utilities. All these challenges make reverse logistics a contemporary area of interest among

Chaihou Zhao; Weiming Liu; Bei Wang

2008-01-01

332

The Application of Random Regression Models in the Genetic Analysis of Monthly Egg Production in Turkeys and a Comparison with Alternative Longitudinal Models  

Microsoft Academic Search

Random regression models (RR) have be- come a popular methodology for the genetic study of longitudinal data since the last decade. The first objective of the current study was to investigate the application of RR models for the genetic analysis of egg production in turkeys. Data collected from a heavy dam line were used to estimate genetic parameters with 2

A. Kranis; G. Su; D. Sorensen; J. A. Woolliams

333

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

334

Genetic analysis of the roles of phytochromes A and B1 in the reversed gravitropic response of the lz-2 tomato mutant  

NASA Technical Reports Server (NTRS)

The lz-2 mutation in tomato (Lycopersicon esculentum) causes conditional reversal of shoot gravitropism by light. This response is mediated by phytochrome. To further elicit the mechanism by which phytochrome regulates the lz-2 phenotype, phytochrome-deficient lz-2 plants were generated. Introduction of au alleles, which severely block chromophore biosynthesis, eliminated the reversal of hypocotyl gravitropism in continuous red and far-red light. The fri1 and tri1 alleles were introduced to specifically deplete phytochromes A and B1, respectively. In dark-grown seedlings, phytochrome A was necessary for response to high-irradiance far-red light, a complete response to low fluence red light, and also mediated the effects of blue light in a far-red reversible manner. Loss of phytochrome B1 alone did not significantly affect the behaviour of lz-2 plants under any light treatment tested. However, dark-grown lz-2 plants lacking both phytochrome A and B1 exhibited reduced responses to continuous red and were less responsive to low fluence red light and high fluence blue light than plants that were deficient for phytochrome A alone. In high light, full spectrum greenhouse conditions, lz-2 plants grew downward regardless of the phytochrome deficiency. These results indicate that phytochromes A and B1 play significant roles in mediating the lz-2 phenotype and that at least one additional phytochrome is involved in reversing shoot gravitropism in this mutant.

Behringer, F. J.; Lomax, T. L.

1999-01-01

335

Time-Reversal Based Range Extension Technique for Ultra-Wideband (UWB) Sensors and Applications in Tactical Communications and Networking.  

National Technical Information Service (NTIS)

This technical report (quarterly) details the work for Office of Naval Research (ONR) by Tennessee Tech. The goal of this project jointly funded by ONR, NSF, and ARO is to build a general purpose testbed with time reversal capability at the transmitter si...

N. Guo P. Zhang R. C. Qiu Y. Song Z. Hu

2008-01-01

336

A novel application of time-reversed acoustics: Salt-dome flank imaging using walkaway VSP surveys  

Microsoft Academic Search

In this paper we present initial results of applying Time-Reversed Acoustics (TRA) technology to salt- dome flank, seismic imaging. We created a set of syn- thetic traces representing a multilevel, walkaway VSP for a model composed of a simplified Gulf of Mexico vertical-velocity gradient and an embedded salt dome. We first applied the concepts of TRA to the synthetic traces

Mark E. Willis; Rongrong Lu; Xander Campman; M. Nafi Toksöz; Yang Zhang; Maarten V. de Hoop

2006-01-01

337

Development and application of a reverse transcriptase polymerase chain reaction to detect Chinese isolates of duck hepatitis virus type 1  

Microsoft Academic Search

We developed a reverse transcriptase polymerase chain reaction (RT-PCR) method for the detection of duck hepatitis virus type 1 (DHV-1) in the tissues of infected and clinically affected ducks and in chick and duck embryos. We found the assay to be effective in detecting the virus in China, where it is being used in studies on the epidemiology of the

Cheng Anchun; Wang Mingshu; Xin Hongyi; Zhu Dekang; Li Xinran; Chen Haijuen; Jia Renyong; Yang Miao

2009-01-01

338

Use of Bayesian networks to dissect the complexity of genetic disease: application to the Genetic Analysis Workshop 17 simulated data  

PubMed Central

Complex diseases are often the downstream event of a number of risk factors, including both environmental and genetic variables. To better understand the mechanism of disease onset, it is of great interest to systematically investigate the crosstalk among various risk factors. Bayesian networks provide an intuitive graphical interface that captures not only the association but also the conditional independence and dependence structures among the variables, resulting in sparser relationships between risk factors and the disease phenotype than traditional correlation-based methods. In this paper, we apply a Bayesian network to dissect the complex regulatory relationships among disease traits and various risk factors for the Genetic Analysis Workshop 17 simulated data. We use the Bayesian network as a tool for the risk prediction of disease outcome.

2011-01-01

339

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.

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

2013-01-01

340

First application of a microsphere-based immunoassay to the detection of genetically modified organisms (GMOs): quantification of Cry1Ab protein in genetically modified maize.  

PubMed

An innovative covalent microsphere immunoassay, based on the usage of fluorescent beads coupled to a specific antibody, was developed for the quantification of the endotoxin Cry1Ab present in MON810 and Bt11 genetically modified (GM) maize lines. In particular, a specific protocol was developed to assess the presence of Cry1Ab in a very broad range of GM maize concentrations, from 0.1 to 100% [weight of genetically modified organism (GMO)/weight]. Test linearity was achieved in the range of values from 0.1 to 3%, whereas fluorescence signal increased following a nonlinear model, reaching a plateau at 25%. The limits of detection and quantification were equal to 0.018 and 0.054%, respectively. The present study describes the first application of quantitative high-throughput immunoassays in GMO analysis. PMID:17300145

Fantozzi, Anna; Ermolli, Monica; Marini, Massimiliano; Scotti, Domenico; Balla, Branko; Querci, Maddalena; Langrell, Stephen R H; Van den Eede, Guy

2007-02-21

341

Development and optimisation of a label-free quantitative proteomic procedure and its application in the assessment of genetically modified tomato fruit.  

PubMed

A key global challenge for plant biotechnology is addressing food security, whereby provision must be made to feed 9 billion people with nutritional feedstuffs by 2050. To achieve this step change in agricultural production new crop varieties are required that are tolerant to environmental stresses imposed by climate change, have better yields, are more nutritious and require less resource input. Genetic modification (GM) and marker-assisted screening will need to be fully utilised to deliver these new crop varieties. To evaluate these varieties both in terms of environmental and food safety and the rational design of traits a systems level characterisation is necessary. To link the transcriptome to the metabolome, quantitative proteomics is required. Routine quantitative proteomics is an important challenge. Gel-based densitometry and MS analysis after stable isotope labeling have been employed. In the present article, we describe the application of a label-free approach that can be used in combination with SDS-PAGE and reverse-phase chromatography to evaluate the changes in the proteome of new crop varieties. The workflow has been optimised for protein coverage, accuracy and robustness, then its application demonstrated using a GM tomato variety engineered to deliver nutrient dense fruit. PMID:23616442

Mora, Leticia; Bramley, Peter M; Fraser, Paul D

2013-06-01

342

Vasectomy reversal  

Microsoft Academic Search

Although vasectomy remains a popular method of contraception, the number of men requesting reversal has risen dramatically.\\u000a The microsurgical Techniques described in this article have yielded excellent results.

Roy A. Brandell; Marc Goldstein

2000-01-01

343

Application of Genetic Algorithms and Neural Networks to the Solution of Inverse Heat Conduction Problems A Tutorial  

Microsoft Academic Search

Genetic Algorithms and Neural Networks are relatively new techniques for optimization and estimation. These techniques can, of course, be applied to the solution of inverse problems. This paper presents a tutorial for application of these techniques to the solution of some simple inverse problems. A description of each of the techniques precedes presentation of the algorithms. MATLAB is used to

Keith A. Woodbury

344

Generalized Predictive Control Using Genetic Algorithms (GAGPC). An Application to Control of a Non-linear Process with Model Uncertainty  

Microsoft Academic Search

Abstract 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

Xavier Blasco Ferragud; Miguel Andres Martínez Iranzo; Juan S. Senent Español; Javier Sanchis

1998-01-01

345

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.

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

2011-01-01

346

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...

347

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

348

Four factor prothrombin complex concentrate (human): review of the pharmacology and clinical application for vitamin K antagonist reversal.  

PubMed

Vitamin K antagonists (VKAs) have been used for decades for the treatment and prophylaxis of thromboembolic events. Due to their wide range of therapeutic indications, they are the most prescribed oral anticoagulant worldwide. However, they are associated with bleeding complications due to their narrow therapeutic range, variability in individual dose responses and laboratory monitoring, and overdoses. Despite off-label use of 3-factor prothrombin complex concentrates and recombinant activated factor VII, until recently, vitamin K and plasma were the only recommended therapeutic options for reversing VKAs in the USA. In 2013, a 4-factor prothrombin complex concentrate (4F-PCC) was approved in the USA for VKA reversal in patients with bleeding or requiring emergency surgery and invasive procedure. Recent randomized controlled clinical trials have shown that 4F-PCC (Kcentra™) is non-inferior for hemostatic efficacy and superior for international normalized ratio correction as compared to plasma and has a similar safety profile. PMID:24650310

Kinard, Theresa N; Sarode, Ravi

2014-04-01

349

Reverse Phase HPLC Separation of Cis-and Trans-Carotenoids and Its Application to ?-Carotenes in Food Materials  

Microsoft Academic Search

Four trans-carotenoids, ?-carotene, ?-carotene, lutein and lycopene, were isomerized with light energy under iodine catalysis and the isomeric mixtures were subjected to reverse phase chromatography on a 5? VYDAC TP-201 column with mobile phases of methanol-chloroform to separate the major isomers. The amounts and properties of the cis-compounds conformed with separations obtained by others from lime and alumina columns. In

W. Forrest Quackenbush

1987-01-01

350

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.

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

2014-01-01

351

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

352

On the application of the genetic algorithm to the predictability problems involving "on-off" switches  

NASA Astrophysics Data System (ADS)

On the application of the genetic algorithm to the predictability problems involving "on-off" switches ZHENG Qin(1,2), DAI Yi(1), ZHANG Lu(1)and LU Xiaoqing(1) (1)Institute of Science, PLA University of Science and Technology, Nanjing 211101, China; (2)State Key Laboratory of Numerical Modeling for Atmospheric Sciences and Geophysical Fluid Dynamics (LASG), Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China Abstract The lower bound of maximum predictable time can be formulated into a constrained nonlinear optimization problem, and the traditional solution to this problem is the filtering method and the conditional nonlinear optimal perturbation (CNOP) method. Usually, the CNOP method is implemented with the help of a gradient descent algorithm based on the adjoint method, which is named as the ADJ-CNOP, hereinafter. However, with the increasing improvement of actual prediction models, more and more physical processes are taken into consideration in models in the form of parameterization, thus giving rise to the "on-off" switch problem, which affects tremendously the effectiveness of the conventional gradient descent algorithm based on the adjoint method. This paper attempts to apply a genetic algorithm (GA) to the CNOP method, named as the GA-CNOP, to solve the predictability problems involving the "on-off" switches. As the precision of the filtering method depends uniquely on the division of the constraint region, its results are taken as benchmarks and a series of comparisons between the ADJ-CNOP and the GA-CNOP are performed. It is revealed that the GA-CNOP can always figure out the accurate lower bound of maximum predictable time even in discontinuous cases, while the ADJ-CNOP, owing to the effect of "on-off" switches, often yields the incorrect lower bound of maximum predictable time. This would suggest that in non-smooth cases, using a GA to solve the predictability problems is more effective than using the conventional optimization algorithm based on gradients, as long as the genetic operators are properly configured.

Zheng, Q.

2011-12-01

353

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.

2013-01-01

354

Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies.  

PubMed

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

355

Application of trishear fault-propagation folding to active reverse faults: examples from the Dalong Fault, Gansu Province, NW China  

NASA Astrophysics Data System (ADS)

Determining accurate fault slip rates at 1 ka to 1 Ma timescales requires well-constrained palinspastic reconstructions of dateable geomorphic and/or geologic markers. Although general kinematic models have been developed to simultaneously reconstruct both bedrock (e.g. bedding and fault attitudes) and neotectonic markers (e.g. strath terraces) along active strike-slip and thrust faults, it is not clear if these models can also account for deformation along steeply dipping (>45°) reverse faults. To address this problem, we have investigated the active, ˜50° dipping, Dalong reverse fault system. This ˜40-km-long fault system forms part of the Aksai restraining stepover along the active, left-slip Altyn Tagh Fault in northwestern China. Our geometric and kinematic analyses show that conventional fault-bend fold models cannot satisfy the steeply-dipping fault geometry we observe in the bedrock record. Likewise, standard fault-propagation fold models fail to match our measurements of a set of fluvial terraces. However, by expanding the trishear model of fault-propagation folding to track both bedrock and neotectonic markers, we are able to match both sets of records. In particular, we have developed trishear kinematic models for two sites (Liuchenzi and Qingyazi) using the numerical modeling program, Fault/Fold v.5.0. This work indicates that an important implication of active trishear fault-propagation folding is that terrace deformation extends for over 1 km on either side of the fault trace. Thus, to accurately measure the total magnitude of vertical separation between matching terraces in the hanging wall and footwall, terrace profiles across active reverse faults must extend 1-2 km on either side of this zone of deformation.

Gold, Ryan D.; Cowgill, Eric; Wang, Xiao-Feng; Chen, Xuan-Hua

2006-02-01

356

Reversible Thermoelectric Nanomaterials  

Microsoft Academic Search

Irreversible effects in thermoelectric materials limit their efficiency and economy for applications in power generation and refrigeration. While electron transport is unavoidably irreversible in bulk materials, here we derive conditions under which reversible diffusive electron transport can be achieved in nanostructured thermoelectric materials. We provide a fundamental thermodynamic explanation for why the optimum density of states in a thermoelectric material

T. E. Humphrey; H. Linke

2005-01-01

357

Antenatal diagnosis of anophthalmia by three-dimensional ultrasound: a novel application of the reverse face view.  

PubMed

The prenatal diagnosis of anophthalmia can be made on the demonstration of absent eye globe and lens on the affected side(s) on two-dimensional ultrasound examination, but when the fetal head position is unfavorable three-dimensional (3D) ultrasound may reveal additional diagnostic sonographic features, including sunken eyelids and small or hypoplastic orbit on the affected side(s). We present two cases of isolated anophthalmia diagnosed on prenatal ultrasound examination in which 3D ultrasound provided additional diagnostic information. The reverse face view provides valuable information about the orbits and the eyeballs for prenatal diagnosis and assessment of anophthalmia. PMID:18570241

Wong, H S; Parker, S; Tait, J; Pringle, K C

2008-07-01

358

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.

Stuart, Gregory R.; Copeland, William C.; Strand, Micheline K.

2009-01-01

359

Application of genetic algorithms for the design of ozone control strategies.  

PubMed

Designing air quality management strategies is complicated by the difficulty in simultaneously considering large amounts of relevant data, sophisticated air quality models, competing design objectives, and unquantifiable issues. For many problems, mathematical optimization can be used to simplify the design process by identifying cost-effective solutions. Optimization applications for controlling nonlinearly reactive pollutants such as tropospheric ozone, however, have been lacking because of the difficulty in representing nonlinear chemistry in mathematical programming models. We discuss the use of genetic algorithms (GAs) as an alternative optimization approach for developing ozone control strategies. A GA formulation is described and demonstrated for an urban-scale ozone control problem in which controls are considered for thousands of pollutant sources simultaneously. A simple air quality model is integrated into the GA to represent ozone transport and chemistry. Variations of the GA formulation for multiobjective and chance-constrained optimization are also presented. The paper concludes with a discussion of the practically of using more sophisticated, regulatory-scale air quality models with the GA. We anticipate that such an approach will be practical in the near term for supporting regulatory decision-making. PMID:10902400

Loughlin, D H; Ranjithan, S R; Baugh, J W; Brill, E D

2000-06-01

360

Simultaneous feature selection and classification based on genetic algorithms: an application to colonic polyp detection  

NASA Astrophysics Data System (ADS)

Selecting a set of relevant features is a crucial step in the process of building robust classifiers. Searching all possible subsets of features is computationally impractical for large number of features. Generally, classifiers are used for the evaluation of the separability of a certain feature subset. The performance of these classifiers depends on some predefined parameters. However, the choice of these parameters for a given classifier is influenced by the given feature subset and vice versa. The computational cost for feature selection would be largely increased by including the selection of optimal parameters for the classifier (for each subset). This paper attempts to tackle the problem by introducing genetic algorithms (GAs) to combine the processes. The proposed approach can choose the most relevant features from a feature set whilst simultaneously optimising the parameters of the classifier. Its performance was tested on a colon polyp database from a cohort study using a weighted support vector machine (SVM) classifier. As a general approach, other classifiers such as artificial neural networks (ANN) and decision trees could be used. This approach could also be applied to other classification problems such as other computer aided detection/diagnosis applications.

Zheng, Yalin; Yang, Xiaoyun; Siddique, Musib; Beddoe, Gareth

2008-04-01

361

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

362

Genetically Modified Networks: A Genetic Algorithm contribution to Space Geodesy. Application to the transformation of SLR and DORIS EOP time series into ITRF2005.  

NASA Astrophysics Data System (ADS)

In this study, we apply Genetic Algorithms (GAs) in order to optimize the referencing (and consequently the precision - stability - and the accuracy) of the EOPs with respect to ITRF2005. These EOPs are derived from SLR or DORIS data at a daily sampling, simultaneously with weekly station positions. GAs are evolutionary algorithms, i.e. stochastic algorithms based on the evolution theory and using some genetic operators such as chromosome crossover and gene mutations. They are currently used for a broad spectrum of activities, from medicine to defence to finance. They have also been used in Earth and Space sciences (remote sensing, geophysics, meteorology, astrophysics, astronomy, etc.) since the early nineties. But, as far as we know, the present work is the first application of GAs in the framework of Space Geodesy. In this work, we use an algorithm based on GAs to find weekly optimal sub-networks over which applying minimum constraints in order to reference EOPs. Each week, the three rotations of the involved terrestrial frames are forced to be zero with respect to ITRF2005 through minimum constraints applied over these sub-networks, which are called Genetically Modified Networks (GMNs). The reference system effects are used as objectives to optimize with GAs. Regarding SLR, our approach provides an improvement of 10 % in accuracy for polar motion in comparison to the results obtained with the network specially designed for EOP referencing by the Analysis Working Group of the International Laser Ranging Service. This improvement of nearly 25 as represents 50 % of the current precision of the IERS 05 C04 reference series. We also show preliminary results regarding such GMNs for the DORIS technique using two different solutions (IGN and CNES/CLS solutions). Finally, for practical applications, we also test, for the SLR and the DORIS techniques, the possible emergence of global core networks to be used for EOP referencing on the basis of GAs.

Coulot, D.; Collilieux, X.; Pollet, A.; Berio, P.; Gobinddass, M. L.; Soudarin, L.; Willis, P.

2009-04-01

363

The Application of Parallel Multipopulation Genetic Algorithms to Dynamic Job-Shop Scheduling  

Microsoft Academic Search

This paper describes the use of parallel multipopulation genetic algorithms (GAs) to meet the dynamic nature of job-shop scheduling.\\u000a A modified genetic technique is adopted by using a specially formulated genetic operator to provide an efficient optimisation\\u000a search. The proposed technique has been successfully implemented using the programming language MATrix LABoratory (MATLAB),\\u000a providing a powerful tool for job-shop scheduling. Comparisons

J. G. Qi; G. R. Burns; D. K. Harrison

2000-01-01

364

Hypospadias in a male (78,XY; SRY-positive) dog and sex reversal female (78,XX; SRY-negative) dogs: clinical, histological and genetic studies.  

PubMed

Hypospadias is rarely reported in dogs. In this study we pre-sent 2 novel cases of this disorder of sexual development and, in addition, a case of hereditary sex reversal in a female with an enlarged clitoris. The first case was a male Moscow watchdog with a normal karyotype (78,XY) and the presence of the SRY gene. In this dog, perineal hypospadias, bilateral inguinal cryptorchidism and testes were observed. The second case, representing the Cocker spaniel breed, had a small penis with a hypospadic orifice of the urethra, bilateral cryptorchidism, testis and a rudimentary gonad inside an ovarian bursa, a normal female karyotype (78,XX) and a lack of the SRY gene. This animal was classified as a compound sex reversal (78,XX, SRY-negative) with the hypospadias syndrome. The third case was a Cocker spaniel female with an enlarged clitoris and internally located ovotestes. Cytogenetic and molecular analyses revealed a normal female karyotype (78,XX) and a lack of the SRY gene, while histology of the gonads showed an ovotesticular structure. This case was classified as a typical hereditary sex reversal syndrome (78,XX, SRY-negative). Molecular studies were focused on coding sequences of the SRY gene (case 1) and 2 candidates for monogenic hypospadias, namely MAMLD1 (mastermind-like domain containing 1) and SRD5A2 (steroid-5-alpha-reductase, alpha polypeptide 2). Sequencing of the entire SRY gene, including 5'- and 3'-flanking regions, did not reveal any mutation. The entire coding sequence of MAMLD1 and SRD5A2 was analyzed in all the intersexes, as well as in 4 phenotypically normal control dogs (3 females and 1 male). In MAMLD1 2 SNPs, including 1 missense substitution in exon 1 (c.128A>G, Asp43Ser), were identified, whereas in SRD5A2 7 polymorphisms, including 1 missense SNP (c.358G>A, Ala120Thr), were found. None of the identified polymorphisms cosegregated with the intersexual phenotype, thus, we cannot confirm that hypospadias may be associated with polymorphism in the coding sequence of the studied genes. PMID:21893969

Switonski, M; Payan-Carreira, R; Bartz, M; Nowacka-Woszuk, J; Szczerbal, I; Colaço, B; Pires, M A; Ochota, M; Nizanski, W

2012-01-01

365

Advancing genetic theory and application by metabolic quantitative trait loci analysis.  

PubMed

This review describes recent advances in the analysis of metabolism using quantitative genetics. It focuses on how recent metabolic quantitative trait loci (QTL) studies enhance our understanding of the genetic architecture underlying naturally variable phenotypes and the impact of this fundamental research on agriculture, specifically crop breeding. In particular, the role of whole-genome duplications in generating quantitative genetic variation within a species is highlighted and the potential uses of this phenomenon presented. Additionally, the review describes how new observations from metabolic QTL mapping analyses are helping to shape and expand the concepts of genetic epistasis. PMID:19525414

Kliebenstein, Danielj

2009-06-01

366

The clinical application of genetic testing in type 2 diabetes: a patient and physician survey  

Microsoft Academic Search

Aims\\/hypothesis  Advances in type 2 diabetes genetics have raised hopes that genetic testing will improve disease prediction, prevention and\\u000a treatment. Little is known about current physician and patient views regarding type 2 diabetes genetic testing. We hypothesised\\u000a that physician and patient views would differ regarding the impact of genetic testing on motivation and adherence.\\u000a \\u000a \\u000a \\u000a \\u000a Methods  We surveyed a nationally representative sample of

R. W. Grant; M. Hivert; J. C. Pandiscio; J. C. Florez; D. M. Nathan; J. B. Meigs

2009-01-01

367

Reverse Logistics.  

National Technical Information Service (NTIS)

The Army has a serious problem with materiel in the supply chain that is moving in the reverse direction. The supply chain is a series of inter- related processes and activities that move supplies and services from the suppliers to the ultimate end users....

J. L. Walden

2001-01-01

368

Genetic polymorphism in varietal identification and genetic improvement  

Microsoft Academic Search

New sources of genetic polymorphisms promise significant additions to the number of useful genetic markers in agricultural plants and animals, and prompt this review of potential applications of polymorphic genetic markers in plant and animal breeding. Two major areas of application can be distinguished. The first is based on the utilization of genetic markers to determine genetic relationships. These applications

M. Soller; J. S. Beckmann

1983-01-01

369

Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution: Exploring the applications of high-resolution genetic interaction mapping of point mutations.  

PubMed

We have achieved a residue-level resolution of genetic interaction mapping - a technique that measures how the function of one gene is affected by the alteration of a second gene - by analyzing point mutations. Here, we describe how to interpret point mutant genetic interactions, and outline key applications for the approach, including interrogation of protein interaction interfaces and active sites, and examination of post-translational modifications. Genetic interaction analysis has proven effective for characterizing cellular processes; however, to date, systematic high-throughput genetic interaction screens have relied on gene deletions or knockdowns, which limits the resolution of gene function analysis and poses problems for multifunctional genes. Our point mutant approach addresses these issues, and further provides a tool for in vivo structure-function analysis that complements traditional biophysical methods. We also discuss the potential for genetic interaction mapping of point mutations in human cells and its application to personalized medicine. PMID:24842270

Braberg, Hannes; Moehle, Erica A; Shales, Michael; Guthrie, Christine; Krogan, Nevan J

2014-07-01

370

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.

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

2010-01-01

371

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

372

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

373

Applications of Molecular Diagnostics: Solid Tumor Genetics Can Determine Clinical Treatment Protocols  

Microsoft Academic Search

Solid tumor diagnosis is now entering an era in which molecular genetics plays an important role. Clinical trials have shown different responses to various therapies that correlate with molecular alterations. Biological determinants related to treatment response markers aimed at individualized therapies are being defined and implemented. Patients are now being treated based on the profile of molecular genetic alterations in

2001-01-01

374

BP network model optimized using the genetic algorithms and the application on fault diagnose of equipments  

Microsoft Academic Search

The BP nerve network has been widely applied on fault diagnosis. The BP network due to adopt search arithmetic along grads drop, therefore there are some problems such as slow convergence rate and easily getting into local infinitesimal. The genetic algorithms has the excellence of rapid searching rate. Therefore, auto-adapt genetic algorithms is adopted to optimize the BP algorithms in

Meng Xianyao; Han Xinjie; Meng Song

2006-01-01

375

Advances in directed protein evolution by recursive genetic recombination: applications to therapeutic proteins  

Microsoft Academic Search

Recent developments in directed evolution technologies combined with innovations in robotics and screening methods have revolutionized protein engineering. These methods are being applied broadly to many fields of biotechnology, including chemical engineering, agriculture and human therapeutics. More specifically, DNA shuffling and other methods of genetic recombination and mutation have resulted in the improvement of proteins of therapeutic interest. Optimizing genetic

Aaron L Kurtzman; Sridhar Govindarajan; Katherine Vahle; Jennifer T Jones; Volker Heinrichs; Phillip A Patten

2001-01-01

376

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

377

Microsatellite loci in the carcinogenic liver fluke, Opisthorchis viverrini and their application as population genetic markers  

Microsoft Academic Search

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

Nonglak Laoprom; Paiboon Sithithaworn; Katsuhiko Ando; Jiraporn Sithithaworn; Sopit Wongkham; Thewarach Laha; Sirawut Klinbunga; Joanne P. Webster; Ross H. Andrews

2010-01-01

378

Cytogenetic map for Anopheles nili: Application for population genetics and comparative physical mapping  

Microsoft Academic Search

Anopheles nili is one of the major malaria vectors in Africa with a wide geographic distribution. However, the taxonomic and population genetic studies on this species are scarce. New research tools are urgently needed to genetically characterize this important malaria vector. In this study, a high-resolution cytogenetic map was developed for An. nili polytene chromosomes. Chromosomes were straightened and subdivided

Maria V. Sharakhova; Christophe Antonio-Nkondjio; Ai Xia; Cyrille Ndo; Parfait Awono-Ambene; Frederic Simard; Igor V. Sharakhov

2011-01-01

379

An empirical assessment of individual-based population genetic statistical techniques: application to British pig breeds  

PubMed Central

Recently developed Bayesian genotypic clustering methods for analysing genetic data offer a powerful tool to evaluate the genetic structure of domestic farm animal breeds. The unit of study with these approaches is the individual instead of the population. We aimed to empirically evaluate various individual-based population genetic statistical methods for characterization of genetic diversity and structure of livestock breeds. Eighteen British pig populations, comprising 819 individuals, were genotyped at 46 microsatellite markers. Three Bayesian genotypic clustering approaches, principle component analysis (PCA) and phylogenetic reconstruction were applied to individual multilocus genotypes to infer the genetic structure and diversity of the British pig breeds. Comparisons of the three Bayesian genotypic clustering methods (, and ) revealed some broad similarities but also some notable differences. Overall, the methods agreed that majority of the British pig breeds are independent genetic units with little evidence of admixture. The three Bayesian genotypic clustering methods provided complementary, biologically credible clustering solutions but at different levels of resolution. detected finer genetic differentiation and in some cases, populations within breeds. Consequently, it estimated a greater number of underlying genetic populations (K, in the notation of Bayesian clustering methods). Two of the Bayesian methods ( and ) and phylogenetic reconstruction provided similar success in assignment of individuals, supporting the use of these methods for breed assignment.

Wilkinson, S; Haley, C; Alderson, L; Wiener, P

2011-01-01

380

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

381

Application of restriction site amplified polymorphism (RSAP) to genetic diversity in Saccharina japonica  

NASA Astrophysics Data System (ADS)

Restriction site amplified polymorphism (RSAP) was used, for the first time, to analyze the genetic structure and diversity of four, mainly cultivated, varieties of the brown alga, Saccharina japonica. Eighty-eight samples from varieties " Rongfu ", " Fujian ", " Ailunwan " and " Shengchanzhong " were used for the genetic analyses. One hundred and ninety-eight bands were obtained using eight combinations of primers. One hundred and ninety-one (96.46%) were polymorphic bands. Nei's genetic diversity was 0.360, and the coefficient of genetic differentiation was 0.357. No inbreeding-type recession was found in the four brown alga varieties and the results of the " Ailunwan " variety using samples from 2 years showed that the variety was becoming less diverse during the selection inherent in the breeding program. Genetic diversity and cluster analyses results were consistent with these genetic relationships. The results show the RSAP method is suitable for genetic analysis. Continuous inbreeding and selection could reduce the genetic diversity effectively; therefore periodical supervision is required.

Zhao, Cui; Liu, Cui; Li, Wei; Chi, Shan; Feng, Rongfang; Liu, Tao

2013-07-01

382

Design of Efficient Reversible Binary Subtractors Based on a New Reversible Gate  

Microsoft Academic Search

Reversible logic has extensive applications in quantum computing, low power VLSI design, quantum dot cellular automata and optical computing. While several researchers have investigated the design of reversible logic elements, there is not much work reported on reversible binary subtractors. In this paper, we propose the design of a new reversible gate called TR gate. Further, we investigate the design

Himanshu Thapliyal; Nagarajan Ranganathan

2009-01-01

383

K-mer natural vector and its application to the phylogenetic analysis of genetic sequences.  

PubMed

Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency. PMID:24858075

Wen, Jia; Chan, Raymond H F; Yau, Shek-Chung; He, Rong L; Yau, Stephen S T

2014-08-01

384

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.

385

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.

2008-10-13

386

Reverse convection  

SciTech Connect

A model of magnetospheric topology for periods when the interplanetary magnetic field (IMF) points northward indicates that reverse convection can readily occur when Earth's dipole or the IMF tilt toward or away from the Sun. In either case, all or part of one tail lobe drapes over the dayside, and the magnetopause merging voltage is applied directly to the ionosphere in that lobe only, to the center or nightside of the polar cap. The overdraped lobe forms layers both earthward and sunward of the magnetopause, similar to layers observed during periods of northward IMF. The model predicts two quasi-steady state patterns of reverse convection: (1) lobe cells in the polar cap of the overdraped lobe, generated by open-to-open flux transfer at the magnetopause and (2) merging cells in both polar caps, generated by closed-to-open flux transfer at the magnetopause and balanced open-to-closed transfer at an internal reconnection site, comparable to the tail merging site for southward IMF. The model also predicts transitional patterns of reverse convection for growing and shrinking polar caps in response to changes in dipole tilt and B[sub x] and in response to a sudden transition from southward to northward IMF. The model predicts theta aurora bar formation on the dawnside polar cap boundary when activation of the internal reconnection site ends polar cap growth. In this view the theta aurora becomes the northward IMF counterpart to substorms.

Crooker, N.U. (Univ. of California, Los Angeles (United States))

1992-12-01

387

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

388

Tazarotene-induced gene 3 is suppressed in basal cell carcinomas and reversed in vivo by tazarotene application.  

PubMed

Basal cell carcinomas are the most common form of skin cancer. Tazarotene is a retinoic acid receptor selective retinoid that upregulates a tumor suppressor, tazarotene-induced gene 3 (TIG-3), in keratinocytes and psoriasis. Expression of TIG-3 in basal cell carcinomas was studied in an opened-label pilot biomarker study of 22 patients with basal cell carcinomas who applied tazarotene 0.1% gel for up to 12 wk prior to excision. Nineteen paired baseline and treated specimens were compared using immunohistochemistry and in situ hybridization. Compared to overlying normal epidermis, TIG-3 protein and mRNA were decreased in 14 and 18 of 19 basal cell carcinomas (74% and 95%), respectively (p < 0.001). Tazarotene treatment was associated with increased TIG-3 protein and mRNA expression in basal cell carcinomas compared to baseline levels (p < or = 0.001 and p = 0.028, respectively). Sixty percent of basal cell carcinomas treated with tazarotene decreased in size by at least 25%. Ten of 19 lesions improved histologically, including three complete responses. There was a correlation between the increased expression of TIG-3 protein and histologic improvement (p = 0.020), suggesting that suppression of TIG-3 may underlie the development of basal cell carcinomas. This association suggests that reversal of TIG-3 expression may help to explain the mechanism of retinoid action in epidermal differentiation and chemoprevention. PMID:14632211

Duvic, Madeleine; Ni, Xiao; Talpur, Rakhashandra; Herne, Kelly; Schulz, Claudia; Sui, Dawen; Ward, Staci; Joseph, Aaron; Hazarika, Parul

2003-10-01

389

Boron as a surrogate for N-nitrosodimethylamine rejection by reverse osmosis membranes in potable water reuse applications.  

PubMed

The results of this study reveal a strong linear correlation (R(2) = 0.95) between the rejections of boron and N-nitrosodimethylamine (NDMA) by six different reverse osmosis (RO) membranes, suggesting that boron can be used as a surrogate for NDMA rejection. This proposal is based on the premise that the rejection of both boric acid and NDMA is governed by steric hindrance and that they have similar molecular dimensions. The concept proposed here is shown to be valid at pH 8 or below where boron exists as the neutral boric acid species and NDMA is also a neutral solute. Observed changes in the rejections of these two species, as a function of permeate fluxes and feed solution temperatures, were also almost identical. Boron rejection increased from 21 to 79%, and the correlation coefficient of the linear regression between boron and NDMA rejections was 0.99 as the permeate flux increased from 5 to 60 L m(-2)h(-1). Similarly, a linear correlation between boron and NDMA rejections was observed as the feed solution temperature increased from 10 to 40 °C. This linear correlation was also validated in a tertiary treated effluent matrix. PMID:23668550

Tu, Kha L; Fujioka, Takahiro; Khan, Stuart J; Poussade, Yvan; Roux, Annalie; Drewes, Jörg E; Chivas, Allan R; Nghiem, Long D

2013-06-18

390

The application of microfiltration-reverse osmosis/nanofiltration to trace organics removal for municipal wastewater reuse.  

PubMed

The fate of organic micropollutans (MPs) in a membrane system based on microfiltration (MF) and reverse osmosis/nanofiltration (RO/NF) has been investigated for the case of wastewater reuse. Both an operating full-scale water reuse plant and a pilot plant were employed, with 22 individual organic compounds at their ambient concentrations studied for the former and the latter employing two target compounds over a range of feed concentrations. Results revealed removal efficiencies higher than 75% for most compounds in the full-scale plant, though mass flow studies on all streams revealed a significant imbalance of material for some compounds. Rejection efficiencies measured for candidate commercial NF and RO membranes tested at pilot scale challenged with a pharmaceutically active compound (ibuprofen, IBU) and an endocrine-disrupting chemical (nonylphenol, NP) exceeded 99%. Permeate concentrations were 0.005-0.14 microg/L for IBU and below the limit of detection for NP. A mass balance of the MPs for the full-scale plant across the MF and RO stages revealed a significant imbalance associated with the challenge of accurate determination of low concentrations. Differences in pilot plant and full-scale data were otherwise attributed to the impact of membrane ageing (and specifically hydrolysis) on RO rejection of the MPs examined. PMID:24617078

Garcia, N; Moreno, J; Cartmell, E; Rodriguez-Roda, I; Judd, S

2013-01-01

391

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

392

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

393

Reverse genetic characterization of two paralogous acetoacetyl CoA thiolase genes in Arabidopsis reveals their importance in plant growth and development.  

PubMed

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. PMID:22332816

Jin, Huanan; Song, Zhihong; Nikolau, Basil J

2012-06-01

394

Ternary Cu2SnS3 cabbage-like nanostructures: large-scale synthesis and their application in Li-ion batteries with superior reversible capacity  

NASA Astrophysics Data System (ADS)

In this paper, novel ternary Cu2SnS3 cabbage-like nanostructures are synthesized on a large scale via a facile solvothermal route. The individual Cu2SnS3 cabbage-like hierarchitecture is constructed from 2D nanosheets with thickness of about 15.6 nm. The Cu2SnS3 electrodes exhibit an initial reversible capacity of 842 mAh g-1 and still reach 621 mAh g-1 after 50 cycles. Such an admirable performance could be related to their 3D porous structural features as well as the high electrical conductivity induced by Cu. The electrochemical properties of the 3D hierarchical nanostructures imply its potential application in high energy density Li-ion batteries.

Qu, Baihua; Li, Hongxing; Zhang, Ming; Mei, Lin; Chen, Libao; Wang, Yanguo; Li, Qiuhong; Wang, Taihong

2011-10-01

395

Cancer risk assessment using genetic panel testing: considerations for clinical application.  

PubMed

With the completion of the Human Genome Project and the development of high throughput technologies, such as next-generation sequencing, the use of multiplex genetic testing, in which multiple genes are sequenced simultaneously to test for one or more conditions, is growing rapidly. Reflecting underlying heterogeneity where a broad range of genes confer risks for one or more cancers, the development of genetic cancer panels to assess these risks represents just one example of how multiplex testing is being applied clinically. There are a number of issues and challenges to consider when conducting genetic testing for cancer risk assessment, and these issues become exceedingly more complex when moving from the traditional single-gene approach to panel testing. Here, we address the practical considerations for clinical use of panel testing for breast, ovarian, and colon cancers, including the benefits, limitations and challenges, genetic counseling issues, and management guidelines. PMID:24599651

Hiraki, Susan; Rinella, Erica S; Schnabel, Freya; Oratz, Ruth; Ostrer, Harry

2014-08-01

396

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.

Sun, Xue; Yu, Weihui; Hu, Cheng

2014-01-01

397

Containment of a genetically engineered microorganism during a field bioremediation application  

Microsoft Academic Search

A field release of a genetically engineered microorganism was performed at the Field Lysimeter Site on the Oak Ridge Reservation.\\u000a Six large lysimeters were filled with soil that had been contaminated with a mixture of naphthalene, phenanthrene, and anthracene.\\u000a A genetically engineered bacterial strain, Pseudomonas fluorescens HK44, was sprayed onto the surface of the soil during soil loading. This strain

C. Z. Ford; G. S. Sayler; R. S. Burlage

1999-01-01

398

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

399

Application of Genetic Bit Analysis (GBA TM ) for allelic selection in plant breeding  

Microsoft Academic Search

Genetic Bit Analysis (GBA) is a relatively new technique developed to score single-nucleotide polymorphisms among alleles. It is currently being used as a genetic diagnostic tool in human paternity tests as well as in pedigree analysis of farm animals. GBA relies on the polymerase chain reaction and enzyme-linked colorimetry to distinguish differences among genotypes. The identification of a single-nucleotide polymorphism

Josefina Alcala; James J. Giovannoni; Leonard M. Pike; Avutu S. Reddy

1997-01-01

400

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.

Valcarcel, Beatriz; Ebbels, Timothy M. D.; Kangas, Antti J.; Soininen, Pasi; Elliot, Paul; Ala-Korpela, Mika; Jarvelin, Marjo-Riitta; de Iorio, Maria

2014-01-01

401

Development and application of SINE multilocus and quantitative genetic markers to study oilseed rape (Brassica napus L.) crops.  

PubMed

A genetic marker system based on the S1 Short Interspersed Elements (SINEs) in the important commercial crop, oilseed rape ( Brassica napus L.) has been developed. SINEs provided a successful multilocus, dominant marker system that was capable of clearly delineating winter- and spring-type crop varieties. Sixteen of 20 varieties tested showed unique profiles from the 17 polymorphic SINE markers generated. The 3' or 5' flank region of nine SINE markers were cloned, and DNA was sequenced. In addition, one putative pre-transposition SINE allele was cloned and sequenced. Two SINE flanking sequences were used to design real-time PCR assays. These quantitative SINE assays were applied to study the genetic structure of eight fields of oilseed rape crops. Studied fields were more genetically diverse than expected for the chosen loci (mean H T = 0.23). The spatial distribution of SINE marker frequencies was highly structured in some fields, suggesting locations of volunteer impurities within the crop. In one case, the assay identified a mislabeling of the crop variety. SINE markers were a useful tool for crop genetics, phylogenetics, variety identification, and purity analysis. The use and further application of quantitative, real-time PCR markers are discussed. PMID:18092752

Allnutt, T R; Roper, K; Henry, C

2008-01-23

402

Comparative Linkage Meta-Analysis Reveals Regionally-Distinct, Disparate Genetic Architectures: Application to Bipolar Disorder and Schizophrenia  

PubMed Central

New high-throughput, population-based methods and next-generation sequencing capabilities hold great promise in the quest for common and rare variant discovery and in the search for ”missing heritability.” However, the optimal analytic strategies for approaching such data are still actively debated, representing the latest rate-limiting step in genetic progress. Since it is likely a majority of common variants of modest effect have been identified through the application of tagSNP-based microarray platforms (i.e., GWAS), alternative approaches robust to detection of low-frequency (1–5% MAF) and rare (<1%) variants are of great importance. Of direct relevance, we have available an accumulated wealth of linkage data collected through traditional genetic methods over several decades, the full value of which has not been exhausted. To that end, we compare results from two different linkage meta-analysis methods—GSMA and MSP—applied to the same set of 13 bipolar disorder and 16 schizophrenia GWLS datasets. Interestingly, we find that the two methods implicate distinct, largely non-overlapping, genomic regions. Furthermore, based on the statistical methods themselves and our contextualization of these results within the larger genetic literatures, our findings suggest, for each disorder, distinct genetic architectures may reside within disparate genomic regions. Thus, comparative linkage meta-analysis (CLMA) may be used to optimize low-frequency and rare variant discovery in the modern genomic era.

Tang, Brady; Thornton-Wells, Tricia; Askland, Kathleen D.

2011-01-01

403

Development and application of a reverse transcriptase polymerase chain reaction to detect Chinese isolates of duck hepatitis virus type 1.  

PubMed

We developed a reverse transcriptase polymerase chain reaction (RT-PCR) method for the detection of duck hepatitis virus type 1 (DHV-1) in the tissues of infected and clinically affected ducks and in chick and duck embryos. We found the assay to be effective in detecting the virus in China, where it is being used in studies on the epidemiology of the disease. We applied this simple and rapid diagnostic method to the detection of DHV isolates grown in chick and duck embryos and in tissues obtained from infected birds. The assay also proved useful for the differentiation of DVH from the duck plague virus (DPV), muscovy parvovirus (MPV), gosling parvovirus (GPV), avian influenza virus (AIV/H5N1), Pasteurella multocida (PA/5:A), Riemerella anatipestifer (RA/serotype 1), and Salmonella enteritidis (SE). The limit of the sensitivity of this method for the detection of DHV-1 RNA was 3 pg/10 microl. As compared to ELISA and virus isolation, the rate of agreement for the detection of experimentally infected livers was 100%; moreover, the RT-PCR method was also capable of detecting DHV-1 RNA from the livers that had been infected and stored at -20 degrees C for 22 years; in contrast, ELISA and virus isolation method could only detect DHV-1 from the livers that had been infected and stored at -20 degrees C for 13 and 11 years, respectively. The rate of positivity in 185 clinically suspected diseased livers subjected to detection by RT-PCR, ELISA, and virus isolation was 89.2%, 69.2%, and 55.7%, respectively. These results indicated that the RT-PCR approach is rapid, sensitive, and reliable for the detection and differentiation of DHV-1 from the other clinical samples and suspected isolates. PMID:18706944

Anchun, Cheng; Mingshu, Wang; Hongyi, Xin; Dekang, Zhu; Xinran, Li; Haijuen, Chen; Renyong, Jia; Miao, Yang

2009-01-01

404

Development and application of a reverse transcriptase polymerase chain reaction to detect Chinese isolates of duck hepatitis virus type 1.  

PubMed

We developed a reverse transcriptase polymerase chain reaction (RT-PCR) method for the detection of duck hepatitis virus type 1 (DHV-1) in the tissues of infected and clinically affected ducks and in chick and duck embryos. We found the assay to be effective in detecting the virus in China, where it is being used in studies on the epidemiology of the disease. We applied this simple and rapid diagnostic method to the detection of DHV isolates grown in chick and duck embryos and in tissues obtained from infected birds. The assay also proved useful for the differentiation of DVH from the duck plague virus (DPV), muscovy parvovirus (MPV), gosling parvovirus (GPV), avian influenza virus (AIV/H5N1), Pasteurella multocida (PA/5:A), Riemerella anatipestifer (RA/serotype 1), and Salmonella enteritidis (SE). The limit of the sensitivity of this method for the detection of DHV-1 RNA was 3 pg/10 microl. As compared to Dot-ELISA and virus isolation, the rate of agreement for the detection of experimentally infected livers was 100%; moreover, the RT-PCR method was also capable of detecting DHV-1 RNA from the livers that had been infected and stored at -20 degrees C for 22 years; in contrast, Dot-ELISA and virus isolation method could only detect DHV-1 from the livers that had been infected and stored at -20 degrees C for 13 and 11 years, respectively. The rate of positivity in 185 clinically suspected diseased livers subjected to detection by RT-PCR, Dot-ELISA, and virus isolation was 89.2%, 69.2%, and 55.7%, respectively. These results indicated that the RT-PCR approach is rapid, sensitive, and reliable for the detection and differentiation of DHV-1 from the other clinical samples and suspected isolates. PMID:19475729

Anchun, Cheng; Mingshu, Wang; Hongyi, Xin; Dekang, Zhu; Xinran, Li; Haijuen, Chen; Renyong, Jia; Miao, Yang

2009-06-01

405

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

406

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.

Bind, Marie-Abele; Coull, Brent; Suh, Helen; Wright, Robert; Baccarelli, Andrea; Vokonas, Pantel; Schwartz, Joel

2014-01-01

407

Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities  

PubMed Central

The goal of sequencing the entire human genome for $1,000 is almost in sight. However, the total costs including DNA sequencing, data management, and analysis to yield a clear data interpretation are unlikely to be lowered significantly any time soon to make studies on a population scale and daily clinical uses feasible. Alternatively, the targeted enrichment of specific groups of disease and biological pathway-focused genes and the capture of up to an entire human exome (~1% of the genome) allowing an unbiased investigation of the complete protein-coding regions in the genome are now routine. Targeted gene capture followed by sequencing with massively parallel next-generation sequencing (NGS) has the advantages of 1) significant cost saving, 2) higher sequencing accuracy because of deeper achievable coverage, 3) a significantly shorter turnaround time, and 4) a more feasible data set for a bioinformatic analysis outcome that is functionally interpretable. Gene capture combined with NGS has allowed a much greater number of samples to be examined than is currently practical with whole-genome sequencing. Such an approach promises to bring a paradigm shift to biomedical research of Mendelian disorders and their clinical diagnoses, ultimately enabling personalized medicine based on one’s genetic profile. In this review, we describe major methodologies currently used for gene capture and detection of genetic variations by NGS. We will highlight applications of this technology in studies of genetic disorders and discuss issues pertaining to applications of this powerful technology in genetic screening and the discovery of genes implicated in syndromic and non-syndromic hearing loss.

Lin, Xi; Tang, Wenxue; Ahmad, Shoeb; Lu, Jingqiao; Colby, Candice C.; Zhu, Jason; Yu, Qing

2013-01-01

408

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

409

Genetic Engineering of Mesenchymal Stem Cells and Its Application in Human Disease Therapy  

PubMed Central

Abstract The use of stem cells for tissue regeneration and repair is advancing both at the bench and bedside. Stem cells isolated from bone marrow are currently being tested for their therapeutic potential in a variety of clinical conditions including cardiovascular injury, kidney failure, cancer, and neurological and bone disorders. Despite the advantages, stem cell therapy is still limited by low survival, engraftment, and homing to damage area as well as inefficiencies in differentiating into fully functional tissues. Genetic engineering of mesenchymal stem cells is being explored as a means to circumvent some of these problems. This review presents the current understanding of the use of genetically engineered mesenchymal stem cells in human disease therapy with emphasis on genetic modifications aimed to improve survival, homing, angiogenesis, and heart function after myocardial infarction. Advancements in other disease areas are also discussed.

Hodgkinson, Conrad P.; Gomez, Jose A.; Mirotsou, Maria

2010-01-01

410

A new hybrid genetic algorithm and its application in the RCPSP  

NASA Astrophysics Data System (ADS)

A new hybrid genetic algorithm is generated in this paper, which is based on the simple genetic algorithm. In this algorithm, some genetic operators such as crossover operator are improved. In the crossover operator, the crossover method based on threshold and the two-points-crossover method are combined into a new hybrid crossover method. An example which is Resource-Constrained Project Scheduling Problem (RCPSP) is given, whose activity network, the execution time and the number of resource required for each activity, selection and crossover operator are also referred. In addition, there are examples to prove the superior of the new algorithm, which is benefit to speed up the evolution and get the optimal solution.

Li, Zheng; Qin, Jinlei

2011-12-01

411

Application of Next Generation Sequencing Upon the Molecular Genetic Diagnosis of Deafness  

PubMed Central

The main objective of this review is to describe the new sequencing technologies called next generation sequencing (NGS) and its utility as a molecular genetic diagnosis tool in a medical field. Sanger method has dominated the genome sequencing industry for the past 30 years since its invention in 1975. It produced first human genome and still remains the gold standard for genome sequencing. However, it cannot meet the needs for enormous genetic data gathering and process because of its relatively long sequencing time and high cost per sample. NGS which parallelise the sequencing process, thereby increasing processing speed at a reduced cost per sample emerged to compensate for the weakness of the previous method. Currently NGS is used in some medical areas and its use is being widened. NGS also plays an important role in a study of genetically heterogenous hearing diseases. NGS is expected to mark a significant milestone in genomic research filed in a near future.

Kim, Bong Jik

2012-01-01

412

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

413

The application of immune genetic algorithm in main steam temperature of PID control of BP network  

NASA Astrophysics Data System (ADS)

In order to overcome the uncertainties, large delay, large inertia and nonlinear property of the main steam temperature controlled object in the power plant, a neural network intelligent PID control system based on immune genetic algorithm and BP neural network is designed. Using the immune genetic algorithm global search optimization ability and good convergence, optimize the weights of the neural network, meanwhile adjusting PID parameters using BP network. The simulation result shows that the system is superior to conventional PID control system in the control of quality and robustness.

Li, Han; Zhen-yu, Zhang

414

The Cre/loxP system in Giardia lamblia: genetic manipulations in a binucleate tetraploid protozoan.  

PubMed

The bacteriophage-derived Cre/loxP system is a valuable tool that has revolutionised genetic and cell biological research in many organisms. We implemented this system in the intestinal parasite Giardia lamblia, an evolutionarily diverged protozoan whose binucleate and tetraploid genome organisation severely limits the application of reverse genetic approaches. We show that Cre-recombinase is functionally expressed in G. lamblia and demonstrate "recycling" of selectable markers. Providing the means for more complex and versatile genetic modifications, this technique massively increases the scope of functional investigations in G. lamblia and other protozoa with similar limitations with respect to genetic manipulation. PMID:24747534

Wampfler, Petra B; Faso, Carmen; Hehl, Adrian B

2014-07-01

415

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

416

Reversible Computation and Reversible Programming Languages  

Microsoft Academic Search

A reversible programming language supports deterministic forward and backward computation. This tutorial focuses on a high-level reversible programming language Janus. In common with other programming paradigms, reversible programming has its own programming methodology. Janus is simple, yet powerful, and its constructs can serve as a model for designing reversible languages in general.