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1

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

2

Application of Reverse Genetics for Producing Attenuated Vaccine Strains against Highly Pathogenic Avian Influenza Viruses  

PubMed Central

ABSTRACT In this study, reverse genetics was applied to produce vaccine candidate strains against highly pathogenic avian influenza viruses (HPAIVs) of the H5N1 subtype. The H5 subtype vaccine strains were generated by a reverse genetics method in a biosafety level 2 facility. The strain contained the HA gene from the H5N1 subtype HPAIV attenuated by genetic modification at the cleavage site, the NA gene derived from the H5N1 subtype HPAI or the H5N3 subtype of avian influenza virus and internal genes from A/Puerto Rico/8/34. Vaccination with an inactivated recombinant virus with oil-emulsion completely protected chickens from a homologous viral challenge with a 640 HAU or 3,200 HAU/vaccination dose. Vaccination with a higher dose of antigen, 3,200 HAU, was effective at increasing survival and efficiently reduced viral shedding even when challenged by a virus of a different HA clade. The feasibility of differentiation of infected from vaccinated animals (DIVA) was demonstrated against a challenge with H5N1 HPAIVs when the recombinant H5N3 subtype viruses were used as the antigens of the vaccine. Our study demonstrated that the use of reverse genetics would be an option to promptly produce an inactivated vaccine with better matching of antigenicity to a circulating strain. PMID:24805906

UCHIDA, Yuko; TAKEMAE, Nobuhiro; SAITO, Takehiko

2014-01-01

3

Influenza reverse genetics: dissecting immunity and pathogenesis.  

PubMed

Reverse genetics systems allow artificial generation of non-segmented and segmented negative-sense RNA viruses, like influenza viruses, entirely from cloned cDNA. Since the introduction of reverse genetics systems over a decade ago, the ability to generate 'designer' influenza viruses in the laboratory has advanced both basic and applied research, providing a powerful tool to investigate and characterise host-pathogen interactions and advance the development of novel therapeutic strategies. The list of applications for reverse genetics has expanded vastly in recent years. In this review, we discuss the development and implications of this technique, including the recent controversy surrounding the generation of a transmissible H5N1 influenza virus. We will focus on research involving the identification of viral protein function, development of live-attenuated influenza virus vaccines, host-pathogen interactions, immunity and the generation of recombinant influenza virus vaccine vectors for the prevention and treatment of infectious diseases and cancer. PMID:24528628

Ye, Siying; Evans, Justin G; Stambas, John

2014-01-01

4

ESTABLISHMENT OF A PIG MODEL FOR THE 1930 H1N1 SWINE INFLUENZA VIRUS AND APPLICATION OF REVERSE GENETICS  

Technology Transfer Automated Retrieval System (TEKTRAN)

The aims of this study were to establish a pig model for the 1930 H1N1 swine influenza virus and its rescue by reverse genetics. Influenza A/swine/IA/15/30 H1N1 (ATCC VR333) is the first influenza virus isolated from swine and genetically related to the 1918 Spanish Flu virus. We inoculated thirty ...

5

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

E-print Network

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

Harman, Mark

6

Reverse Genetics in Ecological Research  

PubMed Central

By precisely manipulating the expression of individual genetic elements thought to be important for ecological performance, reverse genetics has the potential to revolutionize plant ecology. However, untested concerns about possible side-effects of the transformation technique, caused by Agrobacterium infection and tissue culture, on plant performance have stymied research by requiring onerous sample sizes. We compare 5 independently transformed Nicotiana attenuata lines harboring empty vector control (EVC) T-DNA lacking silencing information with isogenic wild types (WT), and measured a battery of ecologically relevant traits, known to be important in plant-herbivore interactions: phytohormones, secondary metabolites, growth and fitness parameters under stringent competitive conditions, and transcriptional regulation with microarrays. As a positive control, we included a line silenced in trypsin proteinase inhibitor gene (TPI) expression, a potent anti-herbivore defense known to exact fitness costs in its expression, in the analysis. The experiment was conducted twice, with 10 and 20 biological replicates per genotype. For all parameters, we detected no difference between any EVC and WT lines, but could readily detect a fitness benefit of silencing TPI production. A statistical power analyses revealed that the minimum sample sizes required for detecting significant fitness differences between EVC and WT was 2–3 orders of magnitude larger than the 10 replicates required to detect a fitness effect of TPI silencing. We conclude that possible side-effects of transformation are far too low to obfuscate the study of ecologically relevant phenotypes. PMID:18253491

Schwachtje, Jens; Kutschbach, Susan; Baldwin, Ian T.

2008-01-01

7

RNA Virus Reverse Genetics and Vaccine Design  

PubMed Central

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

Stobart, Christopher C.; Moore, Martin L.

2014-01-01

8

Reverse Engineering Web Applications  

Microsoft Academic Search

The heterogeneous and dynamic nature of components making up a Web application, the lack of effective programming mechanisms for implementing basic software engineering principles in it, and undisciplined development processes induced by the high pressure of a very short time-to-market, make Web application maintenance a challenging problem. A relevant issue consists of reusing the methodological and technological experience in the

Porfirio Tramontana

2005-01-01

9

Application of Genetic Algorithms for the Design of Large-Scale Reverse Logistic Networks in Europe's Automotive Industry  

Microsoft Academic Search

After providing a brief overview on Europe's legislative situation with regard to the demanded recovering and recycling of end-of-life vehicles the paper characterizes the specifications of a modeling approach describing the design of a recycling network including a large variety of different cooperating actors set at diverse positions on a reverse supply-chain. It advances with a discussion of requirements a

Ralf Schleiffer; Jens Wollenweber; Hans-Juergen Sebastian; Florian Golm; Natasha Kapoustina

2004-01-01

10

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

Microsoft Academic Search

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

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

2008-01-01

11

Biol Cell . Author manuscript Reverse genetics in eukaryotes  

E-print Network

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

Paris-Sud XI, Université de

12

TILLING is an effective reverse genetics technique for Caenorhabditis elegans  

Microsoft Academic Search

BACKGROUND: TILLING (Targeting Induced Local Lesions in Genomes) is a reverse genetic technique based on the use of a mismatch-specific enzyme that identifies mutations in a target gene through heteroduplex analysis. We tested this technique in Caenorhabditis elegans, a model organism in which genomics tools have been well developed, but limitations in reverse genetics have restricted the number of heritable

Erin J Gilchrist; Nigel J O'Neil; Ann M Rose; Monique C Zetka; George W Haughn

2006-01-01

13

Towards Reverse Engineering of Genetic Regulatory Networks Zelmina Lubovac  

E-print Network

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

Chang, Joseph T.

14

Tackling feline infectious peritonitis via reverse genetics.  

PubMed

Feline infectious peritonitis (FIP) is caused by feline coronaviruses (FCoVs) and represents one of the most important lethal infectious diseases of cats. To date, there is no efficacious prevention and treatment, and our limited knowledge on FIP pathogenesis is mainly based on analysis of experiments with field isolates. In a recent study, we reported a promising approach to study FIP pathogenesis using reverse genetics. We generated a set of recombinant FCoVs and investigated their pathogenicity in vivo. The set included the type I FCoV strain Black, a type I FCoV strain Black with restored accessory gene 7b, two chimeric type I/type II FCoVs and the highly pathogenic type II FCoV strain 79-1146. All recombinant FCoVs and the reference strain isolates were found to establish productive infections in cats. While none of the type I FCoVs and chimeric FCoVs induced FIP, the recombinant type II FCoV strain 79-1146 was as pathogenic as the parental isolate. Interestingly, an intact ORF 3c was confirmed to be restored in all viruses (re)isolated from FIP-diseased animals. PMID:25057920

Thiel, Volker; Thiel, Heinz-Jürgen; Tekes, Gergely

2014-07-24

15

Tackling feline infectious peritonitis via reverse genetics.  

PubMed

Feline infectious peritonitis (FIP) is caused by feline coronaviruses (FCoVs) and represents one of the most important lethal infectious diseases of cats. To date, there is no efficacious prevention and treatment, and our limited knowledge on FIP pathogenesis is mainly based on analysis of experiments with field isolates. In a recent study, we reported a promising approach to study FIP pathogenesis using reverse genetics. We generated a set of recombinant FCoVs and investigated their pathogenicity in vivo. The set included the type I FCoV strain Black, a type I FCoV strain Black with restored accessory gene 7b, two chimeric type I/type II FCoVs and the highly pathogenic type II FCoV strain 79-1146. All recombinant FCoVs and the reference strain isolates were found to establish productive infections in cats. While none of the type I FCoVs and chimeric FCoVs induced FIP, the recombinant type II FCoV strain 79-1146 was as pathogenic as the parental isolate. Interestingly, an intact ORF 3c was confirmed to be restored in all viruses (re)isolated from FIP-diseased animals. PMID:25482087

Thiel, Volker; Thiel, Heinz-Jürgen; Tekes, Gergely

2014-11-01

16

Application modeling using reverse engineering techniques  

Microsoft Academic Search

In this work we present techniques and tools that enable effective reverse engineering procedures for web applications that were developed using the promising ASP.NET technology. We deal with model-driven development in its reverse aspect by implementing reverse engineering methods. Our implemented methods model web applications using a well-known, web oriented and robust language, namely WebML. This is, to the authors'

T. Katsimpa; Yannis Panagis; Evangelos Sakkopoulos; Giannis Tzimas; Athanasios K. Tsakalidis

2006-01-01

17

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling  

E-print Network

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

Babu, M. Madan

18

Bayesian Networks Applications in Genetics  

E-print Network

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

Nuel, Gregory

19

Sorting Permutations by Reversals through a Hybrid Genetic Algorithm based on Breakpoint Elimination  

E-print Network

Sorting Permutations by Reversals through a Hybrid Genetic Algorithm based on Breakpoint belongs to P. In this paper, a standard genetic algorithm for solving the problem of sorting by reversals, an improved genetic algorithm is proposed, that in the initial generations applies reversals

Ayala-Rincón, Mauricio

20

TILLING is an effective reverse genetics technique for Caenorhabditis elegans  

PubMed Central

Background TILLING (Targeting Induced Local Lesions in Genomes) is a reverse genetic technique based on the use of a mismatch-specific enzyme that identifies mutations in a target gene through heteroduplex analysis. We tested this technique in Caenorhabditis elegans, a model organism in which genomics tools have been well developed, but limitations in reverse genetics have restricted the number of heritable mutations that have been identified. Results To determine whether TILLING represents an effective reverse genetic strategy for C. elegans we generated an EMS-mutagenised population of approximately 1500 individuals and screened for mutations in 10 genes. A total of 71 mutations were identified by TILLING, providing multiple mutant alleles for every gene tested. Some of the mutations identified are predicted to be silent, either because they are in non-coding DNA or because they affect the third bp of a codon which does not change the amino acid encoded by that codon. However, 59% of the mutations identified are missense alleles resulting in a change in one of the amino acids in the protein product of the gene, and 3% are putative null alleles which are predicted to eliminate gene function. We compared the types of mutation identified by TILLING with those previously reported from forward EMS screens and found that 96% of TILLING mutations were G/C-to-A/T transitions, a rate significantly higher than that found in forward genetic screens where transversions and deletions were also observed. The mutation rate we achieved was 1/293 kb, which is comparable to the mutation rate observed for TILLING in other organisms. Conclusion We conclude that TILLING is an effective and cost-efficient reverse genetics tool in C. elegans. It complements other reverse genetic techniques in this organism, can provide an allelic series of mutations for any locus and does not appear to have any bias in terms of gene size or location. For eight of the 10 target genes screened, TILLING has provided the first genetically heritable mutations which can be used to study their functions in vivo. PMID:17049087

Gilchrist, Erin J; O'Neil, Nigel J; Rose, Ann M; Zetka, Monique C; Haughn, George W

2006-01-01

21

Feline Genetics: Clinical Applications and Genetic Testing  

PubMed Central

DNA testing for domestic cat diseases and appearance traits is a rapidly growing asset for veterinary medicine. Approximately thirty-three genes contain fifty mutations that cause feline health problems or alterations in the cat’s appearance. A variety of commercial laboratories can now perform cat genetic diagnostics, allowing both the veterinary clinician and the private owner to obtain DNA test results. DNA is easily obtained from a cat via a buccal swab using a standard cotton bud or cytological brush, allowing DNA samples to be easily sent to any laboratory in the world. The DNA test results identify carriers of the traits, predict the incidence of traits from breeding programs, and influence medical prognoses and treatments. An overall goal of identifying these genetic mutations is the correction of the defect via gene therapies and designer drug therapies. Thus, genetic testing is an effective preventative medicine and a potential ultimate cure. However, genetic diagnostic tests may still be novel for many veterinary practitioners and their application in the clinical setting needs to have the same scrutiny as any other diagnostic procedure. This article will review the genetic tests for the domestic cat, potential sources of error for genetic testing, and the pros and cons of DNA results in veterinary medicine. Highlighted are genetic tests specific to the individual cat, which are a part of the cat’s internal genome. PMID:21147473

Lyons, Leslie A.

2010-01-01

22

Reverse genetics system for studying human rhinovirus infections.  

PubMed

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

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

2015-01-01

23

Chloroquine Susceptibility and Reversibility in a Plasmodium falciparum Genetic Cross  

PubMed Central

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

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

2011-01-01

24

REVERSE ENGINEERING OF METABOLIC PATHWAYS FROM OBSERVED DATA USING GENETIC PROGRAMMING  

E-print Network

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

Fernandez, Thomas

25

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

E-print Network

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

Fernandez, Thomas

26

A Reverse Genetic Approach to Test Functional Redundancy During Embryogenesis  

PubMed Central

Gene function during embryogenesis is typically defined by loss-of-function experiments, for example by targeted mutagenesis (knockout) in the mouse. In the zebrafish model, effective reverse genetic techniques have been developed using microinjection of gene-specific antisense morpholinos. Morpholinos target an mRNA through specific base-pairing and block gene function transiently by inhibiting translation or splicing for several days during embryogenesis (knockdown). However, in vertebrates such as mouse or zebrafish, some gene functions can be obscured by these approaches due to the presence of another gene that compensates for the loss. This is especially true for gene families containing sister genes that are co-expressed in the same developing tissues. In zebrafish, functional compensation can be tested in a relatively high-throughput manner, by co-injection of morpholinos that target knockdown of both genes simultaneously. Likewise, using morpholinos, a genetic interaction between any two genes can be demonstrated by knockdown of both genes together at sub-threshold levels. For example, morpholinos can be titrated such that neither individual knockdown generates a phenotype. If, under these conditions, co-injection of both morpholinos causes a phenotype, a genetic interaction is shown. Here we demonstrate how to show functional redundancy in the context of two related GATA transcription factors. GATA factors are essential for specification of cardiac progenitors, but this is revealed only by the loss of both Gata5 and Gata6. We show how to carry out microinjection experiments, validate the morpholinos, and evaluate the compensated phenotype for cardiogenesis. PMID:20736915

Rikin, Amir; Rosenfeld, Gabriel E.; McCartin, Kellie; Evans, Todd

2010-01-01

27

Genetic algorithms and their applications  

Microsoft Academic Search

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

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

1996-01-01

28

Reverse Genetics Mediated Recovery of Infectious Murine Norovirus  

PubMed Central

Human noroviruses are responsible for most cases of human gastroenteritis (GE) worldwide and are recurrent problem in environments where close person-to-person contact cannot be avoided 1, 2. During the last few years an increase in the incidence of outbreaks in hospitals has been reported, causing significant disruptions to their operational capacity as well as large economic losses. The identification of new antiviral approaches has been limited due to the inability of human noroviruses to complete a productive infection in cell culture 3. The recent isolation of a murine norovirus (MNV), closely related to human norovirus 4 but which can be propagated in cells 5 has opened new avenues for the investigation of these pathogens 6, 7. MNV replication results in the synthesis of new positive sense genomic and subgenomic RNA molecules, the latter of which corresponds to the last third of the viral genome (Figure 1). MNV contains four different open reading frames (ORFs), of which ORF1 occupies most of the genome and encodes seven non-structural proteins (NS1-7) released from a polyprotein precursor. ORF2 and ORF3 are contained within the subgenomic RNA region and encode the capsid proteins (VP1 and VP2, respectively) (Figure 1). Recently, we have identified that additional ORF4 overlapping ORF2 but in a different reading frame is functional and encodes for a mitochondrial localised virulence factor (VF1) 8. Replication for positive sense RNA viruses, including noroviruses, takes place in the cytoplasm resulting in the synthesis of new uncapped RNA genomes. To promote viral translation, viruses exploit different strategies aimed at recruiting the cellular protein synthesis machinery 9-11. Interestingly, norovirus translation is driven by the multifunctional viral protein-primer VPg covalently linked to the 5' end of both genomic and subgenomic RNAs 12-14. This sophisticated mechanism of translation is likely to be a major factor in the limited efficiency of viral recovery by conventional reverse genetics approaches. Here we report two different strategies based on the generation of murine norovirus-1 (referred to as MNV herewith) transcripts capped at the 5' end. One of the methods involves both in vitro synthesis and capping of viral RNA, whereas the second approach entails the transcription of MNV cDNA in cells expressing T7 RNA polymerase. The availability of these reverse genetics systems for the study of MNV and a small animal model has provided an unprecedented ability to dissect the role of viral sequences in replication and pathogenesis 15-17. PMID:22760450

Thorne, Lucy; Yunus, Muhammad A.; Goodfellow, Ian

2012-01-01

29

Reversible Hydrogels from Self-Assembling Genetically Engineered Protein Block Copolymers  

E-print Network

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

Breedveld, Victor

30

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

31

An Inducible and Reversible Mouse Genetic Rescue System  

Microsoft Academic Search

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

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

2008-01-01

32

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

33

Reverse Genetics Plasmid for Cloning Unstable Influenza A Virus Gene Segments  

PubMed Central

Reverse genetics approaches that enable the generation of recombinant influenza A viruses entirely from plasmids are invaluable for studies on virus replication, morphogenesis, pathogenesis, or transmission. Furthermore, influenza virus reverse genetics is now critical for the development of new vaccines for this human and animal pathogen. Periodically, influenza gene segments are unstable within plasmids in bacteria. The PB2 gene segment of a highly pathogenic avian H5 influenza virus A/Turkey/Ontario/7732/1966 (Ty/Ont) was unstable in commonly available cloning plasmids (e.g., pcDNA3.1/V5-His-TOPO) and in standard influenza virus reverse genetics plasmids (e.g., pHH21), which contain high copy origins of replication. Thus, a low-copy influenza reverse genetics plasmid (pGJ3C3) was developed to enable rapid cloning of unstable influenza A virus genes using ligation-independent recombination-based cloning. The unstable Ty/Ont PB2 gene segment was efficiently cloned using the pGJ3C3 plasmid and this clone was used to rescue a recombinant Ty/Ont virus. This low copy reverse genetics plasmid will be useful for cloning other unstable segments of influenza A viruses in order to rescue recombinant viruses, which will facilitate basic studies and vaccine seed stock production. PMID:21295611

Zhou, Bin; Jerzak, Greta; Scholes, Derek T.; Donnelly, Matthew E.; Li, Yan; Wentworth, David E.

2013-01-01

34

Reverse Engineering of Web Applications: A  

E-print Network

Martin1 Lawson Archer2 1 The University of Liverpool, Department of Computer Science, Ashton street APPLICATIONS: A TECHNICAL REVIEW Reshma Patel1 , Frans Coenen1 , Russell Martin1 , Lawson Archer2 1 Department into a platform where differing applications are able to handle complex transactions, thereby providing

Atkinson, Katie

35

Reversible biomechano-responsive surface based on green fluorescent protein genetically modified with unnatural amino acids.  

PubMed

GFP has been genetically modified at two specific positions of its molecular architecture. These modifications allow its covalent attachment onto PEG brushes grafted on functionalized silicone surfaces. The stretching of this material leads to a reversible decrease of the fluorescence intensity due to stretch-induced forces applying on GFP molecules. PMID:25407087

Longo, Johan; Yao, Chunyan; Rios, César; Chau, Nguyet Trang Thanh; Boulmedais, Fouzia; Hemmerlé, Joseph; Lavalle, Philippe; Schiller, Stefan M; Schaaf, Pierre; Jierry, Loïc

2015-01-01

36

Pharmacological or Genetic Inactivation of the Serotonin Transporter Improves Reversal Learning in Mice  

PubMed Central

Growing evidence supports a major contribution of cortical serotonin (5-hydroxytryptamine, 5-HT) to the modulation of cognitive flexibility and the cognitive inflexibility evident in neuropsychiatric disorders. The precise role of 5-HT and the influence of 5-HT gene variation in mediating this process is not fully understood. Using a touch screen–based operant system, we assessed reversal of a pairwise visual discrimination as an assay for cognitive flexibility. Effects of constitutive genetic or pharmacological inactivation of the 5-HT transporter (5-HTT) on reversal were examined by testing 5-HTT null mice and chronic fluoxetine-treated C57BL/6J mice, respectively. Effects of constitutive genetic loss or acute pharmacological depletion of 5-HT were assessed by testing Pet-1 null mice and para-chlorophenylalanine (PCPA)–treated C57BL/6J mice, respectively. Fluoxetine-treated C57BL/6J mice made fewer errors than controls during the early phase of reversal when perseverative behavior is relatively high. 5-HTT null mice made fewer errors than controls in completing the reversal task. However, reversal in Pet-1 null and PCPA-treated C57BL/6J mice was not different from controls. These data further support an important role for 5-HT in modulating reversal learning and provide novel evidence that inactivating the 5-HTT improves this process. These findings could have important implications for understanding and treating cognitive inflexibility in neuropsychiatric disease. PMID:20032063

Mathur, Poonam; Harvey-White, Judith; Izquierdo, Alicia; Saksida, Lisa M.; Bussey, Timothy J.; Fox, Stephanie; Deneris, Evan; Murphy, Dennis L.; Holmes, Andrew

2010-01-01

37

Human-competitive Applications of Genetic Programming  

E-print Network

Human-competitive Applications of Genetic Programming John R. Koza Stanford Medical Informatics, Department of Medicine, School of Medicine, Department of Electrical Engineering, School of Engineering, Stanford University, Stanford, California 94305 E-mail: koza@stanford.edu Summary: Genetic programming

Fernandez, Thomas

38

On the Starting and Stopping Problem: Application in reversible investments.  

E-print Network

of the power station is an increasing sequence of stopping times = (n)n1 where for n 1, n n+1 and 2n-1 (respOn the Starting and Stopping Problem: Application in reversible investments. S. Hamad solve completely the starting and stopping problem when the dynamics of the system are a general adapted

Jeanblanc, Monique

39

Site-directed mutagenesis and gene deletion using reverse genetics.  

PubMed

Understanding gene function is far easier when tools are available to engineer a bacterial strain lacking a specific gene and phenotypically compare its behavior with the corresponding parental strain. Such mutants could be selected randomly, either by natural selection under particular stress conditions or by random mutagenesis using transposon delivery as described elsewhere in this book. However, with the advent of the genomic era there are now hundreds of bacterial genomes whose sequence is available, and thus, genes can be identified, chosen, and strategies designed to specifically inactivate them. This can be done by using suicide plasmids and is most convenient when the bacterium of interest is easily amenable to genetic manipulation. The method presented here will describe the use of a suicide vector, pKNG101, which allows the selection of a double-recombination event. The first event results in the integration of the pKNG101 derivative carrying the "mutator" fragment onto the chromosome, and could be selected on plates containing appropriate antibiotics. The pKNG101 carries the sacB gene, which induces death when cells are grown on sucrose. Growth on sucrose plates will thus select the second homologous recombination event, which results in removing the plasmid backbone and leaving behind the mutated target gene. This method has been widely used over the last 20 years to inactivate genes in a wide range of gram-negative bacteria and in particular in Pseudomonas aeruginosa. PMID:24818930

Muhl, Daniela; Filloux, Alain

2014-01-01

40

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

NASA Technical Reports Server (NTRS)

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

Liang, Shoudan; Fuhrman, Stefanie; Somogyi, Roland

1998-01-01

41

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

PubMed Central

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

Friedmann, T

1990-01-01

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

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. PMID:20600474

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

44

UTILLdb, a Pisum sativum in silico forward and reverse genetics tool  

PubMed Central

The systematic characterization of gene functions in species recalcitrant to Agrobacterium-based transformation, like Pisum sativum, remains a challenge. To develop a high throughput forward and reverse genetics tool in pea, we have constructed a reference ethylmethane sulfonate mutant population and developed a database, UTILLdb, that contains phenotypic as well as sequence information on mutant genes. UTILLdb can be searched online for TILLING alleles, through the BLAST tool, or for phenotypic information about mutants by keywords. PMID:18302733

Dalmais, Marion; Schmidt, Julien; Le Signor, Christine; Moussy, Francoise; Burstin, Judith; Savois, Vincent; Aubert, Gregoire; Brunaud, Veronique; de Oliveira, Yannick; Guichard, Cecile; Thompson, Richard; Bendahmane, Abdelhafid

2008-01-01

45

Use of Reverse Genetics to Enhance the Oncolytic Properties of Newcastle Disease Virus  

Microsoft Academic Search

Naturally occurring strains of Newcastle disease virus (NDV) have shown oncolytic therapeutic efficacy in preclinical studies and are currently in clinical trials. Here, we have evaluated the possibility to enhance the cancer therapeutic potential of NDV by means of reverse genetics. Mice bearing s.c. implanted CT26 tumors were treated with intratumoral (i.t.) injections of a recombinant NDV modified to contain

Adam Vigil; Osvaldo Martinez; Sa Xiao; Jerome F. Cros; Luis Martinez-Sobrido; Adolfo Garcia-Sastre

2007-01-01

46

The grape microvine - a model system for rapid forward and reverse genetics of grapevines.  

PubMed

A grapevine model system is described that is suitable for rapid forward and reverse genetic studies in small controlled environments. It is based on the Vvgai1 mutant allele that confers a dwarf stature, short generation cycles and continuous flowering ('microvine'). Black and white berry microvine genotypes were developed that can be transformed by Agrobacterium tumefaciens. Near-homozygous lines were created for efficient bi-allelic single nucleotide polymorphism (SNP) marker mapping and mutagenesis studies. A genetic mapping strategy based on picovine-derived microvine progeny populations was used to rapidly phenotype and map the flower sex and fleshless berry loci and identify a new lethal recessive locus, Vvlrl1. The microvine provides a unique model system for rapid genetic studies of grapevine by changing the perennial long life cycle of the plant to one with features and advantages similar to an annual plant. PMID:20374531

Chaïb, Jamila; Torregrosa, Laurent; Mackenzie, Don; Corena, Pat; Bouquet, Alain; Thomas, Mark R

2010-06-01

47

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

48

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

PubMed Central

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

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

2013-01-01

49

Next generation restoration genetics: applications and opportunities.  

PubMed

Restoration ecology is a young scientific discipline underpinning improvements in the rapid global expansion of ecological restoration. The application of molecular tools over the past 20 years has made an important contribution to understanding genetic factors influencing ecological restoration success. Here we illustrate how recent advances in next generation sequencing (NGS) methods are revolutionising the practical contribution of genetics to restoration. Novel applications include a dramatically enhanced capacity to measure adaptive variation for optimal seed sourcing, high-throughput assessment and monitoring of natural and restored biological communities aboveground and belowground, and gene expression analysis as a measure of genetic resilience of restored populations. Challenges remain in data generation, handling and analysis, and how best to apply NGS for practical outcomes in restoration. PMID:24767982

Williams, Anna V; Nevill, Paul G; Krauss, Siegfried L

2014-08-01

50

Introduction to Genetic Engineering and Its Applications  

NSDL National Science Digital Library

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

National Science Foundation GK-12 and Research Experience for Teachers (RET) Programs,

51

Statistical Applications in Genetics and Molecular Biology  

E-print Network

Statistical Applications in Genetics and Molecular Biology Volume 5, Issue 1 2006 Article 5.gilks@mrc-bsu.cam.ac.uk Medical Research Council Laboratory of Molecular Biology, madanm@mrc-lmb.cam.ac.uk Medical Research Council Laboratory of Molecular Biology, sat@mrc-lmb.cam.ac.uk Copyright c 2006 The Berkeley Electronic

Babu, M. Madan

52

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

53

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

PubMed Central

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

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

2013-01-01

54

A Multi-Stage Reverse Logistics Network Problem by Using Hybrid Priority-Based Genetic Algorithm  

NASA Astrophysics Data System (ADS)

Today remanufacturing problem is one of the most important problems regarding to the environmental aspects of the recovery of used products and materials. Therefore, the reverse logistics is gaining become power and great potential for winning consumers in a more competitive context in the future. This paper considers the multi-stage reverse Logistics Network Problem (m-rLNP) while minimizing the total cost, which involves reverse logistics shipping cost and fixed cost of opening the disassembly centers and processing centers. In this study, we first formulate the m-rLNP model as a three-stage logistics network model. Following for solving this problem, we propose a Genetic Algorithm pri (GA) with priority-based encoding method consisting of two stages, and introduce a new crossover operator called Weight Mapping Crossover (WMX). Additionally also a heuristic approach is applied in the 3rd stage to ship of materials from processing center to manufacturer. Finally numerical experiments with various scales of the m-rLNP models demonstrate the effectiveness and efficiency of our approach by comparing with the recent researches.

Lee, Jeong-Eun; Gen, Mitsuo; Rhee, Kyong-Gu

55

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

56

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

57

Application of Genetic Algorithms in Seismic Tomography  

NASA Astrophysics Data System (ADS)

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

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

2010-05-01

58

Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification  

PubMed Central

Many fungi restructured their proteomes through incorporation of serine (Ser) at thousands of protein sites coded by the leucine (Leu) CUG codon. How these fungi survived this potentially lethal genetic code alteration and its relevance for their biology are not understood. Interestingly, the human pathogen Candida albicans maintains variable Ser and Leu incorporation levels at CUG sites, suggesting that this atypical codon assignment flexibility provided an effective mechanism to alter the genetic code. To test this hypothesis, we have engineered C. albicans strains to misincorporate increasing levels of Leu at protein CUG sites. Tolerance to the misincorporations was very high, and one strain accommodated the complete reversion of CUG identity from Ser back to Leu. Increasing levels of Leu misincorporation decreased growth rate, but production of phenotypic diversity on a phenotypic array probing various metabolic networks, drug resistance, and host immune cell responses was impressive. Genome resequencing revealed an increasing number of genotype changes at polymorphic sites compared with the control strain, and 80% of Leu misincorporation resulted in complete loss of heterozygosity in a large region of chromosome V. The data unveil unanticipated links between gene translational fidelity, proteome instability and variability, genome diversification, and adaptive phenotypic diversity. They also explain the high heterozygosity of the C. albicans genome and open the door to produce microorganisms with genetic code alterations for basic and applied research. PMID:23776239

Bezerra, Ana R.; Simões, João; Lee, Wanseon; Rung, Johan; Weil, Tobias; Gut, Ivo G.; Gut, Marta; Bayés, Mónica; Rizzetto, Lisa; Cavalieri, Duccio; Giovannini, Gloria; Bozza, Silvia; Romani, Luigina; Kapushesky, Misha; Moura, Gabriela R.; Santos, Manuel A. S.

2013-01-01

59

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

60

Genetic manipulation of STEP reverses behavioral abnormalities in a fragile X syndrome mouse model  

PubMed Central

Fragile X syndrome (FXS), the most common inherited form of intellectual disability and prevailing known genetic basis of autism, is caused by an expansion in the Fmr1 gene that prevents transcription and translation of fragile X mental retardation protein (FMRP). FMRP binds to and controls translation of mRNAs downstream of metabotropic glutamate receptor (mGluR) activation. Recent work identified striatal-enriched protein tyrosine phosphatase (STEP) as an FMRP target mRNA. STEP opposes synaptic strengthening and promotes synaptic weakening by dephosphorylating its substrates, including ERK1/2, p38, Fyn, Pyk2, and subunits of NMDA and AMPA receptors. Here we demonstrate that STEP translation is dysregulated in Fmr1KO mice, resulting in elevated basal levels of STEP with a concomitant loss of mGluR-dependent STEP translation. We hypothesized that the weakened synaptic strength and behavioral abnormalities reported in FXS may be linked to excess levels of STEP. To test this hypothesis, we reduced or eliminated STEP genetically in Fmr1KO mice. In addition to attenuating audiogenic seizures and seizure-induced c-Fos activation in the periaqueductal gray, genetically reducing STEP in Fmr1KO mice reversed characteristic social abnormalities, including approach, investigation, novelty-induced hyperactivity and anxiety. Loss of STEP also corrected select non-social anxiety-related behaviors in Fmr1KO mice, such as open arm exploration in the elevated plus maze. Our findings indicate that genetically reducing STEP significantly diminishes seizures and restores social and non-social anxiety-related behaviors in Fmr1KO mice, suggesting that strategies to inhibit STEP activity may be effective for treating patients with FXS. PMID:22405502

Goebel-Goody, Susan M.; Wilson-Wallis, Evan D.; Royston, Sara; Tagliatela, Stephanie; Naegele, Janice R.; Lombroso, Paul J.

2014-01-01

61

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

E-print Network

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

Arnold, Jonathan

62

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

PubMed Central

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

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

2014-01-01

63

Establishment of reverse genetics system for infectious bronchitis virus attenuated vaccine strain H120.  

PubMed

Infectious bronchitis virus (IBV) strain H120 was successfully rescued as infectious clone by reverse genetics. Thirteen 1.5-2.8 kb fragments contiguously spanning the virus genome were amplified and cloned into pMD19-T. Transcription grade complete length cDNA was acquired by a modified "No See'm" ligation strategy, which employed restriction enzyme Bsa I and BsmB I and ligated more than two fragments in one T4 ligase reaction. The full-length genomic cDNA was transcribed and its transcript was transfected by electroporation into BHK-21 together with the transcript of nucleocapsid gene. At 48 h post transfection, the medium to culture the transfected BHK-21 cells was harvested and inoculated into 10-days old SPF embryonated chicken eggs (ECE) to replicate the rescued virus. After passage of the virus in ECE five times, the rescued H120 virus (R-H120) was successfully recovered. R-H120 was subsequently identified to possess the introduced silent mutation site in its genome. Some biological characteristics of R-H120 such as growth curve, EID50 and HA titers, were tested and all of them were very similar to its parent strain H120. In addition, both R-H120 and H120 induced a comparable titer of HA inhibition (HI) antibody in immunized chickens and also provided up to 85% of immune protection to the chickens that were challenged with Mass41 IBV strain. The present study demonstrated that construction of infectious clone from IBV vaccine strain H120 is possible and IBV-H120 can be use as a vaccine vector for the development of novel vaccines through molecular recombination and the modified reverse genetics approach. PMID:22999521

Zhou, Ying Shun; Zhang, Yi; Wang, Hong Ning; Fan, Wen Qiao; Yang, Xin; Zhang, An Yun; Zeng, Fan Ya; Zhang, Zhi Kun; Cao, Hai Peng; Zeng, Cheng

2013-02-22

64

Successive transposition explosions in Drosophila melanogaster and reverse transpositions of mobile dispersed genetic elements  

PubMed Central

Transposition outbursts occur in the destabilized Drosophila melanogaster strain ctMR2 carrying a mutation in the locus cut induced by an insertion of mdg4. While the distribution of mobile genetic elements remained unchanged in the great majority of germ cells, in a few cells numerous transpositions had occurred involving mdg (copia-like), fold-back and P-elements. We used in situ hybridization to analyze the distribution of five families of mdg elements in the X-chromosome during several consequent mutational changes in D. melanogaster. Each of them was accompanied by many changes in mdg localization, all of which occurred in one and the same cell. Thus, we could observe the series consisting of up to five successive transposition explosions leading to an almost complete change in the distribution of the mdg elements tested. We also found that in the course of successive transposition explosions, mdg elements often inserted into those sub-sections of the X-chromosome where they had previously been located. This phenomenon, designated as reverse directed transposition, was studied in more detail on insertion into the locus yellow. The rate of reverse transposition of the same mdg element to the corresponding locus was 10–100 times as high as that of primary insertion. In some cases, `the transposon shuttle' into and out of the locus was observed. The existence of `transposition memory' partially explains the specificity of mdg localization in closely related strains as well as the co-ordinated behaviour of different mdg elements in independent transposition explosions. The evolutionary significance of transposition explosions and directed reverse transposition (transposon shuttle) is discussed. ImagesFig. 4. PMID:16453655

Gerasimova, Tatiana I.; Matjunina, Liliya V.; Mizrokhi, Lev J.; Georgiev, Georgii P.

1985-01-01

65

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

66

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

67

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

PubMed Central

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

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

2014-01-01

68

Application of genetic algorithm to steganalysis  

NASA Astrophysics Data System (ADS)

We present a novel application of genetic algorithm (GA) to optimal feature set selection in supervised learning using support vector machine (SVM) for steganalysis. Steganalysis attempts to determine whether a cover object (in our case an image file) contains hidden information. This is a bivariate classification problem: the image either does or does not contain hidden data. Our SVM classifier uses a training set of images with known classification to "learn" how to classify images with unknown classification. The SVM uses a feature set, essentially a set of statistical quantities extracted from the image. The performance of the SVM classifier is heavily dependent on the feature set used. Too many features not only increase computation time but decrease performance, and too few features do not provide enough information for accurate classification. Our steganalysis technique uses entropic features that yield up to 240 features per image. The selection of an optimum feature set is a problem that lends itself well to genetic algorithm optimization. We describe this technique in detail and present a "GA optimized" feature set of 48 features that, for our application, optimizes the tradeoff between computation time and classification accuracy.

Knapik, Timothy; Lo, Ephraim; Marsh, John A.

2006-05-01

69

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

E-print Network

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

70

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

Microsoft Academic Search

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

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

2002-01-01

71

A systemic gene silencing method suitable for high throughput, reverse genetic analyses of gene function in fern gametophytes  

Microsoft Academic Search

BACKGROUND: Ceratopteris richardii is a useful experimental system for studying gametophyte development and sexual reproduction in plants. However, few tools for cloning mutant genes or disrupting gene function exist for this species. The feasibility of systemic gene silencing as a reverse genetics tool was examined in this study. RESULTS: Several DNA constructs targeting a Ceratopteris protoporphyrin IX magnesium chelatase (CrChlI)

George Rutherford; Milos Tanurdzic; Mitsuyasu Hasebe; Jo Ann Banks

2004-01-01

72

Efficient Reversible Montgomery Multiplier and Its Application to Hardware Cryptography  

Microsoft Academic Search

Problem Statement: Arithmetic Logic Unit (ALU) of a crypto-processor and microchips leak information through power consumption. Although the cryptographic protocols are secured against mathematical attacks, the attackers can break the encryption by measuring the energy consumption. Approach: To thwart attacks, this study proposed the use of reversible logic for designing the ALU of a crypto-processor. Ideally, reversible circuits do not

Noor Muhammed Nayeem; Lafifa Jamal; Hasan Babu

2009-01-01

73

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

74

INTERNAL/INTRACAMPUS TRANSFER APPLICATION NCSU Department of Genetics  

E-print Network

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

Langerhans, Brian

75

Time-Reversal and the Adjoint Imaging Method with an Application in Telecommunication  

Microsoft Academic Search

These lecture notes provide a mathematical treatment of time-reversal experiments with a special emphasis on telecommunication.\\u000a A direct link is established between time-reversal experiments and the adjoint imaging method. Based on this relationship,\\u000a several iterative schemes are proposed for optimizing MIMO (multiple-input multiple-output) time-reversal systems in underwater\\u000a acoustic and in wireless communication systems. Whereas in typical imaging applications these iterative

Oliver Dorn; Ecole Superieure

76

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

NASA Technical Reports Server (NTRS)

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

Asbury, Scott C.; Yetter, Jeffrey A.

2000-01-01

77

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

78

Pharmacological and genetic reversal of age dependent cognitive deficits due to decreased presenilin function  

PubMed Central

Alzheimer's disease 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 due to mutations in a single copy of the Presenilin (PS) and Amyloid Precursor Protein (APP) genes. The dominant inheritance pattern of FAD indicates that it may be due to gain or change of function mutations. Studies of FAD-linked forms of presenilin 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 DmGluRA, the inositol trisphosphate receptor (InsP3R) or IPPase 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 InsP3R 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.

2010-01-01

79

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

SciTech Connect

The authors have developed an efficient reverse-genetics protocol that uses expedient pooling and hybridization strategies to identify individual transfer-DNA insertion lines from a collection of 6,000 independently transformed lines in as few as 36 polymerase chain reactions. The authors have used this protocol to systematically isolate Arabidopsis lines containing insertional mutations in individual cytochrome P450 genes. In higher plants P450 genes encode enzymes that perform an exceptionally wide range of functions, including the biosynthesis of primary metabolites necessary for normal growth and development, the biosynthesis of secondary products, and the catabolism of xenobiotics. Despite their importance, progress in assigning enzymatic function to individual P450 gene products has been slow. Here the authors report the isolation of the first 12 such lines, including one (CYP83B1-1) that displays a runt phenotype (small plants with hooked leaves), and three insertions in abundantly expressed genes. The DNAs used in this study are publicly available and can be used to systematically isolate mutants in Arabidopsis.

Winkler, R.G.; Frank, M.R.; Galbraith, D.W.; Feyereisen, R.; Feldmann, K.A. [Univ. of Arizona, Tucson, AZ (United States)] [Univ. of Arizona, Tucson, AZ (United States)

1998-11-01

80

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

PubMed Central

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

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

2001-01-01

81

The reversed dermal graft: surgical procedure and clinical applications.  

PubMed

The reversed dermal graft has been employed in reconstructive plastic surgery for almost 80 years. It is recommended that the dermatologic surgeon use this graft technique whenever a case calls for the combined advantages of the split-thickness skin graft for poorly vascularized areas and the axial pedicle flap appropriate to areas subject to marked mechanical strain. We present cases in which defects on the scalp, sole, palm, and great toe have been covered by reversed dermal graft and split-thickness skin graft in a single operation with excellent results. Our modification of the technique has proved that simultaneous grafting with reversed dermis and split-thickness skin graft produces satisfactory results, reduces postoperative care by 2 weeks, and obviates repeated anesthesia. PMID:9243984

Fratila, A A; Bertlich, R

1997-04-01

82

Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications.  

PubMed Central

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

Fetzner, S; Lingens, F

1994-01-01

83

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

PubMed Central

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

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

2014-01-01

84

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

PubMed

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

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

2014-12-01

85

Application of flux reversal principle for axial flux permanent magnet machines  

NASA Astrophysics Data System (ADS)

Applications of flux reversal machine can be found both for linear and radial flux machines. For axial flux machines, only one application is reported considering a two phase machine. In general, flux reversal effect can produce higher back electromotive forces than other topologies for the less amount of permanent magnets and thus can increase the performance of the machine. Combining the axial structure with the flux reversal effect feature allows higher power density machines suitable for high speed or low speed direct drive applications. Proposed model has a 12-slot stator and a 16-pole variable reluctance rotor. Nd-Fe-B magnets are fixed on the surface of the pole of the stator. The objective of this article is to present an effective method for the design and performance prediction for the axial flux reversal configuration. Basic dimension equations are presented and a two-dimensional equivalent model based on finite element analysis is used for the reduction of the simulation time.

Topor, Marcel; Chun, Yon-Do; Koo, Dae-Hyun; Han, Pil-Wan; Woo, Byung-Chul; Boldea, Ion

2008-04-01

86

Project in population genetics/genomics with applications to archeological genetics  

E-print Network

the genetic relationship between two humans has several applications in genetics, genealogy, archeology from simulations or from available sequence data). This should help to modify those existing methods in order to cope with the specific challenges of low-coverage sequence data. Finally, the modified method

Uppsala Universitet

87

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

88

Applications of terpene analysis in forest genetics  

Microsoft Academic Search

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

James W. Hanover

1992-01-01

89

Reversion mutation in dark variants of luminous bacteria and its application in gene toxicant monitoring  

NASA Astrophysics Data System (ADS)

The luminous intensity of dark variant separated form photobacterium phosphoreum is 1/10000 less than that of wild-type. Ethidium Bromide (EB), Mytomycin C(MC), 2-amino fluorine can all strongly induce reversion mutation for S1 within 24h and increase reversion ratio significantly. The results of experiments indicated that these revertants have stable genetic character and the mutation may take place at gene levels. The mutagenesis to S1 caused by EB, MC and 2-AF was detected and it may be a new rapid, simple and sensitive method of gene toxicant monitoring.

Sun, Yaliang; Guo, Jianli

2001-09-01

90

Application of Genetic Programming to High Energy Physics Event Selection  

E-print Network

We review genetic programming principles, their application to FOCUS data samples, and use the method to study the doubly Cabibbo suppressed decay D+ -> K+ pi+ pi- relative to its Cabibbo favored counterpart, D+ -> K- pi+ pi+. We find that this technique is able to improve upon more traditional analysis methods. To our knowledge, this is the first application of the genetic programming technique to High Energy Physics data.

Link, J M; Anjos, J C; Bediaga, I; Castromonte, C; Göbel, C; Machado, A A; Magnin, J; Massafferri, A; De Miranda, J M; Pepe, I M; Polycarpo, E; Dos Reis, A C; Carrillo, S; Casimiro, E; Cuautle, E; Sánchez-Hernández, A; Uribe, C; Vázquez, F; Agostino, L; Cinquini, L; Cumalat, J P; O'Reilly, B; Segoni, I; Stenson, K; Butler, J N; Cheung, H W K; Chiodini, G; Gaines, I; Garbincius, P H; Garren, L A; Gottschalk, E; Kasper, P H; Kreymer, A E; Kutschke, R; Wang, M; Benussi, L; Bertani, M; Bianco, S; Fabbri, Franco Luigi; Pacetti, S; Zallo, A; Reyes, M; Cawlfield, C; Kim, D Y; Rahimi, A; Wiss, J; Gardner, R; Kryemadhi, A; Chung, Y S; Kang, J S; Ko, B R; Kwak, J W; Lee, K B; Cho, K; Park, H; Alimonti, G; Barberis, S; Boschini, M; Cerutti, A; D'Angelo, P; Di Corato, M; Dini, P; Edera, L; Erba, S; Inzani, P; Leveraro, F; Malvezzi, S; Menasce, D; Mezzadri, M; Moroni, L; Pedrini, D; Pontoglio, C; Prelz, F; Rovere, M; Sala, S; Davenport, T F; Arena, V; Boca, G; Bonomi, G; Gianini, G; Liguori, G; Lopes-Pegna, D; Merlo, M M; Pantea, D; Ratti, S P; Riccardi, C; Vitulo, P; Hernández, H; López, A M; Méndez, H; Paris, A; Quinones, J; Ramírez, J E; Zhang, Y; Wilson, J R; Handler, T; Mitchell, R; Engh, D; Hosack, M; Johns, W E; Luiggi, E; Moore, J E; Nehring, M; Sheldon, P D; Vaandering, E W; Webster, M; Sheaff, M

2005-01-01

91

URCHIN: a reverse ray tracer for astrophysical applications  

NASA Astrophysics Data System (ADS)

We describe URCHIN, a reverse ray-tracing radiative transfer scheme optimized to model self-shielding from the post-reionization ultraviolet (UV) background in cosmological simulations. The reverse ray-tracing strategy provides several benefits over forward ray-tracing codes including: (1) the preservation of adaptive density field resolution; (2) completely uniform sampling of gas elements by rays; (3) the preservation of Galilean invariance; (4) the ability to sample the UV background spectrum with hundreds of frequency bins; and (5) exact preservation of the input UV background spectrum and amplitude in optically thin gas. The implementation described here focuses on smoothed particle hydrodynamics. However, the method can be applied to any density field representation in which resolution elements admit ray intersection tests and can be associated with optical depths. We characterize the errors in our implementation in stages beginning with comparison to known analytic solutions and ending with a realistic model of the z = 3 cosmological UV background incident on to a suite of spherically symmetric models of gaseous galactic haloes.

Altay, Gabriel; Theuns, Tom

2013-09-01

92

Polyglot programming in applications used for genetic data analysis.  

PubMed

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

Nowak, Robert M

2014-01-01

93

Identification of Novel Genes in Arabidopsis Involved in Secondary Cell Wall Formation Using Expression Profiling and Reverse Genetics  

PubMed Central

Forward genetic screens have led to the isolation of several genes involved in secondary cell wall formation. A variety of evidence, however, suggests that the list of genes identified is not exhaustive. To address this problem, microarray data have been generated from tissue undergoing secondary cell wall formation and used to identify genes that exhibit a similar expression pattern to the secondary cell wall–specific cellulose synthase genes IRREGULAR XYLEM1 (IRX1) and IRX3. Cross-referencing this analysis with publicly available microarray data resulted in the selection of 16 genes for reverse genetic analysis. Lines containing an insertion in seven of these genes exhibited a clear irx phenotype characteristic of a secondary cell wall defect. Only one line, containing an insertion in a member of the COBRA gene family, exhibited a large decrease in cellulose content. Five of the genes identified as being essential for secondary cell wall biosynthesis have not been previously characterized. These genes are likely to define entirely novel processes in secondary cell wall formation and illustrate the success of combining expression data with reverse genetics to address gene function. PMID:15980264

Brown, David M.; Zeef, Leo A.H.; Ellis, Joanne; Goodacre, Royston; Turner, Simon R.

2005-01-01

94

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

95

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

96

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. PMID:23144566

Costain, Gregory; Bassett, Anne S

2012-01-01

97

Generation of High-Yielding Influenza A Viruses in African Green Monkey Kidney (Vero) Cells by Reverse Genetics  

PubMed Central

Influenza A viruses are the cause of annual epidemics of human disease with occasional outbreaks of pandemic proportions. The zoonotic nature of the disease and the vast viral reservoirs in the aquatic birds of the world mean that influenza will not easily be eradicated and that vaccines will continue to be needed. Recent technological advances in reverse genetics methods and limitations of the conventional production of vaccines by using eggs have led to a push to develop cell-based strategies to produce influenza vaccine. Although cell-based systems are being developed, barriers remain that need to be overcome if the potential of these systems is to be fully realized. These barriers include, but are not limited to, potentially poor reproducibility of viral rescue with reverse genetics systems and poor growth kinetics and yields. In this study we present a modified A/Puerto Rico/8/34 (PR8) influenza virus master strain that has improved viral rescue and growth properties in the African green monkey kidney cell line, Vero. The improved properties were mediated by the substitution of the PR8 NS gene for that of a Vero-adapted reassortant virus. The Vero growth kinetics of viruses with H1N1, H3N2, H6N1, and H9N2 hemagglutinin and neuraminidase combinations rescued on the new master strain were significantly enhanced in comparison to those of viruses with the same combinations rescued on the standard PR8 master strain. These improvements pave the way for the reproducible generation of high-yielding human and animal influenza vaccines by reverse genetics methods. Such a means of production has particular relevance to epidemic and pandemic use. PMID:14747549

Ozaki, Hiroichi; Govorkova, Elena A.; Li, Chenghong; Xiong, Xiaoping; Webster, Robert G.; Webby, Richard J.

2004-01-01

98

Generation of high-yielding influenza A viruses in African green monkey kidney (Vero) cells by reverse genetics.  

PubMed

Influenza A viruses are the cause of annual epidemics of human disease with occasional outbreaks of pandemic proportions. The zoonotic nature of the disease and the vast viral reservoirs in the aquatic birds of the world mean that influenza will not easily be eradicated and that vaccines will continue to be needed. Recent technological advances in reverse genetics methods and limitations of the conventional production of vaccines by using eggs have led to a push to develop cell-based strategies to produce influenza vaccine. Although cell-based systems are being developed, barriers remain that need to be overcome if the potential of these systems is to be fully realized. These barriers include, but are not limited to, potentially poor reproducibility of viral rescue with reverse genetics systems and poor growth kinetics and yields. In this study we present a modified A/Puerto Rico/8/34 (PR8) influenza virus master strain that has improved viral rescue and growth properties in the African green monkey kidney cell line, Vero. The improved properties were mediated by the substitution of the PR8 NS gene for that of a Vero-adapted reassortant virus. The Vero growth kinetics of viruses with H1N1, H3N2, H6N1, and H9N2 hemagglutinin and neuraminidase combinations rescued on the new master strain were significantly enhanced in comparison to those of viruses with the same combinations rescued on the standard PR8 master strain. These improvements pave the way for the reproducible generation of high-yielding human and animal influenza vaccines by reverse genetics methods. Such a means of production has particular relevance to epidemic and pandemic use. PMID:14747549

Ozaki, Hiroichi; Govorkova, Elena A; Li, Chenghong; Xiong, Xiaoping; Webster, Robert G; Webby, Richard J

2004-02-01

99

Differential Equation Models and Numerical Methods for Reverse Engineering Genetic Regulatory Networks.  

E-print Network

??This dissertation develops and analyzes differential equation-based mathematical models and efficient numerical methods and algorithms for genetic regulatory network identification. The primary objectives of the… (more)

Yoon, Mi Un

2010-01-01

100

Cloned cDNA of A/swine/Iowa/15/1930 internal genes as a candidate backbone for reverse genetics vaccine against influenza A viruses  

PubMed Central

Reverse genetics viruses for influenza vaccine production usually utilize the internal genes of the egg-adapted A/Puerto Rico/8/34 (PR8) strain. This egg-adapted strain provides high production yield in embryonated eggs but does not necessarily give the best yield in mammalian cell culture. In order to generate a reverse genetics viral backbone that is well-adapted to high growth in mammalian cell culture, a swine influenza isolate (A/swine/Iowa/15/30 (H1N1) (rg1930) that was shown to give high yield in Madin-Darby Canine Kidney (MDCK) cells was used as the internal gene donor for reverse genetics plasmids. In this report, the internal genes from rg1930 were used for construction of reverse genetics viruses carrying a cleavage site-modified hemagglutinin (HA) gene and neuraminidase (NA) gene from a highly pathogenic H5N1 virus. The resulting virus (rg1930H5N1) was low pathogenic in vivo. Inactivated rg1930H5N1 vaccine completely protected chickens from morbidity and mortality after challenge with highly pathogenic H5N1. Protective immunity was obtained when chickens were immunized with an inactivated vaccine consisting of at least 29 HA units of the rg1930H5N1 virus. In comparison to the PR8-based reverse genetics viruses carrying the same HA and NA genes from an H5N1 virus, rg1930 based viruses yielded higher viral titers in MDCK and Vero cells. In addition, the reverse genetics derived H3N2 and H5N2 viruses with the rg1930 backbone replicated in MDCK cells better than the cognate viruses with the rgPR8 backbone. It is concluded that this newly established reverse genetics backbone system could serve as a candidate for a master donor strain for development of inactivated influenza vaccines in cell-based systems. PMID:22230579

Lekcharoensuk, Porntippa; Wiriyarat, Witthawat; Petcharat, Nuntawan; Lekcharoensuk, Chalermpol; Auewarakul, Prasert; Richt, Juergen A

2012-01-01

101

Applications of competitor RNA in diagnostic reverse transcription-PCR.  

PubMed

Detection of RNA viruses by reverse transcription (RT)-PCR has proven to be a useful approach for the diagnosis of infections caused by many viral pathogens. However, adequate controls are required for each step of the RT-PCR protocol to ensure the accuracies of diagnostic test results. Heterologous competitor RNA can be used as a control for a number of different aspects of diagnostic RT-PCR. Competitor RNA can be applied to assessments of the efficiency of RNA recovery during extraction procedures, detection of endogenous RT-PCR inhibitors that could lead to false-negative results, and quantification of viral template in samples used for diagnosis; competitor RNA can also be used as a positive control for the RT-PCR. In the present study, heterologous competitor RNA was synthesized by a method that uses two long oligonucleotide primers containing primer binding sites for RT-PCR amplification of porcine reproductive and respiratory syndrome virus or West Nile virus. Amplification of the competitor RNA by RT-PCR resulted in a product that was easily distinguished from the amplification product of viral RNA by agarose gel electrophoresis. Assessment of a variety of RNA samples prepared from routine submissions to a veterinary diagnostic laboratory found that either partial or complete inhibition of the RT-PCR could be demonstrated for approximately 20% of the samples. When inhibition was detected, either dilution of the sample or RNA extraction by an alternative protocol proved successful in eliminating the source of inhibition. PMID:12734248

Kleiboeker, Steven B

2003-05-01

102

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

NASA Technical Reports Server (NTRS)

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

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

1974-01-01

103

Applications of graph theory to landscape genetics  

Microsoft Academic Search

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

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

2008-01-01

104

Genetics in degenerative dementia: current status and applicability.  

PubMed

An increasing number of hereditary neurodegenerative diseases, including autosomal-dominant Alzheimer disease (AD), familial autosomal-dominant frontotemporal dementia (FTD), and heritable Lewy body disease (LBD) have been defined at the molecular level in recent years, making it possible to determine the genotype before the onset of symptoms. The identification of deterministic genes for these common adult-onset genetic diseases is moving the field of genetic counseling toward a new and challenging direction. With the identification of genes associated with AD and FTD, there is considerable interest in the clinical application of genetic information in genetic counseling and testing. Progress in the genetics of dementing disorders and the availability of clinical tests for practicing physicians therefore increases the need for a better understanding of the multifaceted issues associated with genetic testing. The aims of this systematic review are: (1) to underline the need to consider a genetic etiology of AD, FTD, and LBD; (2) to provide clinicians with information necessary to effectively translate genetic diagnosis into clinical practice; and (3) to highlight gaps and uncertainties in the field which will need to be addressed by future research. PMID:24805970

Bruni, Amalia C; Conidi, Maria E; Bernardi, Livia

2014-01-01

105

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

106

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

PubMed

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

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

2014-11-11

107

Genetic Data Simulators and their Applications: An Overview.  

PubMed

Computer simulations have played an indispensable role in the development and applications of statistical models and methods for genetic studies across multiple disciplines. The need to simulate complex evolutionary scenarios and pseudo-datasets for various studies has fueled the development of dozens of computer programs with varying reliability, performance, and application areas. To help researchers compare and choose the most appropriate simulators for their studies, we have created the genetic simulation resources (GSR) website, which allows authors of simulation software to register their applications and describe them with more than 160 defined attributes. This article summarizes the properties of 93 simulators currently registered at GSR and provides an overview of the development and applications of genetic simulators. Unlike other review articles that address technical issues or compare simulators for particular application areas, we focus on software development, maintenance, and features of simulators, often from a historical perspective. Publications that cite these simulators are used to summarize both the applications of genetic simulations and the utilization of simulators. PMID:25504286

Peng, Bo; Chen, Huann-Sheng; Mechanic, Leah E; Racine, Ben; Clarke, John; Gillanders, Elizabeth; Feuer, Eric J

2015-01-01

108

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

E-print Network

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

109

An introduction to genetics and application to Crohn's disease.  

PubMed

Gene-based diagnostics and therapeutics are being explored for application in many areas of healthcare. An understanding of the principles of genomics has become fundamental to patient care within all specialties of nursing and is expected to be included in certification exams in the near future. This introductory article is designed to provide practicing Wound, Ostomy, and Continence nurses with basic information to enhance their abilities to comprehend genetics information, apply it to practice, and translate it to colleagues and patients. Specifics about the genetic basis of Crohn's disease are used to illustrate the application of the concepts described in the article. PMID:17228211

Briones, Tess; Salvadalena, Ginger

2007-01-01

110

Analysis of reverse osmosis system performance using a genetic programming technique  

Microsoft Academic Search

Reverse osmosis (RO) membrane process has been considered a promising technology for water treatment and desalination. However, it is difficult to predict the performance of pilot- or full-scale RO systems because numerous factors are involved in RO performance, including membrane scaling, fouling, and deterioration. This study was intended to develop a practical model for the analysis of pilot-scale RO processes.

Seung-Min Park; Jihee Han; Sangho Lee; Jinsik Sohn; Young-Min Kim; June-Seok Choi; Suhan Kim

2012-01-01

111

Applications of graph theory to landscape genetics  

PubMed Central

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

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

2008-01-01

112

Genetic Algorithm Application in Optimization of Wireless Sensor Networks  

PubMed Central

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

Norouzi, Ali; Zaim, A. Halim

2014-01-01

113

Genetic algorithms and their applications in accelerator physics  

SciTech Connect

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

Hofler, Alicia S. [JLAB

2013-12-01

114

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

115

ORIGINAL ARTICLE A new scoring system in cancer genetics: application  

E-print Network

of cancer due to mutations of genes such as BRCA1 and BRCA2, methods have been proposed to predict incidence of these cancers and the high cost of testing render the exhaustive screening of mutationsORIGINAL ARTICLE A new scoring system in cancer genetics: application to criteria for BRCA1

Paris-Sud XI, Université de

116

Genetic Susceptibility and Survival: Application to Breast Cancer  

E-print Network

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

West, Mike

117

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

Microsoft Academic Search

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

Karen L. Wiebe; Bart Kempenaers

2009-01-01

118

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

ERIC Educational Resources Information Center

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

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

2009-01-01

119

7 Quantum Computing Applications of Genetic Programming  

Microsoft Academic Search

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

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

120

Quantitative genetic versions of Hamilton's rule with empirical applications  

PubMed Central

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

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

2014-01-01

121

Reverse genetic engineering of the human rhinovirus serotype 16 genome to introduce an antibody-detectable tag.  

PubMed

The ability to accurately detect viral proteins during infection is essential for virology research, and the lack of specific antibodies can make this detection difficult. Reverse genetic engineering of virus genomes to alter the wild-type genome is a powerful technique to introduce a detectable tag onto a viral protein. Here we outline a method to incorporate an influenza hemagglutinin epitope tag onto the 2A protease of HRV16. The method uses site-directed mutagenesis PCR to introduce the sequence for the HA antigen onto either the C or N termini of 2A protease while keeping the relevant internal cleavage sites intact. The new viral product is then cloned into a wild-type HRV16 plasmid and transfected into Ohio Hela cells to produce recombinant virus. PMID:25261314

Walker, Erin J; Jensen, Lora M; Ghildyal, Reena

2015-01-01

122

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

E-print Network

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

Wiesinger, J; Satinover, J

2010-01-01

123

Genetic correction using engineered nucleases for gene therapy applications.  

PubMed

Genetic mutations in humans are associated with congenital disorders and phenotypic traits. Gene therapy holds the promise to cure such genetic disorders, although it has suffered from several technical limitations for decades. Recent progress in gene editing technology using tailor-made nucleases, such as meganucleases (MNs), zinc finger nucleases (ZFNs), TAL effector nucleases (TALENs) and, more recently, CRISPR/Cas9, has significantly broadened our ability to precisely modify target sites in the human genome. In this review, we summarize recent progress in gene correction approaches of the human genome, with a particular emphasis on the clinical applications of gene therapy. PMID:24329887

Li, Hongmei Lisa; Nakano, Takao; Hotta, Akitsu

2014-01-01

124

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

125

RNA-interference-based functional genomics in mammalian cells: reverse genetics coming of age  

Microsoft Academic Search

Sequencing of complete genomes has provided researchers with a wealth of information to study genome organization, genetic instability, and polymorphisms, as well as a knowledge of all potentially expressed genes. The identification of all genes encoded in the human genome opens the door for large-scale systematic gene silencing using small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs). With the

Jose Silva; Kenneth Chang; Gregory J Hannon; Fabiola V Rivas

2004-01-01

126

A colorimetric temperature sensor of a cyanine dye supramolecule and its application in reversible switch  

NASA Astrophysics Data System (ADS)

A colorimetric temperature sensor is constructed based on the thermo-responsive switch of a cyanine dye supramolecule. With rising temperature, the supramolecule switches from J- to H-aggregate which is accompanied by obvious changes of absorption spectra and colour. This process can be accurately regulated by changing the concentrations of cyanine dye and metal ions, and it is also reproducible undergo multiple cycles. The results provide an application of cyanine dye supramolecules as a temperature sensor and reversible switch.

Sun, Hongxia; Xiang, Junfeng; Zhang, Xiufeng; Chen, Hongbo; Shi, Yunhua; Yu, Lijia; Yang, Qianfan; Li, Qian; Guan, Aijiao; Tang, Yalin

2014-08-01

127

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

PubMed Central

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

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

2014-01-01

128

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

PubMed

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

Xing, Wanjin; Morigen, Morigen

2014-10-01

129

SMART – Sunflower Mutant population And Reverse genetic Tool for crop improvement  

PubMed Central

Background Sunflower (Helianthus annuus L.) is an important oilseed crop grown widely in various areas of the world. Classical genetic studies have been extensively undertaken for the improvement of this particular oilseed crop. Pertaining to this endeavor, we developed a “chemically induced mutated genetic resource for detecting SNP by TILLING” in sunflower to create new traits. Results To optimize the EMS mutagenesis, we first conducted a “kill curve” analysis with a range of EMS dose from 0.5% to 3%. Based on the observed germination rate, a 50% survival rate i.e. LD50, treatment with 0.6% EMS for 8 hours was chosen to generate 5,000 M2 populations, out of which, 4,763 M3 plants with fertile seed set. Phenotypic characterization of the 5,000 M2 mutagenised lines were undertaken to assess the mutagenesis quality and to identify traits of interest. In the M2 population, about 1.1% of the plants showed phenotypic variations. The sunflower TILLING platform was setup using Endo-1-nuclease as mismatch detection system coupled with an eight fold DNA pooling strategy. As proof-of-concept, we screened the M2 population for induced mutations in two genes related to fatty acid biosynthesis, FatA an acyl-ACP thioesterase and SAD the stearoyl-ACP desaturase and identified a total of 26 mutations. Conclusion Based on the TILLING of FatA and SAD genes, we calculated the overall mutation rate to one mutation every 480 kb, similar to other report for this crop so far. As sunflower is a plant model for seed oil biosynthesis, we anticipate that the developed genetic resource will be a useful tool to identify novel traits for sunflower crop improvement. PMID:23496999

2013-01-01

130

Genetic Diversity of Simian Immunodeficiency Virus Encoding HIV-1 Reverse Transcriptase Persists in Macaques despite Antiretroviral Therapy ?  

PubMed Central

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-SHIVmne, 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

131

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

132

Development and application of biological technologies in fish genetic breeding.  

PubMed

Fish genetic breeding is a process that remolds heritable traits to obtain neotype and improved varieties. For the purpose of genetic improvement, researchers can select for desirable genetic traits, integrate a suite of traits from different donors, or alter the innate genetic traits of a species. These improved varieties have, in many cases, facilitated the development of the aquaculture industry by lowering costs and increasing both quality and yield. In this review, we present the pertinent literatures and summarize the biological bases and application of selection breeding technologies (containing traditional selective breeding, molecular marker-assisted breeding, genome-wide selective breeding and breeding by controlling single-sex groups), integration breeding technologies (containing cross breeding, nuclear transplantation, germline stem cells and germ cells transplantation, artificial gynogenesis, artificial androgenesis and polyploid breeding) and modification breeding technologies (represented by transgenic breeding) in fish genetic breeding. Additionally, we discuss the progress our laboratory has made in the field of chromosomal ploidy breeding of fish, including distant hybridization, gynogenesis, and androgenesis. Finally, we systematically summarize the research status and known problems associated with each technology. PMID:25595050

Xu, Kang; Duan, Wei; Xiao, Jun; Tao, Min; Zhang, Chun; Liu, Yun; Liu, ShaoJun

2015-02-01

133

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

PubMed Central

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

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

2014-01-01

134

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

PubMed Central

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

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

2014-01-01

135

Nash Genetic Algorithms : examples and applications M. Sefrioui  

E-print Network

Nash Genetic Algorithms : examples and applications M. Sefrioui LIP6, University Paris 6 4, Place. A strategy pair (x; y) 2 E#2;F is said to be a Nash equilibrium iff: fE (x; y) = inf x2E fE (x; y) fF (x; y) = inf y2F fF (x; y) It may also be defined by: u = (u 1 ; : : : ; uG ) is a Nash equilibrium iff: 8i; 8v

Coello, Carlos A. Coello

136

Cross flow filtration for radwaste applications reverse osmosis demonstration case studies  

SciTech Connect

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

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

1995-05-01

137

Novel and potential application of cryopreservation to plant genetic transformation.  

PubMed

The world population now is 6.7 billion and is predicted to reach 9 billion by 2050. Such a rapid growing population has tremendously increased the challenge for food security. Obviously, it is impossible for traditional agriculture to ensure the food security, while plant biotechnology offers considerable potential to realize this goal. Over the last 15 years, great benefits have been brought to sustainable agriculture by commercial cultivation of genetically modified (GM) crops. Further development of new GM crops will with no doubt contribute to meeting the requirements for food by the increasing population. The present article provides updated comprehensive information on novel and potential application of cryopreservation to genetic transformation. The major progresses that have been achieved in this subject include (1), long-term storage of a large number of valuable plant genes, which offers a good potential for further development of novel cultivars by genetic transformation; (2), retention of regenerative capacity of embryogenic tissues and protoplasts, which ensures efficient plant regeneration system for genetic transformation; (3), improvement of transformation efficiency and plant regeneration of transformed cells; (4), long-term preservation of transgenic materials with stable expression of transgenes and productive ability of recombinant proteins, which allows transgenic materials to be stored in a safe manner before being analyzed and evaluated, and allows establishment of stable seed stocks for commercial production of homologous proteins. Data provided in this article clearly demonstrate that cryo-technique has an important role to play in the whole chain of genetic transformation. Further studies coupling cryotechnique and genetic transformation are expected to significantly improve development of new GM crops. PMID:22079800

Wang, Biao; Zhang, Zhibo; Yin, Zhenfang; Feng, Chaohong; Wang, Qiaochun

2012-01-01

138

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

139

Reversible Thermal Denaturation of a 60-kDa Genetically Engineered ?-Sheet Polypeptide  

PubMed Central

A de novo 687-amino-acid residue polypeptide with a regular 32-amino-acid repeat sequence, (GA)3GY(GA)3GE(GA)3GH(GA)3GK, forms large ?-sheet assemblages that exhibit remarkable folding properties and, as well, form fibrillar structures. This construct is an excellent tool to explore the details of ?-sheet formation yielding intimate folding information that is otherwise difficult to obtain and may inform folding studies of naturally occurring materials. The polypeptide assumes a fully folded antiparallel ?-sheet/turn structure at room temperature, and yet is completely and reversibly denatured at 125°C, adopting a predominant polyproline II conformation. Deep ultraviolet Raman spectroscopy indicated that melting/refolding occurred without any spectroscopically distinct intermediates, yet the relaxation kinetics depend on the initial polypeptide state, as would be indicative of a non-two-state process. Thermal denaturation and refolding on cooling appeared to be monoexponential with characteristic times of ?1 and ?60 min, respectively, indicating no detectable formation of hairpin-type nuclei in the millisecond timescale that could be attributed to nonlocal “nonnative” interactions. The polypeptide folding dynamics agree with a general property of ?-sheet proteins, i.e., initial collapse precedes secondary structure formation. The observed folding is much faster than expected for a protein of this size and could be attributed to a less frustrated free-energy landscape funnel for folding. The polypeptide sequence suggests an important balance between the absence of strong nonnative contacts (salt bridges or hydrophobic collapse) and limited repulsion of charged side chains. PMID:16891363

Lednev, Igor K.; Ermolenkov, Vladimir V.; Higashiya, Seiichiro; Popova, Ludmila A.; Topilina, Natalya I.; Welch, John T.

2006-01-01

140

Testing for beneficial reversal of dominance during salinity shifts in the invasive copepod Eurytemora affinis, and implications for the maintenance of genetic variation.  

PubMed

Maintenance of genetic variation at loci under selection has profound implications for adaptation under environmental change. In temporally and spatially varying habitats, non-neutral polymorphism could be maintained by heterozygote advantage across environments (marginal overdominance), which could be greatly increased by beneficial reversal of dominance across conditions. We tested for reversal of dominance and marginal overdominance in salinity tolerance in the saltwater-to-freshwater invading copepod Eurytemora affinis. We compared survival of F1 offspring generated by crossing saline and freshwater inbred lines (between-salinity F1 crosses) relative to within-salinity F1 crosses, across three salinities. We found evidence for both beneficial reversal of dominance and marginal overdominance in salinity tolerance. In support of reversal of dominance, survival of between-salinity F1 crosses was not different from that of freshwater F1 crosses under freshwater conditions and saltwater F1 crosses under saltwater conditions. In support of marginal overdominance, between-salinity F1 crosses exhibited significantly higher survival across salinities relative to both freshwater and saltwater F1 crosses. Our study provides a rare empirical example of complete beneficial reversal of dominance associated with environmental change. This mechanism might be crucial for maintaining genetic variation in salinity tolerance in E. affinis populations, allowing rapid adaptation to salinity changes during habitat invasions. PMID:25135455

Posavi, Marijan; Gelembiuk, Gregory William; Larget, Bret; Lee, Carol Eunmi

2014-11-01

141

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

PubMed

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

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

2015-01-15

142

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

PubMed Central

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

2012-01-01

143

Application of Ionic Liquids in High Performance Reversed-Phase Chromatography  

PubMed Central

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

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

2009-01-01

144

Reverse Genetic Screening Identifies Five E-class PPR Proteins Involved in RNA Editing in Mitochondria of Arabidopsis thaliana*  

PubMed Central

RNA editing in flowering plant mitochondria post-transcriptionally alters several hundred nucleotides from C to U, mostly in mRNAs. Several factors required for specific RNA-editing events in plant mitochondria and plastids have been identified, all of them PPR proteins of the PLS subclass with a C-terminal E-domain and about half also with an additional DYW domain. Based on this information, we here probe the connection between E-PPR proteins and RNA editing in plant mitochondria. We initiated a reverse genetics screen of T-DNA insertion lines in Arabidopsis thaliana and investigated 58 of the 150 E-PPR-coding genes for a function in RNA editing. Six genes were identified to be involved in mitochondrial RNA editing at specific sites. Homozygous mutants of the five genes MEF18-MEF22 display no gross disturbance in their growth or development patterns, suggesting that the editing sites affected are not crucial at least in the greenhouse. These results show that a considerable percentage of the E-PPR proteins are involved in the functional processing of site-specific RNA editing in plant mitochondria. PMID:20566637

Takenaka, Mizuki; Verbitskiy, Daniil; Zehrmann, Anja; Brennicke, Axel

2010-01-01

145

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

PubMed Central

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

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

2014-01-01

146

Applications of a formal approach to decipher discrete genetic networks  

PubMed Central

Background A growing demand for tools to assist the building and analysis of biological networks exists in systems biology. We argue that the use of a formal approach is relevant and applicable to address questions raised by biologists about such networks. The behaviour of these systems being complex, it is essential to exploit efficiently every bit of experimental information. In our approach, both the evolution rules and the partial knowledge about the structure and the behaviour of the network are formalized using a common constraint-based language. Results In this article our formal and declarative approach is applied to three biological applications. The software environment that we developed allows to specifically address each application through a new class of biologically relevant queries. We show that we can describe easily and in a formal manner the partial knowledge about a genetic network. Moreover we show that this environment, based on a constraint algorithmic approach, offers a wide variety of functionalities, going beyond simple simulations, such as proof of consistency, model revision, prediction of properties, search for minimal models relatively to specified criteria. Conclusions The formal approach proposed here deeply changes the way to proceed in the exploration of genetic and biochemical networks, first by avoiding the usual trial-and-error procedure, and second by placing the emphasis on sets of solutions, rather than a single solution arbitrarily chosen among many others. Last, the constraint approach promotes an integration of model and experimental data in a single framework. PMID:20646302

2010-01-01

147

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

Microsoft Academic Search

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

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

2009-01-01

148

Identification of genes necessary for wild-type levels of seed phytic acid in Arabidopsis thaliana using a reverse genetics approach  

Microsoft Academic Search

The majority of phosphorus (P) in seeds is found in phytic acid (InsP6) which accumulates as the mixed salt phytate. InsP6 is generally considered to be an anti-nutrient and the development of low phytic acid (lpa) seed crops is of significant interest. We have employed a reverse genetics approach to examine the impact of disrupting\\u000a genes involved in inositol phosphate

Sang-Ic Kim; Thomas H. Tai

2011-01-01

149

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

150

A systemic gene silencing method suitable for high throughput, reverse genetic analyses of gene function in fern gametophytes  

PubMed Central

Background Ceratopteris richardii is a useful experimental system for studying gametophyte development and sexual reproduction in plants. However, few tools for cloning mutant genes or disrupting gene function exist for this species. The feasibility of systemic gene silencing as a reverse genetics tool was examined in this study. Results Several DNA constructs targeting a Ceratopteris protoporphyrin IX magnesium chelatase (CrChlI) gene that is required for chlorophyll biosynthesis were each introduced into young gametophytes by biolistic delivery. Their transient expression in individual cells resulted in a colorless cell phenotype that affected most cells of the mature gametophyte, including the meristem and gametangia. The colorless phenotype was associated with a 7-fold decrease in the abundance of the endogenous transcript. While a construct designed to promote the transient expression of a CrChlI double stranded, potentially hairpin-forming RNA was found to be the most efficient in systemically silencing the endogenous gene, a plasmid containing the CrChlI cDNA insert alone was sufficient to induce silencing. Bombarded, colorless hermaphroditic gametophytes produced colorless embryos following self-fertilization, demonstrating that the silencing signal could be transmitted through gametogenesis and fertilization. Bombardment of young gametophytes with constructs targeting the Ceratopteris filamentous temperature sensitive (CrFtsZ) and uroporphyrin dehydrogenase (CrUrod) genes also produced the expected mutant phenotypes. Conclusion A method that induces the systemic silencing of target genes in the Ceratopteris gametophyte is described. It provides a simple, inexpensive and rapid means to test the functions of genes involved in gametophyte development, especially those involved in cellular processes common to all plants. PMID:15090074

Rutherford, George; Tanurdzic, Milos; Hasebe, Mitsuyasu; Banks, Jo Ann

2004-01-01

151

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

PubMed

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

Hanafy, Sherif M; Schuster, Gerard T

2011-10-01

152

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

2012-03-01

153

Inverse/genetic method and its application in identification of mechanical parameters of interface in composite  

E-print Network

into an inverse approximation problem using the method which includes finite element method and genetic algorithms of interface; Inverse/genetic method; Hybrid analysis; Finite element method 1. Introduction With modernInverse/genetic method and its application in identification of mechanical parameters of interface

Qin, Qinghua

154

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

E-print Network

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

155

New applications of the genetic algorithm for the interpretation of high-resolution spectra1  

E-print Network

804 New applications of the genetic algorithm for the interpretation of high-resolution spectra1 W. An alternative approach is unassigned fits of the spectra using genetic algorithms (GAs) with special cost, genetic algorithm, biomolecules, structure, van der Waals clusters. Résumé : La spectroscopie électronique

Nijmegen, University of

156

Graph Classification Using Genetic Algorithm and Graph Probing Application to Symbol Recognition  

E-print Network

Graph Classification Using Genetic Algorithm and Graph Probing Application to Symbol Recognition classification approach using genetic algorithm and a fast dissimilarity measure between graphs called graph this learning set, a graph based Genetic Algorithm (GA) is applied. Its aim is to generate a set of K graph

Paris-Sud XI, Université de

157

Application of genetic algorithm to the calculation of bound states and local density approximations  

E-print Network

Application of genetic algorithm to the calculation of bound states and local density; accepted 16 November 1994 A novel method, based on genetic algorithms, has been developed and applied. © 1995 American Institute of Physics. I. INTRODUCTION Genetic algorithms GA are global optimization meth

Zeiri, Yehuda

158

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.

159

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

160

The multi-niche crowding genetic algorithm: Analysis and applications  

SciTech Connect

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

Cedeno, W.

1995-09-01

161

Genetic Characterization of a Mammalian Protein-Protein Interaction Domain by Using a Yeast Reverse Two-Hybrid System  

Microsoft Academic Search

Many biological processes rely upon protein-protein interactions. Hence, detailed analysis of these interactions is critical for their understanding. Due to the complexities involved, genetic approaches are often needed. In yeast and phage, genetic characterizations of protein complexes are possible. However, in multicellular organisms, such characterizations are limited by the lack of powerful selection systems. Herein we describe genetic selections that

Marc Vidal; Pascal Braun; Elbert Chen; Jef D. Boeke; Ed Harlow

1996-01-01

162

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

PubMed Central

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

2014-01-01

163

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

164

Innovative applications of genetic algorithms to problems in accelerator physics  

NASA Astrophysics Data System (ADS)

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

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

2013-01-01

165

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

166

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

E-print Network

Volume 10, Issue 1 2011 Article 46 Statistical Applications in Genetics and Molecular Biology Applications in Genetics and Molecular Biology: Vol. 10: Iss. 1, Article 46. DOI: 10 studied by Genzer-Nir et al. has been introduced by germline mosaicism. KEYWORDS: linkage analysis

Friedman, Nir

167

Physics and Application of Streamer Discharge Produced by Polarity-Reversed Voltage Pulse for Environmental Protection Technology  

NASA Astrophysics Data System (ADS)

This paper summarizes physical properties of pulsed streamer discharges caused by very fast polarity-reversals of an applied voltage and remarkable results of discharge treatments using the polarity-reversed voltage pulses in pollution control for exhausted gases and wasted water. The very fast polarity-reversal just after a dc voltage application is produced by direct-grounding of a charged coaxial cable because a traveling wave voltage reciprocates along the cable with a change in its polarity due to impedance mismatching between the grounding end and the coaxial cable. The inception voltage of streamer discharges in an air gap with a glass barrier subjected to the polarity-reversed pulse is much lower than that subjected to a mono-polar single pulse without the dc bias because charges accumulation on the glass surface under the dc field causes field enhancement in the air gap just after the polarity reversal. Due to the space charge effect in the discharge treatment with the polarity-reversed pulses, energy efficiency for removal of pollutants in gases, such as nitrogen oxides and volatile organic compounds produced in various manufacturing processes, can be high as compared with a classical barrier discharge treatment. Experimental results on decomposition of organic compounds in water and on inactivation of microorganisms in water are also reviewed.

Kadowaki, Kazunori; Kitani, Isamu

168

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

169

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

170

F?NANSTA EVR?MSEL ALGOR?TM?K YAKLA?IMLAR: GENET?K ALGOR?TMA UYGULAMALARI EVOLUTIONARY ALGORITHMIC APPROACHES IN FINANCE: APPLICATIONS OF GENETIC ALGORITHMS  

Microsoft Academic Search

The objective of this study is to review genetic algorithms, which are evolution and natural genetic process based stochastic search and optimization techniques, and their financial applications. First, the concepts of evolutionary algorithms and genetic algortihms are explained. Then, literature on the applications of genetic algorithms on finance is reviewed. Financial applications of genetic algoritms are analyzed under two main

Hakan ER; M. Koray

171

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

PubMed

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

Porteri, Corinna

2013-08-01

172

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

NASA Technical Reports Server (NTRS)

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

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

1974-01-01

173

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

174

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

175

High performance and reversible ionic polypeptide hydrogel based on charge-driven assembly for biomedical applications.  

PubMed

In the pursuit of new strategies for the design and synthesis of high performance, physically associated hydrogels, dynamic materials formed through electrostatic interactions can serve as a powerful model. Here, we introduce a convenient strategy to obtain biodegradable hydrogels from ABA triblock ionic polypeptides formed by mixing poly(l-glutamic acid)-block-poly(ethylene glycol)-block-poly(l-glutamic acid) (PGA-PEG-PGA) with poly(l-lysine)-block-poly(ethylene glycol)-block-poly(l-lysine) (PLL-PEG-PLL). The hydrogels showed tunable physical properties, high strength and reversible response. The reactive function groups in the ionic blocks can conjugate with oppositely charged drugs or proteins and allow for further modification. These ionic ABA triblock polyelectrolytes can also encapsulate intact cells without significantly compromising cell viability, suggesting that the hydrogels have excellent cytocompatibility. In vivo evaluation performed in rats with subcutaneous injection indicated that the gels were formed and degraded, and hematoxylin and eosin staining suggested good biocompatibility in vivo. In addition, these advantages, combined with the synthetic accessibility of the copolymer, make this cross-linking system a flexible and powerful new tool for the development of injectable hydrogels for biomedical applications. PMID:25242655

Cui, Haitao; Zhuang, Xiuli; He, Chaoliang; Wei, Yen; Chen, Xuesi

2015-01-01

176

Hybrid Stirling / Reverse Brayton and Multi-stage Brayton Cryocoolers for Space Applications  

NASA Astrophysics Data System (ADS)

Space infrared (IR) sensor applications place demanding requirements on the cryogenic cooling system. These systems must typically have 8+ year life and very high reliability, typically >0.95 at eight years. This has been achieved by several companies, including Raytheon with Stirling-class machines and by Creare with reverse turbo Brayton (RTB) devices. Other requirements virtually always present for space cryocoolers include low mass, high efficiency, and low vibration output. For typical space infrared sensor cryogenic cooling applications, existing Stirling-class cryocoolers (which includes pulse tubes) excel relative to the RTB with respect to mass and often efficiency, but the RTB exports much less vibration. An additional requirement sometimes present for a given payload is that the refrigeration must be provided remotely, perhaps several meters from the ambient environment where the cryocooler machinery typically resides and to which the waste heat must be rejected. A Stirling-class machine cannot meet this last requirement unless it is coupled with a single- or two-phase pumped loop, a cryogenic heat pipe, or a recirculating cooling system. One approach is to combine a Stirling-class machine with a Joule-Thomson (JT) cooling system. Another approach, one that embodies important reliability and integration benefits, is to combine a Stirling-class cryocooler with a RTB cryocooler. The case study results for a particular Stirling-Brayton hybrid system are presented, along with a discussion of its integration characteristics. Such a hybrid system, if properly designed, accentuates the advantages and mitigates the weaknesses of the individual technologies. Finally, the hybrid approach is compared to a straightforward multi-stage RTB cryocooler.

Kirkconnell, C. S.; Zagarola, M. V.; Russo, J. T.

2006-04-01

177

Current and future applications of genetics in primary care medicine.  

PubMed

Individualized medical treatment and prevention based on one's genetic makeup are promises likely to be fulfilled over decades. Already family history is taking a more prominent role in preventive care. Primary care clinicians and geneticists will increasingly collaborate to diagnose and manage genetic conditions: both single-gene disorders and multifactorial diseases such as infections,cancers, cardiovascular disease and mental illness. This will require society, with primary care clinicians in the forefront, to implement means for efficient family history-taking; maintaining private, personally accessible genetic health records; safeguarding people from genetic discrimination; distributing access to scarce genetic specialists and expensive technologies; rectifying lay misconceptions about inheritance; managing emotional responses and family dynamics related to genetic diagnosis; and motivating people at increased familial risk to take preventive action. PMID:15331241

Acheson, Louise S; Wiesner, Georgia L

2004-09-01

178

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

PubMed

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

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

2015-04-15

179

Current Applications of Models of Genetic Effects with Interactions Across the Genome  

PubMed Central

Models of genetic effects integrate the action of genes, regulatory regions and interactions among alleles across the genome. Such theoretical frameworks are critical for applied studies in at least two ways. First, discovering genetic networks with specific effects underlying traits in populations requires the development of models that implement those effects as parameters—adjusting the implementation of epistasis parameters in genetic models has for instance been a requirement for properly testing for epistasis in gene-mapping studies. Second, studying the properties and implications of models of genetic effects that involve complex genetic networks has proven to be valuable, whether those networks have been revealed for particular organisms or inferred to be of interest from theoretical works and simulations. Here I review the current state of development and recent applications of models of genetic effects. I focus on general models aiming to depict complex genotype-to-phenotype maps and on applications of them to networks of interacting loci. PMID:23024608

Álvarez-Castro, José M

2012-01-01

180

Genetic algorithm and the application for job shop group scheduling  

NASA Astrophysics Data System (ADS)

Genetic algorithm (GA) is a heuristic and random search technique mimicking nature. This paper first presents the basic principle of GA, the definition and the function of the genetic operators, and the principal character of GA. On the basis of these, the paper proposes using GA as a new solution method of the job-shop group scheduling problem, discusses the coded representation method of the feasible solution, and the particular limitation to the genetic operators.

Mao, Jianzhong; Wu, Zhiming

1995-08-01

181

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

182

Application Of Genetic Algorithms To The Discovery Of Complex Models For Simulation Studies In Human Genetics  

Microsoft Academic Search

Simulation studies are useful in various disciplines for a number of reasons including the development and evaluation of new computational and statistical methods. This is particularly true in human genetics and genetic epidemiology where new analytical methods are needed for the detection and characterization of disease susceptibility genes whose effects are complex, nonlinear, and partially or solely dependent on the

Jason H. Moore; Lance W. Hahn; Marylyn D. Ritchie; Tricia A. Thornton; Bill C. White

2002-01-01

183

The reverse cholesterol transport pathway improves understanding of genetic networks for fat deposition and muscle growth in beef cattle  

Technology Transfer Automated Retrieval System (TEKTRAN)

In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F1 bulls, 113 ...

184

Application of improved genetic algorithm in camera calibration  

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

185

Application of a genetic algorithm to doping profile identification  

Microsoft Academic Search

This work describes a new approach to CV dopant profiling by means of nonlinear least squares inverse modeling. It is shown that a genetic algorithm can replace standard nonlinear minimization procedure in identification of doping profile parameters. The most important advantages of the genetic algorithm are in its ability to avoid local minima and often in faster convergence in \\

W. Kuzmicz

1996-01-01

186

Applications of probability in molecular population genetics of humans and flies  

E-print Network

Applications of probability in molecular population genetics of humans and flies Andy Clark Cornell/9) + (10/36)}/20 in humans is about 0.0008 Molecular population genetic with a SPARSE multi 5 ATAGCTAGCTAA · Allele 6 CTAGCTAAACG Multi-alignment from a whole genome shotgun · Allele 1

Durrett, Richard

187

Review of capture-recapture methods applicable to noninvasive genetic sampling  

Microsoft Academic Search

The use of noninvasive genetic sampling to identify individual animals for capture-recapture studies has become widespread in the past decade. Strong emphasis has been placed on the field protocols and genetic analyses with fruitful results. Little attention has been paid to the capture-recapture application for this specific type of data beyond stating the effects of assumption violations. Here, we review

PAUL M. L UKACS; KENNETH P. B URNHAM

2005-01-01

188

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

189

Reverse torque failure of screw-shaped implants in baboons: baseline data for abutment torque application.  

PubMed

Torque failure for endosseous implants has been used as a biomechanical measure of anchorage, though the significance of such data is not known. A practical understanding of the resistance to torque failure of implant-tissue interfaces at stage 2 surgery would help in assigning torque levels for implant abutment-screw fastening. The purpose of this study was to measure torque failure levels of commercially pure (CP) titanium, Ti-6Al-4V, hydroxyapatite-coated (HA-coated) screw-shaped implants placed into the maxillae and mandibles of baboons. Implants identical in size were placed into the edentulous posterior maxillae and mandibles of six female baboons (n = 37 each group) using a standardized surgical protocol. Reverse-torque data were collected at postinsertion time intervals ranging from 3 to 4 months using a counterclockwise torque driver and the data were analyzed (repeated measures ANOVA) for torque differences related to time, biomaterial, and jaw. The HA-coated implants exhibited significantly greater torque-removal values compared to both metallic implants (HA: 186.0 Ncm [50.1]; Ti-6Al-4V: 78.6 Ncm [18.1]; CP Ti 74.0 Ncm [24.4]). Analysis of torque interactions with jaw showed no significant difference; however, the mandible was found to be greater than the maxilla in torque resistance for all groups tested. Understanding the risks in inferring animal data to human application, the clinical implications of these data suggest that the recommended torque level of 35 Ncm for abutment fastening may provide a margin of safety for most implants of similar design and material as used in this study.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7744435

Carr, A B; Larsen, P E; Papazoglou, E; McGlumphy, E

1995-01-01

190

Epigenetics and Evolutionary Genetics The Department of Biological Science invites applications for tenure-track faculty  

E-print Network

Epigenetics and Evolutionary Genetics The Department of Biological Science invites applications. For more information see http://www.bio.fsu.edu/genphensearch/ . Epigenetics: Researchers investigating fundamental aspects of chromatin or RNA­ mediated regulation of phenotypic variation, epigenetic mechanisms

Bass, Hank W.

191

Genetic particle filter application to land surface temperature downscaling  

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

192

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

PubMed Central

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

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

2014-01-01

193

Interleaved water and fat imaging and applications to lipid quantitation using the gradient reversal technique  

Microsoft Academic Search

Purpose: To implement and evaluate the gradient reversal- based chemical shift imaging technique to obtain qualita- tive and quantitative spatially-registered fat and water im- ages with high imaging efficiency at very high field. Materials and Methods: A multiecho gradient reversal- based sequence allowing interleaved water-fat imaging during a single acquisition and quantitation of fat\\/water content is presented. The sequence was

Haiying Tang; Ed X. Wu; Richard Kennan; Haiying Liu; Donald S. Williams

2007-01-01

194

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

NASA Technical Reports Server (NTRS)

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

Fiebrich, Rolf-Dieter

1987-01-01

195

Cystic fibrosis genetics: from molecular understanding to clinical application.  

PubMed

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

Cutting, Garry R

2015-01-01

196

Genetically engineered phage fibers and coatings for antibacterial applications  

E-print Network

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

Mao, Joan Y

2009-01-01

197

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

198

Development of A Reverse Genetic System for Infectious Salmon Anemia Virus (ISAV): Rescue of Recombinant Fluorescence Virus Using Salmon ITS-1 Region as a Novel Promoter.  

PubMed

The Infectious salmon anemia (ISA) is a serious disease of marine-farmed Atlantic salmon (Salmo salar) caused by ISA virus (ISAV), belonging to the genus Isavirus, family Orthomyxoviridae. There is an urgent need to understand the virulence factors and pathogenic mechanisms of ISAV and to develop new vaccine approaches. Using a recombinant molecular biology approach, we report for the first time the development of a plasmid based reverse genetic system for ISAV, which includes the use of a novel fish promoter, the Atlantic salmon ITS-1. Salmon cells co-transfected with pSS-URG-based vectors expresings the eight viral RNA segments and four CMV-based vectors that express the four proteins of the ISAV ribonucleoprotein complex allowed the generation of infectious recombinant ISAV (rISAV). We generated three recombinant viruses, a wild type rISAV(901_09) and rISAVr(S6-NotI-HPR) containing a NotI restriction site and rISAV(S6/EGFP-HPR) harbouring the ORF of enhanced green fluorescent protein (EGFP), both within the HPR region of segment 6. All rescued viruses showed replication activity and cytopathic effect in ASK infected cells. The fluorescent recombinant viruses also showed a characteristic cytopathic effect in salmon cells, and the viruses replicated to a titer of 6.5 x 10(5) PFU/ml, similar to that of the wild-type virus. This novel reverse genetics system offers a powerful tool to study the molecular biology of ISAV and develop new generation of ISAV vaccines to prevent and mitigate ISAV infection, which has had a profound effect on the salmon industry. PMID:25480750

Toro-Ascuy, Daniela; Tambley, Carolina; Beltran, Carolina; Mascayano, Carolina; Sandoval, Nicolas; Olivares, Eduardo; Medina, Rafael A; Spencer, Eugenio; Cortez-San Martín, Marcelo

2014-12-01

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

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

201

Clinical Application of Genetics in Management of Colorectal Cancer  

PubMed Central

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

Kim, Eun Ran

2014-01-01

202

Genetics and the general physician: insights, applications and future challenges.  

PubMed

Scientific and technological advances in our understanding of the nature and consequences of human genetic variation are now allowing genetic determinants of susceptibility to common multifactorial diseases to be defined, as well as our individual response to therapy. I review how genome-wide association studies are robustly identifying new disease susceptibility loci, providing insights into disease pathogenesis and potential targets for drug therapy. Some of the remarkable advances being made using current genetic approaches in Crohn's disease, coronary artery disease and atrial fibrillation are described, together with examples from malaria, HIV/AIDS, asthma, prostate cancer and venous thrombosis which illustrate important principles underpinning this field of research. The limitations of current approaches are also noted, highlighting how much of the genetic risk remains unexplained and resolving specific functional variants difficult. There is a need to more clearly understand the significance of rare variants and structural genomic variation in common disease, as well as epigenetic mechanisms. Specific examples from pharmacogenomics are described including warfarin dosage and prediction of abacavir hypersensitivity that illustrate how in some cases such knowledge is already impacting on clinical practice, while in others prospective evaluation of clinical utility and cost-effectiveness is required to define opportunities for personalized medicine. There is also a need for a broader debate about the ethical implications of current advances in genetics for medicine and society. PMID:19737788

Knight, J C

2009-11-01

203

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

EPA Science Inventory

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

204

Extensive Recombination-Induced Disruption of Genetic Interactions Is Highly Deleterious but Can Be Partially Reversed by Small Numbers of Secondary Recombination Events  

PubMed Central

ABSTRACT Although homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary among these is the disruption of favorable coevolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped by either compensatory mutations or secondary recombination events. Here, we used a maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption and the capacity of secondary recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesized two of the most extreme conceivable MSV chimeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimeras were severely defective and apparently noninfectious, neither had individual movement-, encapsidation-, or replication-associated genome regions that were on their own “lethally recombinant.” Surprisingly, mixed inoculations of the chimeras yielded symptomatic infections with viruses with secondary recombination events. These recombinants had only 2 to 6 breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments, and were obviously far more fit than their synthetic parents. It is clearly evident, therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to full recovery, small numbers of secondary recombination events can still yield tremendous fitness gains. IMPORTANCE Recombination between viruses can generate strains with enhanced pathological properties but also runs the risk of producing hybrid genomes with decreased fitness due to the disruption of favorable genetic interactions. Using two synthetic maize streak virus genome chimeras containing alternating genome segments derived from two natural viral strains, we examined both the fitness costs of extreme degrees of recombination (both chimeras had 182 recombination breakpoints) and the capacity of secondary recombination events to recoup these costs. After the severely defective chimeras were introduced together into a suitable host, viruses with between 1 and 3 secondary recombination events arose, which had greatly increased replication and infective capacities. This indicates that even in extreme cases where recombination-induced genetic disruptions are almost lethal, and 91 consecutive secondary recombination events would be required to reconstitute either one of the parental viruses, moderate degrees of fitness recovery can be achieved through relatively small numbers of secondary recombination events. PMID:24789787

Monjane, Adérito L.; Lakay, Francisco; Muhire, Brejnev M.; Pande, Daniel; Varsani, Arvind; Harkins, Gordon; Shepherd, Dionne N.; Rybicki, Edward P.

2014-01-01

205

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

206

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

207

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

208

Genetics  

NSDL National Science Digital Library

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

Doherty, Jennifer; Waldron, Ingrid; Poethig, Scott

209

Genetics  

MedlinePLUS

... made up of strands of genetic information called DNA. Genes are sections of DNA. The location of the gene is called the ... differences occur in less than 1% of the DNA sequence and produce variants of a particular gene ...

210

Application of immersed MF (IMF) followed by reverse osmosis (RO) membrane for wastewater reclamation: A case study in Malaysia.  

PubMed

A pilot scale membrane plant was constructed and monitored in Shah Alam, Malaysia for municipal wastewater reclamation for industrial application purposes. The aim of this study was to verify its suitability under the local conditions and environmental constraints for secondary wastewater reclamation. Immersed-type crossflow microfiltration (IMF) was selected as the pretreatment step before reverse osmosis filtration. Secondary wastewater after chlorine contact tank was selected as feed water. The results indicated that the membrane system is capable of producing a filtrate meeting the requirements of both WHO drinking water standards and Malaysian Effluent Standard A. With the application of an automatic backwash process, IMF performed well in hydraulic performance with low fouling rate being achieved. The investigations showed also that chemical cleaning is still needed because of some irreversible fouling by microorganisms always remains. RO treatment with IMF pretreatment process was significantly applicable for wastewater reuse purposes and promised good hydraulic performance. PMID:18025737

Ujang, Z; Ng, K S; Tg Hamzah, Tg Hazmin; Roger, P; Ismail, M R; Shahabudin, S M; Abdul Hamid, M H

2007-01-01

211

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

PubMed Central

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

2011-01-01

212

Efficient reverse genetics reveals genetic determinants of budding and fusogenic differences between Nipah and Hendra virus and enables real-time monitoring of viral spread in small animal models of henipavirus infection.  

PubMed

Nipah (NiV) and Hendra (HeV) viruses are closely related henipaviruses of the Paramyxovirinae. Spillover from their fruit bat reservoirs can cause severe disease in humans and livestock. Despite their high sequence similarity, NiV and HeV exhibit apparent differences in receptor and tissue tropism, envelope-mediated fusogenicity, replicative fitness, and other pathophysiologic manifestations. To investigate the molecular basis for these differences, we first established a highly efficient reverse genetics system that increased rescue titers by ?3 logs, which offset the difficulty of generating multiple recombinants under constraining BSL-4 conditions. We then substituted singly and in combination, the matrix (M), fusion (F), and attachment glycoprotein (G) genes in mCherry-expressing recombinant NiV (rNiV) with their HeV counterparts. These chimeric but isogenic rNiVs replicated well in primary human endothelial and neuronal cells, indicating efficient heterotypic complementation. The determinants of budding efficiency, fusogenicity, and replicative fitness were dissociable: HeV-M budded more efficiently than NiV-M, accounting for the early higher replicative titers of HeV-M-bearing chimeras, while the enhanced fusogenicity of NiV-G-bearing chimeras did not correlate with increased replicative fitness. Furthermore, to facilitate spatiotemporal studies on henipavirus pathogenesis, we generated a Firefly luciferase-expressing NiV and monitored virus replication and spread in infected interferon-?/? receptor knockout mice via bioluminescence imaging. While intraperitoneal inoculation resulted in neuroinvasion following systemic spread and respiratory tract replication, intranasal inoculation resulted in confined spread to regions corresponding to olfactory bulbs and salivary glands before subsequent neuroinvasion. This optimized henipavirus reverse genetics system will facilitate future investigations into the growing numbers of novel henipa-like viruses. PMID:25392218

Yun, Tatyana; Park, Arnold; Hill, Terence E; Pernet, Olivier; Beaty, Shannon M; Juelich, Terry L; Smith, Jennifer K; Zhang, Lihong; Wang, Yao E; Vigant, Frederic; Gao, Junling; Wu, Ping; Lee, Benhur; Freiberg, Alexander N

2014-11-12

213

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. PMID:22253801

van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

2012-01-01

214

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

PubMed

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

Hurtado, Ana

2015-01-01

215

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

216

Exfoliative Toxin Detection Using Reversed Passive Latex Agglutination: Clinical and Epidemiologic Applications  

Microsoft Academic Search

A rapid and simple method for detecting exfoliative toxin serotypes A and B from clinical isolates has been developed as a test kit (EXT-RPLA; Denka Seiken Co. Ltd., Niigata, Japan). This method is based on reversed passive latex agglutination. The detection limit of the EXT-RPLA observed for purified exfoliative toxin serotypes A and B was 1 ng\\/ml. We evaluated the

ATSUSHI KAWABATA; SATOSHI ICHIYAMA; YOSHITSUGU IINUMA; YOSHINORI HASEGAWA; MICHIO OHTA; KAORU SHIMOKATA

1997-01-01

217

Equilibrium paradigm for field-reversed configurations and application to experiments  

Microsoft Academic Search

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

Loren C. Steinhauer; T. P. Intrator

2009-01-01

218

Equilibrium paradigm for field-reversed configurations and application to experiments  

Microsoft Academic Search

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

Loren C. Steinhauer; T. P. Intrator

2009-01-01

219

Clinical application of genetically modified T cells in cancer therapy.  

PubMed

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

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

2014-05-01

220

Clinical application of genetically modified T cells in cancer therapy  

PubMed Central

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

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

2014-01-01

221

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

222

Clinical application of exome sequencing in undiagnosed genetic conditions  

PubMed Central

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

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

2012-01-01

223

Tools for genetic manipulations in Corynebacterium glutamicum and their applications  

Microsoft Academic Search

Corynebacterium glutamicum is an important industrial producer of various amino acids with great potential for the production of other metabolites.\\u000a The complete genome sequences of two C. glutamicum strains were determined and the use of genome-based approaches (transcriptomics, proteomics, metabolomics, and fluxomics)\\u000a provided large amounts of data on the metabolism of this bacterium and its regulation. Many tools for genetic

Jan Nešvera; Miroslav Pátek

2011-01-01

224

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

225

DNA marker applications to molecular genetics and genomics in tomato  

PubMed Central

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

2013-01-01

226

The K65R mutation in HIV-1 reverse transcriptase: genetic barriers, resistance profile and clinical implications  

PubMed Central

Resistance to antiviral therapy is the limiting factor in the successful management of HIV. In general, the K65R mutation is rarely selected (1.7–4%) with tenofovir disoproxil fumarate (TDF), abacavir (ABC), didanosine (ddI), and stavudine (d4T), as compared with the high incidence (>40%) of thymidine analog mutations associated with zidovudine and d4T. The high barrier to the development of K65R may reflect a combination of factors, including the high potency of K65R-selecting drugs, including recommended TDF/emtricitabine and ABC/lamivudine (ABC/3TC) combinations; the partial (low–intermediate level) profile of cross-resistance conferred by K65R to TDF, ABC and 3TC; the favorable viral fitness constraint imposed by K65R and the 3TC/emtricitabine-associated M184V mutations; the bidirectional antagonism between the K65R and thymidine analog mutation pathways; and unique RNA structural considerations in the region surrounding codon 65. Nevertheless, surprisingly high levels of treatment failures and K65R resistance may be associated with triple nucleoside analog regimens. The use of TDF + ABC, TDF + ddI and ABC + d4T in combination with 3TC or emtricitabine should be avoided. This selection of K65R may be reduced by the inclusion of zidovudine in two–four nucleoside reverse-transcriptase regimens. Clinical studies have demonstrated an increased frequency of K65R in association with suboptimal d4T and ddI regimens, as well as nevirapine and its resistance mutations Y181C and G190A. The potential for the development of the K65R mutation in subtype C is particularly problematic wherein a signature KKK nucleotide motif, at codons 64, 65 and 66 in reverse transcriptase, appear to lead to template pausing, facilitating the selection of K65R. Optimizing regimens may attenuate the emergence of K65R, leading to better long-term treatment management in different geographic settings. TDF-based regimens are the leading candidates for first- and second-line therapy, microbicides and chemoprophylaxis strategies. PMID:20190870

Brenner, Bluma G; Coutsinos, Dimitrios

2010-01-01

227

Development and characterization of a reverse genetic system for studying dengue virus serotype 3 strain variation and neutralization.  

PubMed

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. PMID:22389731

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

2012-01-01

228

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

229

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

E-print Network

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

Paris-Sud XI, Université de

230

Multi-Niche Crowding in Genetic Algorithms and its Application to the Assembly of DNA Restriction-Fragments  

E-print Network

Multi-Niche Crowding in Genetic Algorithms and its Application to the Assembly of DNA Restriction the optima of a multi-modal function. A genetic algorithm that uses multi-niche crowding permits us to do words: Genetic algorithms, multi-modal functions, DNA restriction fragment assembly, human genome

Vemuri, Rao

231

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

232

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

PubMed

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

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

2011-08-01

233

Application of Genetic Algorithms in Nonlinear Heat Conduction Problems  

PubMed Central

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

Khan, Waqar A.

2014-01-01

234

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

235

Optimal transition probability of reversible data hiding for general distortion metrics and its applications.  

PubMed

Recently, a recursive code construction (RCC) approaching the rate-distortion bound of reversible data hiding (RDH) was proposed. However, to estimate the rate-distortion bound or execute RCC, one should first estimate the optimal transition probability matrix (OTPM). By previous methods, OTPM can be effectively estimated only for some specific distortion metrics, such as square error distortion or L1 -Norm. In this paper, we proposed a unified framework of estimating the OTPM for general distortion metrics, with which we can calculate the rate-distortion bound of RDH for general cases and extend RCC to improve state-of-the-art RDH schemes based on any distortion metrics. PMID:25248187

Zhang, Weiming; Hu, Xiaocheng; Li, Xiaolong; Nenghai, Yu

2015-01-01

236

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

237

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

PubMed

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

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

2010-01-01

238

Genetics  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

239

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

240

Application of Silica-Based Hyper-Crosslinked Sulfonate-Modified Reversed Stationary Phases for Separating Highly Hydrophilic Basic Compounds  

PubMed Central

The separation and determination of hydrophilic basic compounds are of great importance in many fields including clinical and biological research, pharmaceutical development and forensic analysis. However, the most widely used analytical separation technique in these disciplines, reversed-phase liquid chromatography (RPLC), usually does not provide sufficient retention for several of the important classes of highly hydrophilic basic compounds including catecholamines, many drug metabolites and many drugs of abuse. Commonly eluents having little or no organic modifier and/or strong ion pairing agents must be used to achieve sufficient retention and separation. Use of highly aqueous eluents can lead to column failure by dewetting, resulting in poor retention, selectivity, reproducibility and slow recovery of performance. The use of a strong ion pairing agent to increase retention renders the separation incompatible with mass spectrometric detection and complicates preparative separations. This paper describes the successful applications of a novel type of silica-based, hyper-crosslinked, sulfonate-modified reversed stationary phase, denoted as ?SO3-HC-C8-L, for the separation of highly hydrophilic cations and related compounds by a hydrophobically assisted cation-exchange mechanism. Compared to conventional reversed-phases, the ?SO3-HC-C8-L phase showed significantly improved retention and separation selectivity. Concurrently, due to the presence of both cation-exchange and reversed-phase retention mechanisms and the high acid stability of hyper-crosslinked phases, the separation can be optimized by changing the type or concentration of ionic additive or organic modifier, and by varying the column temperature. In addition, gradients generated by programming the concentration of either the ionic additive or the organic modifier can be applied to reduce the analysis time without compromising resolution. Furthermore, remarkably different chromatographic selectivities, especially toward cationic solutes, were observed upon comparison of the ?SO3-HC-C8-L phase with conventional reversed-phases. We believe that the combination of these two types of stationary phases will be very useful in two-dimensional liquid chromatography. PMID:18617181

Luo, Hao; Ma, Lianjia; Paek, Changyub; Carr, Peter W.

2008-01-01

241

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

242

Application of Genetic Algorithm to Hexagon-Based Motion Estimation  

PubMed Central

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

Cheng, Wan-Shu

2014-01-01

243

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

244

Time reversal of scattering wavefield with applications for imaging fault damaged zones close to bimaterial interfaces  

NASA Astrophysics Data System (ADS)

We demonstrate that a time-reverse mirror (TRM) of data recorded by an array of broadband surface seismometers distributed across a bimaterial fault interface separating two quarter spaces, one of which includes a damaged zone with high crack density, can be used to image the spatial distribution of the damage. The generic cases presented in this study consider the damaged zone to be a region containing many thin, elliptical cracks randomly distributed laterally next to the fault and extending vertically down, in the medium with slower average S-wave velocity. The incident seismic wave is produced by a strike-slip line source corresponding to slip right on the fault plane at some prescribed depth. We first solve the forward problem, i.e. compute the full waveform synthetic seismogram at each element of the array using a boundary integral numerical scheme. Then we subtract the incident wave from each seismogram and time-reverse only the scattered wavefield, last phase first, back to their origin. The results show that the computed image can be obtained with high resolution for an array aperture size comparable to four times the largest length scale (width or depth) of the damage zone, and a seismometer interval distance comparable to one quarter of the smallest wavelength considered in the calculations. We present results of such images for several random realizations of crack distribution.

Benites, R. A.; Ben-Zion, Y.

2010-12-01

245

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.

246

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

ERIC Educational Resources Information Center

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

Gary, Ronald K.

2004-01-01

247

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

248

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. PMID:23055839

Bardhan, Jaydeep P.; Altman, Michael D.

2009-01-01

249

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

250

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

Microsoft Academic Search

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

Morteza Montazeri-Gh; Amir Poursamad; Babak Ghalichi

2006-01-01

251

Stock Portfolio Evaluation: An Application of Genetic-Programming-Based Technical Analysis  

E-print Network

Stock Portfolio Evaluation: An Application of Genetic- Programming-Based Technical Analysis Liad to predictability of stock. When attempting to create an efficient portfolio of stocks, there are numerous factors. By using a set of fitness heuristics over a population of stock portfolios, the goal is to find a portfolio

Fernandez, Thomas

252

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

E-print Network

based, counterparts [1, 2]. Sub-populations, in fact, may allow sometimes a better control on populationSub-population policies for a parallel multiobjective genetic algorithm with applications to wing. The population selection and mating phase is kept dis- tinct from the population fitness evaluation loop

Coello, Carlos A. Coello

253

Computing genetic evaluations through application of generalized least squares to an animal model  

E-print Network

Computing genetic evaluations through application of generalized least squares to an animal model G.F.S. HUDSON Department of Animal Sciences, University of Maryland, College Park, Maryland 20742, U.S.A. Summary The animal model for performance data is rewritten in the form of a fixed model with uncorrelated

Paris-Sud XI, Université de

254

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

Microsoft Academic Search

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

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

1999-01-01

255

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

E-print Network

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

Gleeson, Joseph G.

256

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

SciTech Connect

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

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

1996-05-01

257

Applications of landscape genetics in conservation biology: concepts and challenges  

E-print Network

2009 / Accepted: 31 December 2009 / Published online: 2 February 2010 � Springer Science+Business Media, the application of Bayesian methods, inference from landscape resistance and a shift from population Isolation by distance Á Landscape resistance Á Sampling design Á Simulation modelling Introduction Habitat

258

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. PMID:11238393

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

2001-01-01

259

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

PubMed

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. PMID:11238393

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

2001-03-01

260

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

261

Orbit determination by genetic algorithm and application to GEO observation  

NASA Astrophysics Data System (ADS)

This paper demonstrates an initial orbit determination method that solves the problem by a genetic algorithm using two well-known solutions for the Lambert's problem: universal variable method and Battin method. This paper also suggests an intuitive error evaluation method in terms of rotational angle and orbit shape by separating orbit elements into two groups. As reference orbit, mean orbit elements (original two-lines elements) and osculating orbit elements considering the J2 effect are adopted and compared. Our proposed orbit determination method has been tested with actual optical observations of a geosynchronous spacecraft. It should be noted that this demonstration of the orbit determination is limited to one test case. This observation was conducted during approximately 70 min on 2013/05/15 UT. Our method was compared with the orbit elements propagated by SGP4 using the TLE of the spacecraft. The result indicates that our proposed method had a slightly better performance on estimating orbit shape than Gauss's methods and Escobal's method by 120 km. In addition, the result of the rotational angle is closer to the osculating orbit elements than the mean orbit elements by 0.02°, which supports that the estimated orbit is valid.

Hinagawa, Hideaki; Yamaoka, Hitoshi; Hanada, Toshiya

2014-02-01

262

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

Microsoft Academic Search

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

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

1999-01-01

263

Virus-induced gene silencing (VIGS) as a reverse genetic tool to study development of symbiotic root nodules.  

PubMed

Virus-induced gene silencing (VIGS) can provide a shortcut to plants with altered expression of specific genes. Here, we report that VIGS of the Nodule inception gene (Nin) can alter the nodulation phenotype and Nin gene expression in Pisum sativum. PsNin was chosen as target because of the distinct non-nodulating phenotype of nin mutants in P. sativum, Lotus japonicus, and Medicago truncatula. The vector based on Pea early browning virus (PEBV) was engineered to carry one of three nonoverlapping fragments (PsNinA, PsNinB, and PsNinC) derived from the PsNin cDNA. Vector inoculation was mediated by agroinfiltration and, 2 weeks later, a Rhizobium leguminosarum bv. viceae culture was added in order to induce root nodulation. At this time point, it was estimated that systemic silencing was established because leaves of reference plants inoculated with PEBV carrying a fragment of Phytoene desaturase displayed photo bleaching. Three weeks after Rhizobium spp. application, plants inoculated with a control vector nodulated normally, whereas nodulation was almost eliminated in plants inoculated with a vector carrying PsNinA and PsNinC. For plants inoculated with a vector carrying PsNinB, nodulation was reduced by at least 45%. Down-regulation of PsNin transcripts in plants inoculated with vectors carrying PsNin cDNA fragments was confirmed and these plants displayed a relative increase in the root/shoot ratio, as expected if nitrogen fixation had been impaired. PMID:18624636

Constantin, G D; Grønlund, M; Johansen, I E; Stougaard, J; Lund, O S

2008-06-01

264

Genetics  

NSDL National Science Digital Library

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

Goodfellow, Miss

2007-10-23

265

Genetics  

NSDL National Science Digital Library

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

The Tech Museum of Innovation

2004-01-01

266

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

267

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

268

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

269

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

NASA Astrophysics Data System (ADS)

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.

1984-10-01

270

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

PubMed Central

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

Newman, Robert H.; Zhang, Jin

2014-01-01

271

Genetic and epigenetic variations in iPSCs: potential causes and implications for application  

PubMed Central

The ability to reprogram somatic cells to induced pluripotent stem cells (iPSCs) has revolutionized the field of regenerative medicine. However, recent studies on the genetic and epigenetic variations in iPSCs have raised concerns that these variations may compromise the utility of iPSCs. In this Perspective, we review the current understanding of genetic and epigenetic variations in iPSCs, trace their causes, discuss the implications of these variations for iPSC applications, and propose approaches to cope with these variations. PMID:23910082

Liang, Gaoyang; Zhang, Yi

2013-01-01

272

Towards a Better Comprehensibility of Web Applications: Lessons Learned from Reverse Engineering Experiments  

Microsoft Academic Search

The rapid diffusion of the Internet has triggered a growing request for new Web sites and Web applications (WA). Due to the pressing market demand, new WAs are usually developed in a very short time, while existing WAs are modified frequently and quickly. In these conditions, well-known software engineering principles are not usually applied, and well-defined software processes and methodologies

Giuseppe A. Di Lucca; Anna Rita Fasolino; Porfirio Tramontana

2002-01-01

273

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

274

Bis sigma-bond dihydrogen and borane ruthenium complexes: bonding nature, catalytic applications, and reversible hydrogen release.  

PubMed

Hydrogen, the simplest element in the periodic table, plays a tremendous role in organic and inorganic chemistry. For years, it was inconceivable that dihydrogen could be bound to a metal center without breaking the H-H bond. Thus, oxidative addition of H(2) was universally recognized as a key elementary step in hydrogenation processes. In 1984, Kubas and co-workers reported the first example of a complex in which dihydrogen was coordinated to a metal center without breaking of the H-H bond. This opened a new area in coordination chemistry: sigma-complexes were born, complementing the well-known Werner-type family of complexes. Since then, hundreds of stable dihydrogen complexes have been isolated, and their properties have been investigated in detail. By comparison, very little information is available for the analogous class of sigma-borane complexes, in which sigma-H-B bonds are complexed to a metal (in the manner of H-H bonds in sigma-dihydrogen complexes). Since the first example published in 1996 by Hartwig and co-workers, very few sigma-borane complexes have been isolated. Scientists have maintained a continuous interest in catalytic hydrogenation reactions. Almost a century ago, in 1912, Paul Sabatier, the father of the hydrogenation process, received the Nobel prize, and the selection of Noyori and Knowles in 2001 for their studies on enantioselective catalyzed hydrogenations amply demonstrates the ongoing importance of the field. Moreover, during the past decade, dihydrogen has attracted considerable attention as a possible "fuel of the future". This endeavor has furthered interest in sigma-borane complexes, as more and more evidence links their chemistry to that of amine-borane derivatives. Indeed, ammonia-borane (NH(3)BH(3)) is attracting significant interest for hydrogen storage applications. One of the main limitations is the lack of reversibility associated with the production of dehydrogenated (BNH)(x) materials. Of major importance will be a better understanding of the coordination of H(2) to a metal center, and more generally of the coordination of H-E bonds (E = B, C), which are likely to play a critical role in the reversible dehydrogenation process. In this Account, we review our recent results in the field of dihydrogen and borane activation, with a specific focus on the problem of reversible dehydrogenation pathways. We concentrate on the chemistry of ruthenium complexes incorporating two sigma-ligands: either two dihydrogen or two sigma-B-H bonds. We describe our synthetic strategies to prepare such unusual structures. Their characterization is discussed in detail, highlighting the importance of an experimental and theoretical approach (NMR, structural, and theoretical studies). Some catalytic applications are discussed and put into context, and their reactivity toward reversible hydrogen release is detailed. PMID:19586012

Alcaraz, Gilles; Grellier, Mary; Sabo-Etienne, Sylviane

2009-10-20

275

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. PMID:19609385

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

2008-01-01

276

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

PubMed Central

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

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

1997-01-01

277

Biochemistry, genetics, and applications of exopolysaccharide production in Streptococcus thermophilus: a review.  

PubMed

Many strains of Streptococcus thermophilus synthesize extracellular polysaccharides. These molecules may be produced as capsules that are tightly associated with the cell, or they may be liberated into the medium as a loose slime (i.e., "ropy" polysaccharide). Although the presence of exopolysaccharide does not confer any obvious advantage to growth or survival of S. thermophilus in milk, in situ production by this species or other dairy lactic acid bacteria typically imparts a desirable "ropy" or viscous texture to fermented milk products. Recent work has also shown that exopolysaccharide-producing S. thermophilus can enhance the functional properties of Mozzarella cheese, but they are not phage-proof. As our understanding of the genetics, physiology, and functionality of bacterial exopolysaccharides continues to improve, novel applications for polysaccharides and polysaccharide-producing cultures are likely to emerge inside and outside the dairy industry. This article provides an overview of biochemistry, genetics, and applications of exopolysaccharide production in S. thermophilus. PMID:12647947

Broadbent, J R; McMahon, D J; Welker, D L; Oberg, C J; Moineau, S

2003-02-01

278

Application of Genetic Algorithms for Microwave Oven Design: Power Efficiency Optimization  

Microsoft Academic Search

In this work we present power efficiency optimization for microwave ovens by means of genetic algorithms (GA). Two kind of\\u000a microwave applicators are analyzed in this case: cylindrical and rectangular ones. In the first case, optimization of the\\u000a oven uses cavity dimensions, waveguide feeding location and polarization as design parameters. In the second case, waveguide\\u000a slots are used to feed

Juan Monzó-cabrera; Alejandro Díaz-morcillo; Elsa Domínguez-tortajada; Antonio Lozano-guerrero

2007-01-01

279

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.

280

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

281

Nested quantization index modulation for reversible watermarking and its application to healthcare information management systems.  

PubMed

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. PMID:22194776

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

2012-01-01

282

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. PMID:22194776

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

2012-01-01

283

Post-Doctoral Fellowships The Department of Biostatistics and Center for Statistical Genetics invite applications for post-  

E-print Network

Post-Doctoral Fellowships The Department of Biostatistics and Center for Statistical Genetics. Applicants should have a doctoral degree in Biostatistics, Genetics, Computer Science, Epidemiology (734-763-4901), c/o Peggy White (ppwhite@umich.edu, 734-936-1004), Department of Biostatistics, School

Queitsch, Christine

284

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

E-print Network

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

285

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

PubMed Central

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

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

2014-01-01

286

Molecular characterization with RAPD-PCR: Application of genetic diagnostics to biological control of the sweetpotato whitefly  

Technology Transfer Automated Retrieval System (TEKTRAN)

The application of genetic diagnostics under the umbrella of classical taxonomy was imperative for successful development and delivery of the biological control program against the sweet potato whitefly, Bemisia tabaci Gennadius biotype B (= silverleaf whitefly, B. argentifolii Bellows and Perring)....

287

A Quantitative, High-Throughput Reverse Genetic Screen Reveals Novel Connections between Pre–mRNA Splicing and 5? and 3? End Transcript Determinants  

PubMed Central

Here we present the development and implementation of a genome-wide reverse genetic screen in the budding yeast, Saccharomyces cerevisiae, that couples high-throughput strain growth, robotic RNA isolation and cDNA synthesis, and quantitative PCR to allow for a robust determination of the level of nearly any cellular RNA in the background of 5,500 different mutants. As an initial test of this approach, we sought to identify the full complement of factors that impact pre–mRNA splicing. Increasing lines of evidence suggest a relationship between pre–mRNA splicing and other cellular pathways including chromatin remodeling, transcription, and 3? end processing, yet in many cases the specific proteins responsible for functionally connecting these pathways remain unclear. Moreover, it is unclear whether all pathways that are coupled to splicing have been identified. As expected, our approach sensitively detects pre–mRNA accumulation in the vast majority of strains containing mutations in known splicing factors. Remarkably, however, several additional candidates were found to cause increases in pre–mRNA levels similar to that seen for canonical splicing mutants, none of which had previously been implicated in the splicing pathway. Instead, several of these factors have been previously implicated to play roles in chromatin remodeling, 3? end processing, and other novel categories. Further analysis of these factors using splicing-sensitive microarrays confirms that deletion of Bdf1, a factor that links transcription initiation and chromatin remodeling, leads to a global splicing defect, providing evidence for a novel connection between pre–mRNA splicing and this component of the SWR1 complex. By contrast, mutations in 3? end processing factors such as Cft2 and Yth1 also result in pre–mRNA splicing defects, although only for a subset of transcripts, suggesting that spliceosome assembly in S. cerevisiae may more closely resemble mammalian models of exon-definition. More broadly, our work demonstrates the capacity of this approach to identify novel regulators of various cellular RNAs. PMID:22479188

Albulescu, Laura-Oana; Sabet, Nevin; Gudipati, Mohanram; Stepankiw, Nicholas; Bergman, Zane J.; Huffaker, Tim C.; Pleiss, Jeffrey A.

2012-01-01

288

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

PubMed Central

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

Hill, William G.

2014-01-01

289

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

PubMed

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

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

2013-03-01

290

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

PubMed Central

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

2014-01-01

291

A study on the inventory and pricing model for reverse logistics: An application on reuse of refillable containers  

Microsoft Academic Search

Enterprises apply reverse logistics through recycling, repairing, and remanufacturing processes to reduce resource consumption and waste generation for the environment. To effectively manipulate reverse logistic activities of a refillable container, this paper proposes an integrated inventory and pricing model to deal with the problems of inventory control, production schedule, and pricing decisions. We formulate a profit function and then examine

H. L. Huang; H. M. Chen; C. C. Lo

2008-01-01

292

Genetic Counseling Program Information  

E-print Network

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

Berdichevsky, Victor

293

47MCGAUGH ET AL. Applications of Modern Genetic Tools Defining Turtle Diversity: Proceedings of a Workshop on Genetics, Ethics, and Taxonomy of Freshwater Turtles and Tortoises  

E-print Network

in studies of conser- vation, evolution, and ecology of turtles. We show how standard approaches such as DNA to traditional field practices in illuminating the evolution and ecology of turtles. We illustrate how standard47MCGAUGH ET AL. ­ Applications of Modern Genetic Tools Defining Turtle Diversity: Proceedings

Feldman, Chris R

294

On inferring and interpreting genetic population structure - applications to conservation, and the estimation of pairwise genetic relatedness.  

E-print Network

??The presence of population structure is ubiquitous in most wild populations of species. Detecting genetic population structure and understanding its consequences for the evolutionary trajectories… (more)

Sethuraman, Arun

2013-01-01

295

Applications of Genetically Modified Tools to Safety Assessment in Drug Development  

PubMed Central

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

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

2010-01-01

296

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

PubMed

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

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

2014-01-01

297

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

PubMed Central

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

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

2014-01-01

298

Contribution of genetics to ecological restoration.  

PubMed

Ecological restoration of degraded ecosystems has emerged as a critical tool in the fight to reverse and ameliorate the current loss of biodiversity and ecosystem services. Approaches derived from different genetic disciplines are extending the theoretical and applied frameworks on which ecological restoration is based. We performed a search of scientific articles and identified 160 articles that employed a genetic approach within a restoration context to shed light on the links between genetics and restoration. These articles were then classified on whether they examined association between genetics and fitness or the application of genetics in demographic studies, and on the way the studies informed restoration practice. Although genetic research in restoration is rapidly growing, we found that studies could make better use of the extensive toolbox developed by applied fields in genetics. Overall, 41% of reviewed studies used genetic information to evaluate or monitor restoration, and 59% provided genetic information to guide prerestoration decision-making processes. Reviewed studies suggest that restoration practitioners often overlook the importance of including genetic aspects within their restoration goals. Even though there is a genetic basis influencing the provision of ecosystem services, few studies explored this relationship. We provide a view of research gaps, future directions and challenges in the genetics of restoration. PMID:25377524

Mijangos, Jose Luis; Pacioni, Carlo; Spencer, Peter B S; Craig, Michael D

2015-01-01

299

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

300

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

301

Reversible depletion of synaptic vesicles induced by application of high external potassium to the frog neuromuscular junction  

PubMed Central

1. Reversible depletion of synaptic vesicles from frog cutaneous pectoris neuromuscular junctions was studied by application of a Ringer solution containing 115 mM-K propionate. 2. During the release of transmitter, the synaptic vesicle membrane is added to the axolemmal membrane. Under the conditions of high K+-induced release, the synaptic vesicle membrane accumulates as folds formed in the region of the axolemmal membrane between the active zones. In depleted terminals, large vesicular structures appear and the evidence shows that some of them (possibly all) are formed as axolemmal infoldings. During formation of such infoldings the active zones remain fixed in position with respect to the post-junctional membrane. 3. During recovery in normal Ringer solution, which followed 30 min depolarization in high K+ Ringer solution, spontaneous m.e.p.p.s were detected as early as 9 min after the start of the recovery period and the average time for their reappearance was 17 min. 4. At the end of a 20 min recovery period which followed K+ depolarization, small accumulations of synaptic vesicles were again found within the terminal close to the active zones. At this time coated vesicles and coated pits were seen associated with the prejunctional axolemma and its infoldings. It appears that synaptic vesicles are re-formed directly from these coated vesicles. 5. After 60 min recovery from K+ depolarization, at which time stimulation of the motor nerve induced a muscle twitch, the structure of the terminals closely resembled that of control preparations. 6. The entire synaptic vesicle recycling process can take place in the absence of the neurone soma. ImagesPlate 3Plate 1Plate 2 PMID:308538

Gennaro, Joseph F.; Nastuk, William L.; Rutherford, Dorothy T.

1978-01-01

302

Using Reverse Genetics to Manipulate the NSs Gene of the Rift Valley Fever Virus MP-12 Strain to Improve Vaccine Safety and Efficacy  

PubMed Central

Rift Valley fever virus (RVFV), which causes hemorrhagic fever, neurological disorders or blindness in humans, and a high rate abortion and fetal malformation in ruminants1, has been classified as a HHS/USDA overlap select agent and a risk group 3 pathogen. It belongs to the genus Phlebovirus in the family Bunyaviridae and is one of the most virulent members of this family. Several reverse genetics systems for the RVFV MP-12 vaccine strain2,3 as well as wild-type RVFV strains 4-6, including ZH548 and ZH501, have been developed since 2006. The MP-12 strain (which is a risk group 2 pathogen and a non-select agent) is highly attenuated by several mutations in its M- and L-segments, but still carries virulent S-segment RNA3, which encodes a functional virulence factor, NSs. The rMP12-C13type (C13type) carrying 69% in-frame deletion of NSs ORF lacks all the known NSs functions, while it replicates as efficient as does MP-12 in VeroE6 cells lacking type-I IFN. NSs induces a shut-off of host transcription including interferon (IFN)-beta mRNA7,8 and promotes degradation of double-stranded RNA-dependent protein kinase (PKR) at the post-translational level.9,10 IFN-beta is transcriptionally upregulated by interferon regulatory factor 3 (IRF-3), NF-kB and activator protein-1 (AP-1), and the binding of IFN-beta to IFN-alpha/beta receptor (IFNAR) stimulates the transcription of IFN-alpha genes or other interferon stimulated genes (ISGs)11, which induces host antiviral activities, whereas host transcription suppression including IFN-beta gene by NSs prevents the gene upregulations of those ISGs in response to viral replication although IRF-3, NF-kB and activator protein-1 (AP-1) can be activated by RVFV7. . Thus, NSs is an excellent target to further attenuate MP-12, and to enhance host innate immune responses by abolishing the IFN-beta suppression function. Here, we describe a protocol for generating a recombinant MP-12 encoding mutated NSs, and provide an example of a screening method to identify NSs mutants lacking the function to suppress IFN-beta mRNA synthesis. In addition to its essential role in innate immunity, type-I IFN is important for the maturation of dendritic cells and the induction of an adaptive immune response12-14. Thus, NSs mutants inducing type-I IFN are further attenuated, but at the same time are more efficient at stimulating host immune responses than wild-type MP-12, which makes them ideal candidates for vaccination approaches. PMID:22083261

Kalveram, Birte; Lihoradova, Olga; Indran, Sabarish V.; Ikegami, Tetsuro

2011-01-01

303

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

PubMed

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

Groshong, Ashley M; Blevins, Jon S

2014-01-01

304

Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network  

PubMed Central

Background It is widely accepted that genetic regulatory systems are 'modular', in that the whole system is made up of smaller 'subsystems' corresponding to specific biological functions. Most attempts to identify modules in genetic regulatory systems have relied on the topology of the underlying network. However, it is the temporal activity (dynamics) of genes and proteins that corresponds to biological functions, and hence it is dynamics that we focus on here for identifying subsystems. Results Using Boolean network models as an exemplar, we present a new technique to identify subsystems, based on their dynamical properties. The main part of the method depends only on the stable dynamics (attractors) of the system, thus requiring no prior knowledge of the underlying network. However, knowledge of the logical relationships between the network components can be used to describe how each subsystem is regulated. To demonstrate its applicability to genetic regulatory systems, we apply the method to a model of the Drosophila segment polarity network, providing a detailed breakdown of the system. Conclusion We have designed a technique for decomposing any set of discrete-state, discrete-time attractors into subsystems. Having a suitable mathematical model also allows us to describe how each subsystem is regulated and how robust each subsystem is against perturbations. However, since the subsystems are found directly from the attractors, a mathematical model or underlying network topology is not necessarily required to identify them, potentially allowing the method to be applied directly to experimental expression data. PMID:17961242

Irons, David J; Monk, Nicholas AM

2007-01-01

305

The Design of Potter Horns for THz Applications Using a Genetic Algorithm  

NASA Astrophysics Data System (ADS)

We describe the design and performance of Potter horns at millimetre and submillimetre wavelength employing a novel software package that we have developed, using Genetic Algorithm. The horn is easy to fabricate and exhibits excellent beam circularity and low cross polarization over a 15% bandwidth which is sufficient for many applications. Excitation of the required higher order modes is done by either a step or a flare discontinuity at the horn throat. In each case we provide design curves that give the optimum parameters of the horn geometry as a function of frequency and beamwidth. The range of values provided covers the parameters required for the design of horns for telescope feeds and various other instruments. The design curves show clearly that the flare-step performance is superior to the traditional groove-step Potter horn. The simulations for designing these horns were carried out at millimetre and submillimetre wavelengths but the results can be scaled to lower or higher frequencies. A key component in the design method is the optimization software that searches for the correct magnitude and location of the flare discontinuities. We have developed a software package based on the combination of modal matching, a genetic algorithm (GA) and downhill simplex optimization. The genetic code is first used to locate the proximity of the global minimum. The set of parameters obtained are then used as a starting point for the simplex method, which refines the parameters to the required accuracy.

Kittara, P.; Jiralucksanawong, A.; Yassin, G.; Wangsuya, S.; Leech, J.

2007-12-01

306

Genetic programming  

Microsoft Academic Search

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

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

2000-01-01

307

Biological engineering applications of feedforward neural networks designed and parameterized by genetic algorithms.  

PubMed

Two neural network (NN) applications in the field of biological engineering are developed, designed and parameterized by an evolutionary method based on the evolutionary process of genetic algorithms. The developed systems are a fault detection NN model and a predictive modeling NN system. An indirect or 'weak specification' representation was used for the encoding of NN topologies and training parameters into genes of the genetic algorithm (GA). Some a priori knowledge of the demands in network topology for specific application cases is required by this approach, so that the infinite search space of the problem is limited to some reasonable degree. Both one-hidden-layer and two-hidden-layer network architectures were explored by the GA. Except for the network architecture, each gene of the GA also encoded the type of activation functions in both hidden and output nodes of the NN and the type of minimization algorithm that was used by the backpropagation algorithm for the training of the NN. Both models achieved satisfactory performance, while the GA system proved to be a powerful tool that can successfully replace the problematic trial-and-error approach that is usually used for these tasks. PMID:15963690

Ferentinos, Konstantinos P

2005-09-01

308

Hybrid Algorithms for Fuzzy Reverse Supply Chain Network Design  

PubMed Central

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

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

2014-01-01

309

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

310

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

311

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

312

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

E-print Network

1 Sex-Role Reversal and "Dominance Genes" in African Cichlid Fish The broad scope of my research and molecular techniques. The current focus of my research with African Cichlid Fishes aims to understand conditions and thus represent evolutionary adaptation. I seek support of the Jordan Endowment Award

Renn, Susan C.P.

313

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

PubMed Central

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

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

2014-01-01

314

Reversible Sterilization  

ERIC Educational Resources Information Center

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

Largey, Gale

1977-01-01

315

Reversing vasectomy.  

PubMed

Advances in surgical techniques have made the reversal of vasectomy a realistic prospect. Currently, some 3% of patients request the reversal of vasectomy. Reversal techniques include macroscopic vasovasostomy, vasovasostomy with optical loupe magnification, and microsurgical methods. All of these methods have demonstrated acceptable rates of patency and pregnancy. Common to the success of these methods is the accurate apposition of mucosa to mucosa. The results of uniting the straight segments of the vas are better than those obtained with vasoepididymostomy. Recent reports indicate up to 80% patency and 30% pregnancy rates after macrosurgical anastomosis and up to 90% patency and 40% pregnancy rates after microsurgery. Operation failure could result from the following: poor anastomotic surgical technique, infection leading to fibrosis, formation of anastomotic sperm and suture granulomas, more than 10 years elapsing between the vasectomy and the reversal, and the removal of either too long a portion of the vas or part of the convoluted portion of the vas during the initial vasectomy. Although uncommon, some complications during the reversal procedure have been reported. As the reports indicate, pregnancy and patency differ significantly. Several explanations exist: 1) semen quality after reversal may be poor; 2) a secondary anastomotic stricture in the vas may gradually develop; 3) pressure mediated local changes may affect the testis and epididymis; 4) there might be a an injury to the sympathetic nerve fibers in the vas sheath; 5) antibodies to sperm may be present. While reversal is possible, the article cautions that the public should not consider vasectomy a reversible method of birth control. PMID:1392787

Banerjee, A K; Simpson, A

1992-05-01

316

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

PubMed Central

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

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

2013-01-01

317

Genetic algorithm with age structure and its application to self-organizing manufacturing system  

Microsoft Academic Search

The genetic algorithm has recently been demonstrated its effectiveness in optimization issues, but it has two major problems: a premature local convergence and a bias by the genetic drift. In order to solve these problems, we propose a new genetic algorithm with an age structure of a continuous generation model. The new genetic algorithm is applied to a self-organizing manufacturing

Naoyuki KUBOTA; Toshio FUKUDA; Fumihito ARAI; Koji SHIMOJIMA

1994-01-01

318

Development and application of a hexaplex reverse transcription polymerase chain reaction for screening global Citrus tristeza virus isolates  

Technology Transfer Automated Retrieval System (TEKTRAN)

The discovery of the diversity of Citrus tristeza virus (CTV) genotypes has complicated detection and diagnostic measures. To simplify the identification and differentiation of CTV genotypes, an efficient multiplex reverse transcription polymerase chain reaction (M-RT-PCR) technique for the screenin...

319

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

ERIC Educational Resources Information Center

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

Gilman, Rich; Connor, Nancy; Haney, Michelle

2005-01-01

320

Development and application of a hexaplex reverse transcription polymerase chain reaction for screening global citrus tristeza virus isolates  

Technology Transfer Automated Retrieval System (TEKTRAN)

The discovery of the diversity of Citrus tristeza virus (CTV) genotypes has complicated detection and diagnostic measures. To simplify the identification and differentiation of CTV genotypes, an efficient multiplex reverse transcription polymerase chain reaction (M-RT-PCR) technique for the screenin...

321

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

E-print Network

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

Fernandez, Thomas

322

Diagnostic application of an extensive gene panel for leber congenital amaurosis with severe genetic heterogeneity.  

PubMed

Leber congenital amaurosis (LCA) is a genetically heterogeneous disorder and the most severe form of inherited retinal dystrophy. We report results of a diagnostic application of an extensive gene panel composed of 204 retinal dystrophy-related genes and discuss its feasibility as a diagnostic tool. Nineteen unrelated LCA patients were included in the study: two patients for validation purposes of our gene panel, 15 previously analyzed patients with no identified mutations, and two previously unanalyzed patients. Genetic diagnosis for each patient was conducted according to whether the variants were consistent with the known inheritance pattern of each gene. We identified two heterozygous or homozygous pathogenic variants in seven of 19 patients. On the basis of mutation information, clinical features were re-reviewed, and clinical diagnoses for two patients were revised from LCA to LCA-related disorders. In addition, a coverage simulation was performed to determine the optimal depth of coverage of the gene panel. Using our gene panel, we diagnosed LCA and LCA-related disorders in 36.8% of patients and one or more deleterious variants or variants of unknown significance in 89.5% of patients. Molecular diagnosis using this extensive gene panel is expected to facilitate diagnosis of retinal dystrophy and help provide proper treatment to patients, although further analyses is needed for a complete clinical validation. PMID:25445212

Seong, Moon-Woo; Seo, Soo Hyun; Yu, Young Suk; Hwang, Jeong-Min; Cho, Sung Im; Ra, Eun Kyung; Park, Hyunwoong; Lee, Seung Jun; Kim, Ji Yeon; Park, Sung Sup

2015-01-01

323

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

PubMed Central

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

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

2014-01-01

324

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

325

Multi-objective optimization of reverse osmosis desalination units using different adaptations of the non-dominated sorting genetic algorithm (NSGA)  

Microsoft Academic Search

Multi-objective optimization using genetic algorithm (GA) is carried out for the desalination of brackish and sea water using spiral wound or tubular modules. A few sample optimization problems involving two and three objective functions are solved, both for the operation of an existing plant (which is almost trivial), as well as, for the design of new plants (associated with a

Chandan Guria; Prashant K. Bhattacharya; Santosh K. Gupta

2005-01-01

326

A Reverse Genetic System Provides a Powerful Tool in the Design of Foot-and-Mouth Disease Viruses with Enhanced Properties  

Technology Transfer Automated Retrieval System (TEKTRAN)

The fact that the foot-and-mouth disease viral (FMDV) RNA can be made infectious in the absence of other components of the virion allows the recovery of genetically engineered new viruses from in vitro-generated RNA molecules. We utilize infectious cDNA technology to produce recombinant FMDV, retain...

327

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...

328

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

329

Synthesis of carboxylated poly(NIPAAm) oligomers and their application to form thermo-reversible polymer-enzyme conjugates.  

PubMed

A thermo-reversible poly(N-isopropylacrylamide) poly(NIPAAm) oligomer with a carboxyl functional end group has been synthesized by radical polymerization using beta-mercaptopropionic acid as a chain transfer reagent. This polymer has been conjugated to an enzyme, beta-D-glucosidase, to form a thermo-reversible water soluble-insoluble polymer-enzyme conjugate. This conjugate can be used for separation, recovery and recycle of an enzyme simply by applying small temperature changes to the reaction medium. In contrast to the random polymer-enzyme conjugates reported in the literature, in this study the enzyme is coupled to each polymer chain by a single end attachment. These preliminary studies show that the conjugated enzyme exhibits very high retention of activity (> 90%) compared to the native enzyme and shows improved thermal stability. PMID:8025032

Chen, G; Hoffman, A S

1994-01-01

330

Sequence analysis of the large (L) polymerase gene and trailer of the peste des petits ruminants virus vaccine strain Nigeria 75/1: expression and use of the L protein in reverse genetics.  

PubMed

The large (L) polymerase gene and the 5'-terminal UTR of the genome of peste des petits ruminants virus (PPRV), vaccine strain Nigeria 75/1, were cloned and sequenced. The L protein was also expressed in eukaryotic cells and its polymerase activity was quantitatively measured in a PPR reverse genetics assay using a reporter minigenome. Comparative sequence analysis of this functional L gene with corresponding genes of other morbilliviruses showed a degree of conservation exceeding 70%. The multiple sequence alignment and the phylogenetic study of L gene discriminated the morbilliviruses in 6 clusters, which are more closely related to Tupaia and Henipaviruses than to other paramyxoviruses. Important protein domains and functional motifs of the L polymerase of the PPRV Nigeria 75/1 vaccine were also identified by using different bioinformatics tools. PMID:19540279

Minet, C; Yami, M; Egzabhier, B; Gil, P; Tangy, F; Brémont, M; Libeau, G; Diallo, A; Albina, E

2009-10-01

331

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

Microsoft Academic Search

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

Shijie Deng

1999-01-01

332

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

E-print Network

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

333

A simian-human immunodeficiency virus carrying the rt gene from Chinese CRF01_AE strain of HIV is sensitive to nucleoside reverse transcriptase inhibitors and has a highly genetic stability in vivo.  

PubMed

Human immunodeficiency virus (HIV)-1 subtype CRF01_AE is one of the major HIV-1 subtypes that dominate the global epidemic. However, its drug resistance, associated mutations, and viral fitness have not been systemically studied, because available chimeric simian-HIVs (SHIVs) usually express the HIV-1 reverse transcriptase (rt) gene of subtype B HIV-1, which is different from subtype CRF01_AE HIV-1. In this study, a recombinant plasmid, pRT-SHIV/AE, was constructed to generate a chimeric RT-SHIV/AE by replacing the rt gene of simian immunodeficiency virus (SIVmac239) with the counterpart of Chinese HIV-1 subtype CRF01_AE. The infectivity, replication capacity, co-receptor tropism, drug sensitivity, and genetic stability of RT-SHIV/AE were characterized. The new chimeric RT-SHIV/AE effectively infected and replicated in human T cell line and rhesus peripheral blood mononuclear cells (rhPBMC). The rt gene of RT-SHIV/AE lacked the common mutation (T215I) associated with drug resistance. RT-SHIV-AE retained infectivity and immunogenicity, similar to that of its counterpart RT-SHIV/TC virus following intravenous inoculation in Chinese rhesus macaque. RT-SHIV-AE was more sensitive to nucleoside reverse transcriptase inhibitors (NRTIs) than the RT-SHIV/TC. RT-SHIV/AE was genetically stable in Chinese rhesus macaque. The new chimeric RT-SHIV/AE may be a valuable tool for evaluating the efficacy of the rt-based antiviral drugs against the subtype CRF01_AE HIV-1. PMID:24709063

Wang, Wei; Yao, Nan; Ju, Bin; Dong, Zhihui; Cong, Zhe; Jiang, Hong; Qin, Chuan; Wei, Qiang

2014-06-01

334

Reversal by L-arginine of a dysfunctional arginine\\/nitric oxide pathway in the endothelium of the genetic diabetic BB rat  

Microsoft Academic Search

Summary   We examined the effects of acute supplementation with arginine in vitro on endothelium-dependent relaxation in aortic rings\\u000a taken from female genetic, diabetes-prone BB rats. Sensitivity to norepinephrine-induced contraction was unaltered in rings\\u000a of diabetic BB rats compared to rings from non-diabetic littermates. In precontracted rings, acetylcholine produced a concentration-dependent\\u000a relaxation which was impaired by diabetes. This relaxation was blocked

G. M. Pieper; W. Siebeneich; G. Moore-Hilton; A. M. Roza

1997-01-01

335

Rapid on-chip genetic detection microfluidic platform for real world applications.  

PubMed

The development of genetic detection protocols for field applications is an important aspect of modern medical diagnostic technology and environmental monitoring. In this paper, we report a rapid, portable, and inexpensive DNA hybridization technique using a bead-based microfluidic platform that functions by passing fluorescently labeled target DNA through a chamber packed with functionalized beads within a microfluidic channel. DNA hybridization is then assessed using a digital camera attached to a Clare Chemical DR-45M dark reader non-UV transilluminator that uses visible light as an excitation source and a blue and amber filter to reveal fluorescence. This microfluidic approach significantly enhances hybridization by reducing the diffusion time between target DNA and the silica surface. The use of probe-functionalized beads as solid support also enhances the sensitivity and limit of detection due to a larger surface area per unit volume. This platform could be adapted for use in medical applications and environmental monitoring, including the detection of harmful organisms in the ballast water of ships. PMID:19693342

Senapati, Satyajyoti; Mahon, Andrew R; Gordon, Jason; Nowak, Carsten; Sengupta, Shramik; Powell, Thomas H Q; Feder, Jeffrey; Lodge, David M; Chang, Hsueh-Chia

2009-01-01

336

Rapid on-chip genetic detection microfluidic platform for real world applications  

PubMed Central

The development of genetic detection protocols for field applications is an important aspect of modern medical diagnostic technology and environmental monitoring. In this paper, we report a rapid, portable, and inexpensive DNA hybridization technique using a bead-based microfluidic platform that functions by passing fluorescently labeled target DNA through a chamber packed with functionalized beads within a microfluidic channel. DNA hybridization is then assessed using a digital camera attached to a Clare Chemical DR-45M dark reader non-UV transilluminator that uses visible light as an excitation source and a blue and amber filter to reveal fluorescence. This microfluidic approach significantly enhances hybridization by reducing the diffusion time between target DNA and the silica surface. The use of probe-functionalized beads as solid support also enhances the sensitivity and limit of detection due to a larger surface area per unit volume. This platform could be adapted for use in medical applications and environmental monitoring, including the detection of harmful organisms in the ballast water of ships. PMID:19693342

Senapati, Satyajyoti; Mahon, Andrew R.; Gordon, Jason; Nowak, Carsten; Sengupta, Shramik; Powell, Thomas H. Q.; Feder, Jeffrey; Lodge, David M.; Chang, Hsueh-Chia

2009-01-01

337

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

EPA Science Inventory

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

338

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

Microsoft Academic Search

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

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

2008-01-01

339

Reversible concentric ring microfluidic interconnects  

E-print Network

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

Thompson, Mary Kathryn, 1980-

2004-01-01

340

Reverse osmosis reverses conventional wisdom with Superfund cleanup success  

SciTech Connect

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

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

1994-09-01

341

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

342

A school-based application of modified habit reversal for Tourette syndrome via a translator: a case study.  

PubMed

A school-based modified habit reversal intervention was utilized with an adolescent diagnosed with Tourette syndrome who recently immigrated from Mexico. Because the student possessed little proficiency of the English language, an interpreter was needed to help implement the procedure. The frequency of motor tics markedly decreased from baseline to intervention across classroom settings. Results of two follow-up phases revealed that motor tic levels remained below those observed in the baseline phase. Implications and limitations of these findings are noted. PMID:16204418

Gilman, Rich; Connor, Nancy; Haney, Michelle

2005-11-01

343

New hydrophilic interaction/reversed-phase mixed-mode stationary phase and its application for analysis of nonionic ethoxylated surfactants.  

PubMed

We have developed a new stationary phase that combines both hydrophilic interaction and reversed-phase characteristics. The new phase is based on high-purity, porous and spherical silica gel functionalized with a silyl ligand consisting of both hydrophilic and hydrophobic functionalities. This phase can be operated in both HILIC mode (high organic solvent) and RPLC mode (low organic solvent). An optimal balance of hydrophilic and hydrophobic moieties on the silica surface provides unique chromatographic properties that make it useful for determination of alkyl chain distribution and degree of ethoxylation (EO number) of nonionic ethoxylated surfactants. PMID:18184616

Liu, Xiaodong; Pohl, Christopher

2008-05-16

344

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

345

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

346

Vasectomy reversal.  

PubMed

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

Belker, A M

1987-02-01

347

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

348

Linear genetic programming application for successive-station monthly streamflow prediction  

NASA Astrophysics Data System (ADS)

In recent decades, artificial intelligence (AI) techniques have been pronounced as a branch of computer science to model wide range of hydrological phenomena. A number of researches have been still comparing these techniques in order to find more effective approaches in terms of accuracy and applicability. In this study, we examined the ability of linear genetic programming (LGP) technique to model successive-station monthly streamflow process, as an applied alternative for streamflow prediction. A comparative efficiency study between LGP and three different artificial neural network algorithms, namely feed forward back propagation (FFBP), generalized regression neural networks (GRNN), and radial basis function (RBF), has also been presented in this study. For this aim, firstly, we put forward six different successive-station monthly streamflow prediction scenarios subjected to training by LGP and FFBP using the field data recorded at two gauging stations on Çoruh River, Turkey. Based on Nash-Sutcliffe and root mean squared error measures, we then compared the efficiency of these techniques and selected the best prediction scenario. Eventually, GRNN and RBF algorithms were utilized to restructure the selected scenario and to compare with corresponding FFBP and LGP. Our results indicated the promising role of LGP for successive-station monthly streamflow prediction providing more accurate results than those of all the ANN algorithms. We found an explicit LGP-based expression evolved by only the basic arithmetic functions as the best prediction model for the river, which uses the records of the both target and upstream stations.

Danandeh Mehr, Ali; Kahya, Ercan; Yerdelen, Cahit

2014-09-01

349

Linking genetically-defined neurons to behavior through a broadly applicable silencing allele  

PubMed Central

Summary Tools for suppressing synaptic transmission gain power when able to target highly selective neuron subtypes, thereby sharpening attainable links between neuron type, behavior, and disease; and when able to silence most any neuron subtype, thereby offering broad applicability. Here we present such a tool, RC::PFtox, that harnesses breadth in scope along with high cell-type selection via combinatorial gene expression to deliver tetanus toxin light chain (tox), an inhibitor of vesicular neurotransmission. When applied in mice, we observed cell-type specific disruption of vesicle exocytosis accompanied by loss of excitatory postsynaptic currents and commensurately perturbed behaviors. Among various test populations, we applied RC::PFtox to silence serotonergic neurons, en masse or a subset defined combinatorially. Of the behavioral phenotypes observed upon en masse serotonergic silencing, only one mapped to the combinatorially defined subset. These findings provide evidence for separability by genetic lineage of serotonin-modulated behaviors; collectively, these findings demonstrate broad utility of RC::PFtox for dissecting neuron functions. PMID:19679071

Kim, Jun Chul.; Cook, Melloni N.; Carey, Megan R.; Shen, Chung; Regehr, Wade G.; Dymecki, Susan M.

2009-01-01

350

Pragmatic Language in autism and fragile X syndrome: Genetic and clinical applications  

PubMed Central

Evidence suggests a strong genetic basis to autism. Our research program focuses on identifying genetically meaningful phenotypes in autism, through family-genetic and cross-population methods, with a particular focus on language and social phenotypes that have been shown to aggregate in families of individuals with autism. In this article, we discuss recent findings from family study research implicating particular language and personality features as markers for genetic liability to autism and fragile X syndrome and FMR1-related variation in relatives. We conclude with consideration of the clinical implications of such findings. PMID:24660047

Losh, Molly; Martin, Gary E.; Klusek, Jessica; Hogan-Brown, Abigail L.

2013-01-01

351

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

352

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

353

The Science of Breeding and Its Application to the Breeder Genetic Algorithm (BGA)  

Microsoft Academic Search

The breeder genetic algorithm (BGA) models artificial selection as performed by human breeders. The science of breeding is based on advanced statistical methods. In this paper a connection between genetic algorithm theory and the science of breeding is made. We show how the response to selection equation and the concept of heritability can be applied to predict the behavior of

Heinz Mühlenbein; Dirk Schlierkamp-voosen

1993-01-01

354

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

355

Application of the microsatellite technique for analyzing genetic diversity in shrimp breeding programs  

Microsoft Academic Search

The microsatellite technique was employed to demonstrate the use of genetic markers as a genetic analysis tool to manage breeding programs of cultured species. This technique was used on a total of 312 P. vannamei shrimp from Population 1 (Sinaloa, Mexico), Population 2 (Ecuador), Population 3 (hybrid of Population 1 X Population 2), Population 4 (Oaxaca, Mexico), a Guatemalan stock,

Greg M. Wolfus; Denise K. Garcia; Acacia Alcivar-Warren

1997-01-01

356

Teaching Applied Genetics and Molecular Biology to Agriculture Engineers. Application of the European Credit Transfer System  

ERIC Educational Resources Information Center

We have been teaching applied molecular genetics to engineers and adapted the teaching methodology to the European Credit Transfer System. We teach core principles of genetics that are universal and form the conceptual basis of most molecular technologies. The course then teaches widely used techniques and finally shows how different techniques…

Weiss, J.; Egea-Cortines, M.

2008-01-01

357

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

358

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

359

Application of sequence and genetic stratigraphic concepts to Carboniferous coal-bearing strata: an example from the Black Warrior basin, USA  

Microsoft Academic Search

Carboniferous strata provide an excellent example on which to test the application of genetic stratigraphic and sequence stratigraphic concepts. Both approaches are employed in the evaluation of the coal-bearing strata of the Black Warrior basin, south-eastern USA. Bounding hiatal surfaces have been recognized in the succession of rock that includes the Mary Lee coal zone. Within the framework of genetic

Robert A. Gastaldo; Timothy M. Demko; Yuejin Liu

1993-01-01

360

Tomato TILLING Technology: Development of a Reverse Genetics Tool for the Efficient Isolation of Mutants from Micro-Tom Mutant Libraries  

PubMed Central

To accelerate functional genomic research in tomato, we developed a Micro-Tom TILLING (Targeting Induced Local Lesions In Genomes) platform. DNA pools were constructed from 3,052 ethyl methanesulfonate (EMS) mutant lines treated with 0.5 or 1.0% EMS. The mutation frequency was calculated by screening 10 genes. The 0.5% EMS population had a mild mutation frequency of one mutation per 1,710 kb, whereas the 1.0% EMS population had a frequency of one mutation per 737 kb, a frequency suitable for producing an allelic series of mutations in the target genes. The overall mutation frequency was one mutation per 1,237 kb, which affected an average of three alleles per kilobase screened. To assess whether a Micro-Tom TILLING platform could be used for efficient mutant isolation, six ethylene receptor genes in tomato (SlETR1–SlETR6) were screened. Two allelic mutants of SlETR1 (Sletr1-1 and Sletr1-2) that resulted in reduced ethylene responses were identified, indicating that our Micro-Tom TILLING platform provides a powerful tool for the rapid detection of mutations in an EMS mutant library. This work provides a practical and publicly accessible tool for the study of fruit biology and for obtaining novel genetic material that can be used to improve important agronomic traits in tomato. PMID:21965606

Okabe, Yoshihiro; Asamizu, Erika; Saito, Takeshi; Matsukura, Chiaki; Ariizumi, Tohru; Brès, Cécile; Rothan, Christophe; Mizoguchi, Tsuyoshi; Ezura, Hiroshi

2011-01-01

361

Optimization of reversible sequential circuits  

E-print Network

In recent years reversible logic has been considered as an important issue for designing low power digital circuits. It has voluminous applications in the present rising nanotechnology such as DNA computing, Quantum Computing, low power VLSI and quantum dot automata. In this paper we have proposed optimized design of reversible sequential circuits in terms of number of gates, delay and hardware complexity. We have designed the latches with a new reversible gate and reduced the required number of gates, garbage outputs, and delay and hardware complexity. As the number of gates and garbage outputs increase the complexity of reversible circuits, this design will significantly enhance the performance. We have proposed reversible D-latch and JK latch which are better than the existing designs available in literature.

Sayem, Abu Sadat Md

2010-01-01

362

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

363

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

364

Phylogenetic and Genetic Analysis of Feline Immunodeficiency Virus gag, pol, and env Genes from Domestic Cats Undergoing Nucleoside Reverse Transcriptase Inhibitor Treatment or Treatment-Naïve Cats in Rio de Janeiro, Brazil? †  

PubMed Central

Feline immunodeficiency virus (FIV) is the Lentivirus responsible for an immunodeficiency-like disease in domestic cats (Felis catus). FIV is divided into five phylogenetic subtypes (A, B, C, D, and E), based on genetic diversity. Knowledge of the geographical distribution of subtypes is relevant for understanding different disease progressions and for vaccine development. In this study, viral sequences of 26 infected cats from Rio de Janeiro, 8 undergoing treatment with zidovudine (AZT) for at least 5 years, were successfully amplified from blood specimens. gag capsid (CA), pol reverse transcriptase (RT), and env gp120 (V3-V4) regions were analyzed to determine subtypes and to evaluate potential mutations related to antiretroviral drug resistance among treated cats. Subtyping based on phylogenetic analysis was performed by the neighbor-joining and maximum likelihood methods. All of the sequences clustered with subtype B in the three regions, exhibiting low genetic variability. Additionally, we found evidence that the same virus is circulating in animals in close contact. The analysis of FIV RT sequences identified two new putative mutations related to drug resistance located in the RT “finger” domain, which has 60% identity to human immunodeficiency virus (HIV) sequence. Amino acid change K?R at codons 64 and 69 was found in 25% and 37.5% of the treated animals, respectively. These signatures were comparable to K65R and K70R thymidine-associated mutations found in the HIV-1 HXB2 counterpart. This finding strongly suggests a position correlation between the mutations found in FIV and the K65R and K70R substitutions from drug-resistant HIV-1 strains. PMID:18550661

Martins, Angelica N.; Medeiros, Sheila O.; Simonetti, Jose P.; Schatzmayr, Hermann G.; Tanuri, Amílcar; Brindeiro, Rodrigo M.

2008-01-01

365

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.

366

High capacity, reversible alloying reactions in SnSb/C nanocomposites for Na-ion battery applications  

SciTech Connect

A new SnSb/C nanocomposite based on Na alloying reactions is demonstrated as anode for Na-ion battery applications. The electrode can achieve an exceptionally high capacity (544 mA h g?1, almost double that of intercalation carbon materials), good rate capacity and cyclability (80% capacity retention over 50 cycles) for Na-ion storage.

Xiao, Lifen; Cao, Yuliang; Xiao, Jie; Wang, Wei; Kovarik, Libor; Nie, Zimin; Liu, Jun

2012-04-04

367

Application of reversed-phase high-performance liquid chromatography with fluorimetric detection for simultaneous assessment of global DNA and total RNA methylation in Lepidium sativum: effect of plant exposure to Cd(II) and Se(IV).  

PubMed

In the present work, application of the previously established reversed-phase liquid chromatography procedure based on fluorescent labeling of cytosine and methylcytosine moieties with 2-bromoacetophenone (HPLC-FLD) is presented for simultaneous evaluation of global DNA and total RNA methylation at cytosine carbon 5. The need for such analysis was comprehended from the recent advances in the field of epigenetics that highlight the importance of non-coding RNAs in DNA methylation and suggest that RNA methylation might play a similar role in the modulation of genetic information, as previously demonstrated for DNA. In order to adopt HPLC-FLD procedure for DNA and RNA methylation analysis in a single biomass extract, two extraction procedures with different selectivity toward nucleic acids were examined, and a simplified calibration was designed allowing for evaluation of methylation percentage based on the ratio of chromatographic peak areas: cytidine/5-methylcytidine for RNA and 2'-deoxycytidine/5-methyl-2'-deoxycytidine for DNA. As a proof of concept, global DNA and total RNA methylation were determined in Lepidium sativum hydroponically grown in the presence of different Cd(II) or Se(IV) concentrations, expecting that plant exposure to abiotic stress might affect not only global DNA but also total RNA methylation. The results obtained showed the increase of DNA methylation in the treated plants up to concentration levels 2 mg L(-1) Cd and 1 mg L(-1) Se in the growth medium. For higher stressors' concentration, global DNA methylation tended to decrease. Most importantly, an inverse correlation was found between DNA and RNA methylation levels (r = -0.6788, p = 0.031), calling for further studies of this particular modification of nucleic acids in epigenetic context. PMID:23322354

Yanez Barrientos, Eunice; Wrobel, Kazimierz; Lopez Torres, Adolfo; Gutiérrez Corona, Felix; Wrobel, Katarzyna

2013-03-01

368

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

369

Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)  

PubMed Central

Molecular markers are a highly valuable tool for creating genetic maps. Like in many other crops, sugar beet (Beta vulgaris L.) breeding is increasingly supported by the application of such genetic markers. Single nucleotide polymorphism (SNP) based markers have a high potential for automated analysis and high-throughput genotyping. We developed a bioinformatics workflow that uses Sanger and 2nd-generation sequence data for detection, evaluation and verification of new transcript-associated SNPs from sugar beet. RNAseq data from one parent of an established mapping population were produced by 454-FLX sequencing and compared to Sanger ESTs derived from the other parent. The workflow established for SNP detection considers the quality values of both types of reads, provides polymorphic alignments as well as selection criteria for reliable SNP detection and allows painless generation of new genetic markers within genes. We obtained a total of 14,323 genic SNPs and InDels. According to empirically optimised settings for the quality parameters, we classified these SNPs into four usability categories. Validation of a subset of the in silico detected SNPs by genotyping the mapping population indicated a high success rate of the SNP detection. Finally, a total of 307 new markers were integrated with existing data into a new genetic map of sugar beet which offers improved resolution and the integration of terminal markers. PMID:25302600

Holtgräwe, Daniela; Sörensen, Thomas Rosleff; Viehöver, Prisca; Schneider, Jessica; Schulz, Britta; Borchardt, Dietrich; Kraft, Thomas; Himmelbauer, Heinz; Weisshaar, Bernd

2014-01-01

370

Application of Genetic Algorithm to Optimal Design of Central Air-Conditioning Water System  

E-print Network

The optimal design of air-conditioning water system is an optimization problem of functions that depend on a series of nonlinear discrete multi-variables.Many traditional methods are not satisfactory when applied in this field. However, genetic...

Feng, X.; Zou, Y.; Long, W.

2006-01-01

371

Genetics of Type 2 Diabetes: Insights into the Pathogenesis and Its Clinical Application  

PubMed Central

With rapidly increasing prevalence, diabetes has become one of the major causes of mortality worldwide. According to the latest studies, genetic information makes substantial contributions towards the prediction of diabetes risk and individualized antidiabetic treatment. To date, approximately 70 susceptibility genes have been identified as being associated with type 2 diabetes (T2D) at a genome-wide significant level (P < 5 × 10?8). However, all the genetic loci identified so far account for only about 10% of the overall heritability of T2D. In addition, how these novel susceptibility loci correlate with the pathophysiology of the disease remains largely unknown. This review covers the major genetic studies on the risk of T2D based on ethnicity and briefly discusses the potential mechanisms and clinical utility of the genetic information underlying T2D. PMID:24864266

Sun, Xue; Yu, Weihui; Hu, Cheng

2014-01-01

372

Genetic Regulation of Platelet Receptor Expression and Function: Application in Clinical Practice and Drug Development  

PubMed Central

Understanding genetic contributions to platelet function could have profound clinical ramifications for personalizing platelet-directed pharmacotherapy, by providing insight into the risks and possible benefits associated with specific genotypes. This article represents an integrated summary of presentations related to genetic regulation of platelet receptor expression and function given at the Fifth Annual Platelet Colloquium in January 2010. It is supplemented with additional highlights from the literature covering 1) approaches to determining and evidence for the associations of genetic variants with platelet hypo- and hyperresponsive phenotypes, 2) the ramifications of these polymorphisms with regard to clinical responses to antiplatelet therapies, and 3) the role of platelet function/genetic testing in guiding antiplatelet therapy. PMID:21084706

Williams, Marlene S.; Weiss, Ethan J.; Sabatine, Marc S.; Bray, Paul F.; Simon, Daniel I.; Bahou, Wadie F.; Becker, Lewis C.; Parise, Leslie V.; Dauerman, Harold L.; French, Patricia A.; Becker, Richard C.; Smyth, Susan S.

2014-01-01

373

The Use of Prior Distributions to Learn Genetic Olivier Gevaert1  

E-print Network

of a struc- ture prior for reverse-engineering genetic networks with Bayesian network models can improve more reliable models of genetic networks. 1 Introduction Reverse engineering genetic networks has been and extensions of Bayesian networks are popular models for reverse engineering genetic networks ([5, 15, 9, 10

374

Applications of the Saccharomyces cerevisiae Flp-FRT System in Bacterial Genetics  

Microsoft Academic Search

The Flp-FRT site-specific recombinationsystem from Saccharomyces cerevisiae is a powerful and efficient tool for high-throughput genetic analysis of bacteria in the postgenomic era. This review highlights the features of the Flp-FRT system, describes current bacterial genetic methods incorporating this technology and, finally, suggests potential future uses of this system. In combination with improved allele replacement methods, recyclable FRT mutagenesis cassettes,

Herbert P. Schweizer

2003-01-01

375

Shape Matching and Recognition Base on Genetic Algorithm and Application to Plant Species Identification  

Microsoft Academic Search

\\u000a In this paper an efficient shape matching and recognition approach based on genetic algorithm is proposed and successfully\\u000a applied to plant special identification. Firstly, a Douglas-Peucker approximation algorithm is adopted to the original shape\\u000a and a new shape representation is used to form the sequence of invariant attributes. Then a genetic algorithm for shape matching\\u000a is proposed to do the

Ji-xiang Du; Xiao-Feng Wang; Xiao Gu

2005-01-01

376

Control of Wettability of Carbon Nanotube Array by Reversible Dry Oxidation for Superhydrophobic Coating and Supercapacitor Applications  

NASA Astrophysics Data System (ADS)

In this thesis, dry chemical modification methods involving UV/ozone, oxygen plasma, and vacuum annealing treatments are explored to precisely control the wettability of CNT arrays. The effect of oxidation using UV/ozone and oxygen plasma treatments is highly reversible as long as the O/C ratio of the CNT arrays is kept below 18%. At O/C ratios higher than 18%, the effect of oxidation is no longer reversible. This irreversible oxidation is caused by irreversible changes to the CNT atomic structure during the oxidation process. During the oxidation process, CNT arrays undergo three different processes. For CNT arrays with O/C ratios lower than 40%, the oxidation process results in the functionalization of CNT outer walls by oxygenated groups. Although this functionalization process introduces defects, vacancies and micropores opening, the graphitic structure of the CNT is still largely intact. For CNT arrays with O/C ratios between 40% and 45%, the oxidation process results in the etching of CNT outer walls. This etching process introduces large scale defects and holes that can be obviously seen under TEM at high magnification. Most of these holes are found to be several layers deep and, in some cases, a large portion of the CNT side walls are cut open. For CNT arrays with O/C ratios higher than 45%, the oxidation process results in the exfoliation of the CNT walls and amorphization of the remaining CNT structure. This amorphization process can be implied from the disappearance of C-C sp2 peak in the XPS spectra associated with the pi-bond network. The impact behavior of water droplet impinging on superhydrophobic CNT arrays in a low viscosity regime is investigated for the first time. Here, the experimental data are presented in the form of several important impact behavior characteristics including critical Weber number, volume ratio, restitution coefficient, and maximum spreading diameter. As observed experimentally, three different impact regimes are identified while another impact regime is proposed. These regimes are partitioned by three critical Weber numbers, two of which are experimentally observed. The volume ratio between the primary and the secondary droplets is found to decrease with the increase of Weber number in all impact regimes other than the first one. In the first impact regime, this is found to be independent of Weber number since the droplet remains intact during and subsequent to the impingement. Experimental data show that the coefficient of restitution decreases with the increase of Weber number in all impact regimes. The rate of decrease of the coefficient of restitution in the high Weber number regime is found to be higher than that in the low and moderate Weber number. Experimental data also show that the maximum spreading factor increases with the increase of Weber number in all impact regimes. The rate of increase of the maximum spreading factor in the high Weber number regime is found to be higher than that in the low and moderate Weber number. Phenomenological approximations and interpretations of the experimental data, as well as brief comparisons to the previously proposed scaling laws, are shown here. Dry oxidation methods are used for the first time to characterize the influence of oxidation on the capacitive behavior of CNT array EDLCs. The capacitive behavior of CNT array EDLCs can be tailored by varying their oxygen content, represented by their O/C ratio. The specific capacitance of these CNT arrays increases with the increase of their oxygen content in both KOH and Et4NBF4/PC electrolytes. As a result, their gravimetric energy density increases with the increase of their oxygen content. However, their gravimetric power density decreases with the increase of their oxygen content. The optimally oxidized CNT arrays are able to withstand more than 35,000 charge/discharge cycles in Et4NBF4/PC at a current density of 5 A/g while only losing 10% of their original capacitance. (Abstract shortened by UMI.)

Aria, Adrianus Indrat

377

In Peter Aiken and Elizabeth Burd, editors, Proc. 8th Working Conference on Reverse Engineering. IEEE, Los Alamitos, 2001 Application of UML Associations and Their Adornments in Design Recovery  

E-print Network

­ stractions from a combination of code, existing design doc­ umentation (if available), personal experience. IEEE, Los Alamitos, 2001 Application of UML Associations and Their Adornments in Design Recovery Ralf: UML class diagrams, association, adorn­ ment, aggregation, composition, reverse engineering, de­ sign

Gogolla, Martin - Fachbereich 3

378

Personalized MultiStage Decision Support in Reverse Logistics Management  

Microsoft Academic Search

Reverse logistics has gained increasing importance as a profitable and sustainable business strategy. As a reverse logistics chain has strong internal and external linkages, the management of a reverse logistics chain becomes an area of organizational competitive advantage, in particular, with the growth of e-commerce applications. To effectively manage a reverse logistics chain always involves a decision optimization issue in

Jie Lu; Guangquan Zhang

2005-01-01

379

Molecular diagnosis of inheritable neuromuscular disorders. Part II: Application of genetic testing in neuromuscular disease.  

PubMed

Molecular genetic advances have led to refinements in the classification of inherited neuromuscular disease, and to methods of molecular testing useful for diagnosis and management of selected patients. Testing should be performed as targeted studies, sometimes sequentially, but not as wasteful panels of multiple genetic tests performed simultaneously. Accurate diagnosis through molecular testing is available for the vast majority of patients with inherited neuropathies, resulting from mutations in three genes (PMP22, MPZ, and GJB1); the most common types of muscular dystrophies (Duchenne and Becker, facioscapulohumeral, and myotonic dystrophies); the inherited motor neuron disorders (spinal muscular atrophy, Kennedy's disease, and SOD1 related amyotrophic lateral sclerosis); and many other neuromuscular disorders. The role of potential multiple genetic influences on the development of acquired neuromuscular diseases is an increasingly active area of research. PMID:15704143

Greenberg, Steven A; Walsh, Ronan J

2005-04-01

380

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

381

I ARTICLE........ A Genetic Linkage Map of the Mouse: Current Applications and Future Prospects  

E-print Network

Technological advances have made possible the development of high-resolution genetic linkage maps for the mouse. These maps in turn offer exciting prospects for understanding mammalian genome evolution through comparative mapping, for developing mouse models of human disease, and for identifying the function of all genes in the organism. (RFLPs) on Southern (DNA) blots; more recently, many have been developed that can be assayed by the polymerase chain reaction (PCR). Interspeciflc Crosses Historically, the mouse has been the mammal of choice for genetic analysis primarily because of its short gestation period and large litter sizes, the availability of inbred strains, and the ability to perform controlled matings. The mouse has also served

Neal G. Copel; Nancy A. Jenkins; Debra J. Gilbert; Lois J. Maitais; Joyce C. Miller; William F. Dietrich; Alix Weaver; Stephen E. Lincoln; Robert G. Steen; Uncoln D. Stein; Joseph H. Nadeau; Eric S. L

382

Genetic variation and its maintenance  

SciTech Connect

This book contains several papers divided among three sections. The section titles are: Genetic Diversity--Its Dimensions; Genetic Diversity--Its Origin and Maintenance; and Genetic Diversity--Applications and Problems of Complex Characters.

Roberts, D.F.; De Stefano, G.F.

1986-01-01

383

Application of a single-objective, hybrid genetic algorithm approach to pharmacokinetic model building.  

PubMed

A limitation in traditional stepwise population pharmacokinetic model building is the difficulty in handling interactions between model components. To address this issue, a method was previously introduced which couples NONMEM parameter estimation and model fitness evaluation to a single-objective, hybrid genetic algorithm for global optimization of the model structure. In this study, the generalizability of this approach for pharmacokinetic model building is evaluated by comparing (1) correct and spurious covariate relationships in a simulated dataset resulting from automated stepwise covariate modeling, Lasso methods, and single-objective hybrid genetic algorithm approaches to covariate identification and (2) information criteria values, model structures, convergence, and model parameter values resulting from manual stepwise versus single-objective, hybrid genetic algorithm approaches to model building for seven compounds. Both manual stepwise and single-objective, hybrid genetic algorithm approaches to model building were applied, blinded to the results of the other approach, for selection of the compartment structure as well as inclusion and model form of inter-individual and inter-occasion variability, residual error, and covariates from a common set of model options. For the simulated dataset, stepwise covariate modeling identified three of four true covariates and two spurious covariates; Lasso identified two of four true and 0 spurious covariates; and the single-objective, hybrid genetic algorithm identified three of four true covariates and one spurious covariate. For the clinical datasets, the Akaike information criterion was a median of 22.3 points lower (range of 470.5 point decrease to 0.1 point decrease) for the best single-objective hybrid genetic-algorithm candidate model versus the final manual stepwise model: the Akaike information criterion was lower by greater than 10 points for four compounds and differed by less than 10 points for three compounds. The root mean squared error and absolute mean prediction error of the best single-objective hybrid genetic algorithm candidates were a median of 0.2 points higher (range of 38.9 point decrease to 27.3 point increase) and 0.02 points lower (range of 0.98 point decrease to 0.74 point increase), respectively, than that of the final stepwise models. In addition, the best single-objective, hybrid genetic algorithm candidate models had successful convergence and covariance steps for each compound, used the same compartment structure as the manual stepwise approach for 6 of 7 (86 %) compounds, and identified 54 % (7 of 13) of covariates included by the manual stepwise approach and 16 covariate relationships not included by manual stepwise models. The model parameter values between the final manual stepwise and best single-objective, hybrid genetic algorithm models differed by a median of 26.7 % (q? = 4.9 % and q? = 57.1 %). Finally, the single-objective, hybrid genetic algorithm approach was able to identify models capable of estimating absorption rate parameters for four compounds that the manual stepwise approach did not identify. The single-objective, hybrid genetic algorithm represents a general pharmacokinetic model building methodology whose ability to rapidly search the feasible solution space leads to nearly equivalent or superior model fits to pharmacokinetic data. PMID:22767341

Sherer, Eric A; Sale, Mark E; Pollock, Bruce G; Belani, Chandra P; Egorin, Merrill J; Ivy, Percy S; Lieberman, Jeffrey A; Manuck, Stephen B; Marder, Stephen R; Muldoon, Matthew F; Scher, Howard I; Solit, David B; Bies, Robert R

2012-08-01

384

Reverse-Genetic Analysis of the Two Biotin-Containing Subunit Genes of the Heteromeric Acetyl-Coenzyme A Carboxylase in Arabidopsis Indicates a Unidirectional Functional Redundancy1[C][W][OA  

PubMed Central

The heteromeric acetyl-coenzyme A carboxylase catalyzes the first and committed reaction of de novo fatty acid biosynthesis in plastids. This enzyme is composed of four subunits: biotin carboxyl-carrier protein (BCCP), biotin carboxylase, ?-carboxyltransferase, and ?-carboxyltransferase. With the exception of BCCP, single-copy genes encode these subunits in Arabidopsis (Arabidopsis thaliana). Reverse-genetic approaches were used to individually investigate the physiological significance of the two paralogous BCCP-coding genes, CAC1A (At5g16390, codes for BCCP1) and CAC1B (At5g15530, codes for BCCP2). Transfer DNA insertional alleles that completely eliminate the accumulation of BCCP2 have no perceptible effect on plant growth, development, and fatty acid accumulation. In contrast, transfer DNA insertional null allele of the CAC1A gene is embryo lethal and deleteriously affects pollen development and germination. During seed development the effect of the cac1a null allele first becomes apparent at 3-d after flowering, when the synchronous development of the endosperm and embryo is disrupted. Characterization of CAC1A antisense plants showed that reducing BCCP1 accumulation to 35% of wild-type levels, decreases fatty acid accumulation and severely affects normal vegetative plant growth. Detailed expression analysis by a suite of approaches including in situ RNA hybridization, promoter:reporter transgene expression, and quantitative western blotting reveal that the expression of CAC1B is limited to a subset of the CAC1A-expressing tissues, and CAC1B expression levels are only about one-fifth of CAC1A expression levels. Therefore, a likely explanation for the observed unidirectional redundancy between these two paralogous genes is that whereas the BCCP1 protein can compensate for the lack of BCCP2, the absence of BCCP1 cannot be tolerated as BCCP2 levels are not sufficient to support heteromeric acetyl-coenzyme A carboxylase activity at a level that is required for normal growth and development. PMID:21030508

Li, Xu; Ilarslan, Hilal; Brachova, Libuse; Qian, Hui-Rong; Li, Ling; Che, Ping; Wurtele, Eve Syrkin; Nikolau, Basil J.

2011-01-01

385

An application of genetic and tabu searches to the freight railroad operating plan problem  

Microsoft Academic Search

This paper addresses the joint train-scheduling and demand-flow problem for a major US freight railroad. No efficient optimization techniques are known to solve the NP-hard combinatorial optimization problem. Genetic search is used to find acceptable solutions; however, its performance is found to deteriorate as the problem size grows. A \\

Michael Francis Gorman

1998-01-01

386

Genetic algorithms for the application of Activated Sludge Model No. 1  

Microsoft Academic Search

The genetic algorithm (GA) has been integrated into the IWA ASM No.1 to calibrate important stoichiometric and kinetic parameters. The evolutionary feature of GA was used to configure the multiple local optima as well as the global optimum. The objective function of optimization was designed to minimize the difference between estimated and measured effluent concentrations at the activated sludge system.

S. Kim; H. Lee; J. Kim; C. Kim; J. Ko; H. Woo

2002-01-01

387

A genetic linkage map of the mouse: Current applications and future prospects  

SciTech Connect

Technological advances have made possible the development of high-resolution genetic linkage maps for the mouse. These maps in turn offer exciting prospects for understanding mammalian genome evolution through comparative mapping, for developing mouse models of human disease, and for identifying the function of all genes in the organism.

Copeland, N.G.; Jenkins, N.A.; Gilbert, D.J. (Frederick Cancer Research and Development Center, MD (United States)); Eppig, J.T.; Maltais, L.J.; Nadeau, J.H. (Jackson Laboratory, Bar Harbor, ME (United States)); Miller, J.C.; Dietrich, W.F.; Weaver, A.; Lincoln, S.E.; Steen, R.G.; Steing, L.D.; Lander, E.S. (Whitehead Institute for Biomedical Research, Cambridge, MA (United States))

1993-10-01

388

Genetic-based fuzzy image filter and its application to image processing.  

PubMed

In this paper, we propose a Genetic-based Fuzzy Image Filter (GFIF) to remove additive identical independent distribution (i.i.d.) impulse noise from highly corrupted images. The proposed filter consists of a fuzzy number construction process, a fuzz filtering process, a genetic learning process, and an image knowledge base. First, the fuzzy number construction process receives sample images or the noise-free image and then constructs an image knowledge base for the fuzzy filtering process. Second, the fuzzy filtering process contains a parallel fuzzy inference mechanism, a fuzzy mean process, and a fuzzy decision process to perform the task of noise removal. Finally, based on the genetic algorithm, the genetic learning process adjusts the parameters of the image knowledge base. By the experimental results, GFIF achieves a better performance than the state-of-the-art filters based on the criteria of Peak-Signal-to-Noise-Ratio (PSNR), Mean-Square-Error (MSE), and Mean-Absolute-Error (MAE). On the subjective evaluation of those filtered images, GFIF also results in a higher quality of global restoration. PMID:16128454

Lee, Chang-Shing; Guo, Shu-Mei; Hsu, Chin-Yuan

2005-08-01

389

Application of genetic algorithm (GA) technique on demand estimation of fossil fuels in Turkey  

Microsoft Academic Search

The main objective is to investigate Turkey's fossil fuels demand, projection and supplies by using the structure of the Turkish industry and economic conditions. This study develops scenarios to analyze fossil fuels consumption and makes future projections based on a genetic algorithm (GA). The models developed in the nonlinear form are applied to the coal, oil and natural gas demand

Olcay Ersel Canyurt; Harun Kemal Ozturk

2008-01-01

390

The Application of Genetically Engineered Herpes Simplex Viruses to the Treatment of Experimental Brain Tumors  

Microsoft Academic Search

Due to lack of effective therapy, primary brain tumors are the focus of intense investigation of novel experimental approaches that use vectors and recombinant viruses. Therapeutic approaches have been both indirect, whereby vectors are used, or direct to allow for direct cell killing by the introduced virus. Genetically engineered herpes simplex viruses are currently being evaluated as an experimental approach

Samita S. Andreansky; Bin He; G. Yancey Gillespie; Liliana Soroceanu; James Markert; Joany Chou; Bernard Roizman; Richard J. Whitley

1996-01-01

391

GENETIC DETECTION OF EDWARDSIELLA ICTALURI: APPLICATION IN A CHANNEL CATFISH SELECTIVE BREEDING PROGRAM  

Technology Transfer Automated Retrieval System (TEKTRAN)

Sensitive detection of ESC (Enteric Septicemia of Catfish) is important to the successful development of a selective breeding program for ESC resistance in channel catfish. Therefore, a genetic assay using quantitative PCR (polymerase chain reaction) was developed for early detection of E. ictaluri...

392

Clinical applications of fetal sex determination in maternal blood in a preimplantation genetic diagnosis centre  

Microsoft Academic Search

BACKGROUND: Couples with a risk of transmitting X-linked diseases who are included in a preimplantation genetic diagnosis (PGD) programme need early and rapid fetal sex determination in two situations. The first situation is for the control of embryo sexing after PGD and the second situation is for those couples having a spontaneous pregnancy before the start of their PGD cycle.

Gerard Tachdjian; Nelly Frydman; Francois Audibert; Pierre Ray; Violaine Kerbrat

393

Genetic clustering for automatic evolution of clusters and application to image classification  

Microsoft Academic Search

In this article the searching capability of genetic algorithms has been exploited for automatically evolving the number of clusters as well as proper clustering of any data set. A new string representation, comprising both real numbers and the do not care symbol, is used in order to encode a variable number of clusters. The Davies–Bouldin index is used as a

Sanghamitra Bandyopadhyay; Ujjwal Maulik

2002-01-01

394

Application of triplex PCR for identification of genetically modified organism in foods  

Microsoft Academic Search

A multiplex method for detection of genetically modified organism (GMO) in various foods has been developed based on PCR-identification\\u000a of cauliflower mosaic virus (CMV) 35S-promoter. It allows avoiding false positive signals due to contamination of plant raw\\u000a material with CMV.

E. S. Bulygina; M. V. Sukhacheva; B. K. Bumazhkin; B. B. Kuznetsov

2010-01-01

395

The application of molecular genetic approaches to the study of human evolution  

Microsoft Academic Search

The past decade of advances in molecular genetic technology has heralded a new era for all evolutionary studies, but especially the science of human evolution. Data on various kinds of DNA variation in human populations have rapidly accumulated. There is increasing recognition of the importance of this variation for medicine and developmental biology and for understanding the history of our

L. Luca Cavalli-Sforza; Marcus W. Feldman

2003-01-01

396

Genetics and epigenetics in major psychiatric disorders: dilemmas, achievements, applications, and future scope.  

PubMed

No specific gene has been identified for any major psychiatric disorder, including schizophrenia, in spite of strong evidence supporting a genetic basis for these complex and devastating disorders. There are several likely reasons for this failure, ranging from poor study design with low statistical power to genetic mechanisms such as polygenic inheritance, epigenetic interactions, and pleiotropy. Most study designs currently in use are inadequate to uncover these mechanisms. However, to date, genetic studies have provided some valuable insight into the causes and potential therapies for psychiatric disorders. There is a growing body of evidence suggesting that the understanding of the genetic etiology of psychiatric illnesses, including schizophrenia, will be more successful with integrative approaches considering both genetic and epigenetic factors. For example, several genes including those encoding dopamine receptors (DRD2, DRD3, and DRD4), serotonin receptor 2A (HTR2A) and catechol-O-methyltransferase (COMT) have been implicated in the etiology of schizophrenia and related disorders through meta-analyses and large, multicenter studies. There is also growing evidence for the role of DRD1, NMDA receptor genes (GRIN1, GRIN2A, GRIN2B), brain-derived neurotrophic factor (BDNF), and dopamine transporter (SLC6A3) in both schizophrenia and bipolar disorder. Recent studies have indicated that epigenetic modification of reelin (RELN), BDNF, and the DRD2 promoters confer susceptibility to clinical psychiatric conditions. Pharmacologic therapy of psychiatric disorders will likely be more effective once the molecular pathogenesis is known. For example, the hypoactive alleles of DRD2 and the hyperactive alleles of COMT, which degrade the dopamine in the synaptic cleft, are associated with schizophrenia. It is likely that insufficient dopaminergic transmission in the frontal lobe plays a role in the development of negative symptoms associated with this disorder. Antipsychotic therapies with a partial dopamine D2 receptor agonist effect may be a plausible alternative to current therapies, and would be effective in symptom reduction in psychotic individuals. It is also possible that therapies employing dopamine D1/D2 receptor agonists or COMT inhibitors will be beneficial for patients with negative symptoms in schizophrenia and bipolar disorder. The complex etiology of schizophrenia, and other psychiatric disorders, warrants the consideration of both genetic and epigenetic systems and the careful design of experiments to illumine the genetic mechanisms conferring liability for these disorders and the benefit of existing and new therapies. PMID:15952869

Abdolmaleky, Hamid M; Thiagalingam, Sam; Wilcox, Marsha

2005-01-01

397

Reversible phosphorylation in mitochondria.  

E-print Network

??Mitochondria represent an underappreciated site of regulation by reversible phosphorylation. Our work has focused on the identification of proteins involved in regulating mitochondria by reversible… (more)

Rardin, Matthew James

2008-01-01

398

Microfluidic on-chip capture-cycloaddition reaction to reversibly immobilize small molecules or multi-component structures for biosensor applications.  

PubMed

Methods for rapid surface immobilization of bioactive small molecules with control over orientation and immobilization density are highly desirable for biosensor and microarray applications. In this Study, we use a highly efficient covalent bioorthogonal [4+2] cycloaddition reaction between trans-cyclooctene (TCO) and 1,2,4,5-tetrazine (Tz) to enable the microfluidic immobilization of TCO/Tz-derivatized molecules. We monitor the process in real-time under continuous flow conditions using surface plasmon resonance (SPR). To enable reversible immobilization and extend the experimental range of the sensor surface, we combine a non-covalent antigen-antibody capture component with the cycloaddition reaction. By alternately presenting TCO or Tz moieties to the sensor surface, multiple capture-cycloaddition processes are now possible on one sensor surface for on-chip assembly and interaction studies of a variety of multi-component structures. We illustrate this method with two different immobilization experiments on a biosensor chip; a small molecule, AP1497 that binds FK506-binding protein 12 (FKBP12); and the same small molecule as part of an immobilized and in situ-functionalized nanoparticle. PMID:24084440

Tassa, Carlos; Liong, Monty; Hilderbrand, Scott; Sandler, Jason E; Reiner, Thomas; Keliher, Edmund J; Weissleder, Ralph; Shaw, Stanley Y

2013-01-01

399

Forward and reverse mutagenesis in C. elegans  

PubMed Central

Mutagenesis drives natural selection. In the lab, mutations allow gene function to be deciphered. C. elegans is highly amendable to functional genetics because of its short generation time, ease of use, and wealth of available gene-alteration techniques. Here we provide an overview of historical and contemporary methods for mutagenesis in C. elegans, and discuss principles and strategies for forward (genome-wide mutagenesis) and reverse (target-selected and gene-specific mutagenesis) genetic studies in this animal. PMID:24449699

Kutscher, Lena M.; Shaham, Shai

2014-01-01

400

Potential applications of cryogenic technologies to plant genetic improvement and pathogen eradication.  

PubMed

Rapid increases in human populations provide a great challenge to ensure that adequate quantities of food are available. Sustainable development of agricultural production by breeding more productive cultivars and by increasing the productive potential of existing cultivars can help meet this demand. The present paper provides information on the potential uses of cryogenic techniques in ensuring food security, including: (1) long-term conservation of a diverse germplasm and successful establishment of cryo-banks; (2) maintenance of the regenerative ability of embryogenic tissues that are frequently the target for genetic transformation; (3) enhancement of genetic transformation and plant regeneration of transformed cells, and safe, long-term conservation for transgenic materials; (4) production and maintenance of viable protoplasts for transformation and somatic hybridization; and (5) efficient production of pathogen-free plants. These roles demonstrate that cryogenic technologies offer opportunities to ensure food security. PMID:24681087

Wang, Biao; Wang, Ren-Rui; Cui, Zhen-Hua; Bi, Wen-Lu; Li, Jing-Wei; Li, Bai-Quan; Ozudogru, Elif Aylin; Volk, Gayle M; Wang, Qiao-Chun

2014-01-01

401

Applications and limitations of genetically modified mouse models in drug discovery and development.  

PubMed

Genetically modified mouse models in which a specific gene is removed or replaced have proven to be powerful tools for identification/validation of target gene and scientific understanding of molecular mechanisms underlying drug-induced toxicity through mechanistic studies. In spite of the advantage, there are significant limitations of genetically modified mouse models. Modification of a given gene does not always result in the anticipated phenotype. In some instances, phenotypes of targeted mouse mutants were not those predicted from the presumed function of the given genes, while other null mutants revealed no apparent defects. Furthermore, the phenotypic outcome can be influenced by many environmental and genetic factors. Therefore, interpretation of the significance of the findings from studies using genetically modified mouse models is not always as straightforward as one would expect, especially when desire is to extrapolate the findings to humans. Interestingly, many humanized mouse models have been generated for evaluating the function and regulation of cytochrome P450 (CYP) enzymes. Our fascination with humanized animals dates back to ancients. For example, the Great Sphinx of Giza, a large half-human and half-lion statue, is believed to have been built by Egyptians about 4500 years ago. Although the creation of humanized animals that carry a particular human CYP gene provides useful tools for scientific understanding of the function and regulation of the CYP enzyme, these humanized mouse models are not so useful in prediction of human pharmacokinetics in a quantitative sense. Accordingly, it is important to keep in mind that an animal engineered to express a human gene and its protein is still an animal. PMID:18537578

Lin, Jiunn H

2008-06-01

402

Sustainable Development and Norwegian Genetic Engineering Regulations: Applications, Impacts, and Challenges  

Microsoft Academic Search

The main purpose of The NorwegianGene Technology Act (1993) is to enforcecontainment of genetically modified organisms(GMOs) and control of GMO releases.Furthermore, the Act intends to ensure that``production and use of GMOs should take placein an ethically and socially justifiable way,in accordance with the principle of sustainabledevelopment and without detrimental effects tohealth and the environment.'' Hence it isobvious that, for the

Anne Ingeborg Myhr; Terje Traavik

2003-01-01

403

Application of Microsatellite Markers to Population Genetics Studies of Japanese Flounder Paralichthys olivaceus  

Microsoft Academic Search

:   We examined population genetic structure by means of microsatellite analysis among 7 Japanese flounder (Paralichthys olivaceus) populations collected from coastal sea areas around Japan. As was expected, all of the 11 microsatellite loci examined were\\u000a variable in all populations (number of alleles per locus, 15.2–18.2; average of expected heterozygosity, 0.74–0.78). Eleven\\u000a population pairs in 21 possible pairwise comparisons showed

Masashi Sekino; Motoyuki Hara

2001-01-01

404

A mixed integer genetic algorithm used in biological and chemical defense applications  

Microsoft Academic Search

There are many problems in security and defense that require a robust optimization technique, including those that involve\\u000a the release of a chemical or biological contaminant. Our problem, in particular, is computing the parameters to be used in\\u000a modeling atmospheric transport and dispersion given field sensor measurements of contaminant concentration. This paper discusses\\u000a using a genetic algorithm for addressing this

Sue Ellen Haupt; Randy L. Haupt; George S. Young

2011-01-01

405

Application of rapd in the determination of genetic fidelity in micropropagated Drosera plantlets  

Microsoft Academic Search

Summary  Random amplified polymorphic DNA (RAPD) markers were used to verify the clonal fidelity of two micropropagated Drosera species, D. anglica and D. binata, which were regenerated by adventitious budding from leaf explants and shoot tips, respectively. Twenty arbitrary decamers\\u000a were used to screen 15 randomly selected plantlets of each species. No genetic variation was detected among D. binata regenerants, whereas

Anna Kawiak; Ewa ?ojkowska

2004-01-01

406

The application of molecular genetic approaches to the study of human evolution  

Microsoft Academic Search

doi:10.1038\\/ng1113 The past decade of advances in molecular genetic technology has heralded a new era for all evolutionary stud- ies, but especially the science of human evolution. Data on various kinds of DNA variation in human popula- tions have rapidly accumulated. There is increasing recognition of the importance of this variation for medicine and developmental biology and for understanding the

L. Luca Cavalli-Sforza; Marcus W. Feldman

2003-01-01

407

The Application of Genetic Algorithm Based Support Vector Machine for Image Quality Evaluation  

Microsoft Academic Search

\\u000a In this paper, we have proposed a novel image quality evaluation algorithm based on the Visual Difference Predictor(VDP),\\u000a a classical method of estimating the visual similarity between an image under test and its reference one. Compared with state-of-the-art\\u000a image quality evaluation algorithms, this method have employed a genetic algorithm based support vector machine, instead of\\u000a linear or nonlinear mathematical models,

Li Cui; SongYun Xie

2011-01-01

408

Improved Quantum Genetic Algorithm and Its Application in Nutritional Diet Optimization  

Microsoft Academic Search

An improved quantum genetic algorithm (IQGA) is proposed to avoid declining of the searching ability for multi-peak function optimization and multi-genes chromosome encoding problem. Improvements include adjusting initialization way of chromosome's genes, changing elitist strategy and introducing partial population disaster strategy. Experimental results on continuous multi-peak function optimization and actual nutritional diet optimization show that IQGA is superior to traditional

Youbo Lv; Dong Li

2008-01-01

409

Optimization of fuels from waste composition with application of genetic algorithm.  

PubMed

The objective of this article is to elaborate a method to optimize the composition of the fuels from sewage sludge (PBS fuel - fuel based on sewage sludge and coal slime, PBM fuel - fuel based on sewage sludge and meat and bone meal, PBT fuel - fuel based on sewage sludge and sawdust). As a tool for an optimization procedure, the use of a genetic algorithm is proposed. The optimization task involves the maximization of mass fraction of sewage sludge in a fuel developed on the basis of quality-based criteria for the use as an alternative fuel used by the cement industry. The selection criteria of fuels composition concerned such parameters as: calorific value, content of chlorine, sulphur and heavy metals. Mathematical descriptions of fuel compositions and general forms of the genetic algorithm, as well as the obtained optimization results are presented. The results of this study indicate that the proposed genetic algorithm offers an optimization tool, which could be useful in the determination of the composition of fuels that are produced from waste. PMID:24718361

Ma?gorzata, Wzorek

2014-05-01

410

Application of AFLP markers for population genetic study on half-smooth tongue sole Cynoglossus semilaevis  

NASA Astrophysics Data System (ADS)

The genetic diversity of wild and hatchery populations of half-smooth tongue sole Cynoglossus semilaevis, based on observation of amplified fragment length polymorphism (AFLP) was described. Two hundred individuals from four wild populations, Laizhou (LZ), Weihai (WH), Qingdao (QD), Rizhao (RZ), and one hatchery population, Mingbo (MB), were screened using eight different AFLP primer combinations. A total of 384 loci were screened in the five studied populations. 48.4%, 51.3%, 50.7%, 49.3% and 45.8% of these loci were polymorphic among the individuals tested in the LZ, WH, QD, RZ and MB populations, respectively. The number of polymorphic loci detected by single primer combinations ranged from 17 to 35. The average heterozygosity of the LZ, WH, QD, RZ and MB populations was 0.072, 0.093, 0.092, 0.090 and 0.063, respectively. The WH population showed the highest genetic diversity in terms of total number of AFLP bands, total number of polymorphic bands, average heterozygosity and percentage of low frequency (0-0.2) polymorphic loci among all the populations, while the LZ population was the lowest among the wild populations. Compared with the wild populations, the hatchery population showed a low genetic viability.

Liu, Yunguo; Li, Junfeng; Ye, Naihao

2011-05-01

411

Reverse engineering of geometric models - an introduction  

Microsoft Academic Search

ABSTRACT IN MANY AREAS OF INDUSTRY, IT IS DESIRABLE TO CREATE GEOMETRIC MODELS OF EXISTING OB JECTS FOR WHICH NO SUCH MODEL IS AVAILABLE. THIS PAPER REVIEWS THE PROCESS OF REVERSE ENGINEERING OF SHAPES. AFTER IDENTIFYING THE PURPOSE OF REVERSE ENGINEERING AND THE MAIN APPLICATION AREAS, THE MOST IMPORTANT ALGORITHMIC STEPS ARE OUTLINED AND VARIOUS RECONSTRUCTION STRATEGIES ARE PRE-SENTED. PROS

Tamás Várady; Ralph R. Martin; Jordan Cox

1997-01-01

412

Application of Massively Parallel Sequencing to Genetic Diagnosis in Multiplex Families with Idiopathic Sensorineural Hearing Impairment  

PubMed Central

Despite the clinical utility of genetic diagnosis to address idiopathic sensorineural hearing impairment (SNHI), the current strategy for screening mutations via Sanger sequencing suffers from the limitation that only a limited number of DNA fragments associated with common deafness mutations can be genotyped. Consequently, a definitive genetic diagnosis cannot be achieved in many families with discernible family history. To investigate the diagnostic utility of massively parallel sequencing (MPS), we applied the MPS technique to 12 multiplex families with idiopathic SNHI in which common deafness mutations had previously been ruled out. NimbleGen sequence capture array was designed to target all protein coding sequences (CDSs) and 100 bp of the flanking sequence of 80 common deafness genes. We performed MPS on the Illumina HiSeq2000, and applied BWA, SAMtools, Picard, GATK, Variant Tools, ANNOVAR, and IGV for bioinformatics analyses. Initial data filtering with allele frequencies (<5% in the 1000 Genomes Project and 5400 NHLBI exomes) and PolyPhen2/SIFT scores (>0.95) prioritized 5 indels (insertions/deletions) and 36 missense variants in the 12 multiplex families. After further validation by Sanger sequencing, segregation pattern, and evolutionary conservation of amino acid residues, we identified 4 variants in 4 different genes, which might lead to SNHI in 4 families compatible with autosomal dominant inheritance. These included GJB2 p.R75Q, MYO7A p.T381M, KCNQ4 p.S680F, and MYH9 p.E1256K. Among them, KCNQ4 p.S680F and MYH9 p.E1256K were novel. In conclusion, MPS allows genetic diagnosis in multiplex families with idiopathic SNHI by detecting mutations in relatively uncommon deafness genes. PMID:23451214

Wu, Chen-Chi; Lin, Yin-Hung; Lu, Ying-Chang; Chen, Pei-Jer; Yang, Wei-Shiung; Hsu, Chuan-Jen; Chen, Pei-Lung

2013-01-01

413

Application of massively parallel sequencing to genetic diagnosis in multiplex families with idiopathic sensorineural hearing impairment.  

PubMed

Despite the clinical utility of genetic diagnosis to address idiopathic sensorineural hearing impairment (SNHI), the current strategy for screening mutations via Sanger sequencing suffers from the limitation that only a limited number of DNA fragments associated with common deafness mutations can be genotyped. Consequently, a definitive genetic diagnosis cannot be achieved in many families with discernible family history. To investigate the diagnostic utility of massively parallel sequencing (MPS), we applied the MPS technique to 12 multiplex families with idiopathic SNHI in which common deafness mutations had previously been ruled out. NimbleGen sequence capture array was designed to target all protein coding sequences (CDSs) and 100 bp of the flanking sequence of 80 common deafness genes. We performed MPS on the Illumina HiSeq2000, and applied BWA, SAMtools, Picard, GATK, Variant Tools, ANNOVAR, and IGV for bioinformatics analyses. Initial data filtering with allele frequencies (<5% in the 1000 Genomes Project and 5400 NHLBI exomes) and PolyPhen2/SIFT scores (>0.95) prioritized 5 indels (insertions/deletions) and 36 missense variants in the 12 multiplex families. After further validation by Sanger sequencing, segregation pattern, and evolutionary conservation of amino acid residues, we identified 4 variants in 4 different genes, which might lead to SNHI in 4 families compatible with autosomal dominant inheritance. These included GJB2 p.R75Q, MYO7A p.T381M, KCNQ4 p.S680F, and MYH9 p.E1256K. Among them, KCNQ4 p.S680F and MYH9 p.E1256K were novel. In conclusion, MPS allows genetic diagnosis in multiplex families with idiopathic SNHI by detecting mutations in relatively uncommon deafness genes. PMID:23451214

Wu, Chen-Chi; Lin, Yin-Hung; Lu, Ying-Chang; Chen, Pei-Jer; Yang, Wei-Shiung; Hsu, Chuan-Jen; Chen, Pei-Lung

2013-01-01

414

Nonparametric Methods for Incorporating Genomic Information Into Genetic Evaluations: An Application to Mortality in Broilers  

PubMed Central

Four approaches using single-nucleotide polymorphism (SNP) information (F?-metric model, kernel regression, reproducing kernel Hilbert spaces (RKHS) regression, and a Bayesian regression) were compared with a standard procedure of genetic evaluation (E-BLUP) of sires using mortality rates in broilers as a response variable, working in a Bayesian framework. Late mortality (14–42 days of age) records on 12,167 progeny of 200 sires were precorrected for fixed and random (nongenetic) effects used in the model for genetic evaluation and for the mate effect. The average of the corrected records was computed for each sire. Twenty-four SNPs seemingly associated with late mortality were included in three methods used for genomic assisted evaluations. One thousand SNPs were included in the Bayesian regression, to account for markers along the whole genome. The posterior mean of heritability of mortality was 0.02 in the E-BLUP approach, suggesting that genetic evaluation could be improved if suitable molecular markers were available. Estimates of posterior means and standard deviations of the residual variance were 24.38 (3.88), 29.97 (3.22), 17.07 (3.02), and 20.74 (2.87) for E-BLUP, the linear model on SNPs, RKHS regression, and the Bayesian regression, respectively, suggesting that RKHS accounted for more variance in the data. The two nonparametric methods (kernel and RKHS regression) fitted the data better, having a lower residual sum of squares. Predictive ability, assessed by cross-validation, indicated advantages of the RKHS approach, where accuracy was increased from 25 to 150%, relative to other methods. PMID:18430951

González-Recio, Oscar; Gianola, Daniel; Long, Nanye; Weigel, Kent A.; Rosa, Guilherme J. M.; Avendaño, Santiago

2008-01-01

415

Transforming the Untransformable: Application of Direct Transformation To Manipulate Genetically Staphylococcus aureus and Staphylococcus epidermidis  

PubMed Central

ABSTRACT The strong restriction barrier present in Staphylococcus aureus and Staphylococcus epidermidis has limited functional genomic analysis to a small subset of strains that are amenable to genetic manipulation. Recently, a conserved type IV restriction system termed SauUSI (which specifically recognizes cytosine methylated DNA) was identified as the major barrier to transformation with foreign DNA. Here we have independently corroborated these findings in a widely used laboratory strain of S. aureus. Additionally, we have constructed a DNA cytosine methyltransferase mutant in the high-efficiency Escherichia coli cloning strain DH10B (called DC10B). Plasmids isolated from DC10B can be directly transformed into clinical isolates of S. aureus and S. epidermidis. We also show that the loss of restriction (both type I and IV) in an S. aureus USA300 strain does not have an impact on virulence. Circumventing the SauUSI restriction barrier, combined with an improved deletion and transformation protocol, has allowed the genetic manipulation of previously untransformable strains of these important opportunistic pathogens. IMPORTANCE  Staphylococcal infections place a huge burden on the health care sector due both to their severity and also to the economic impact of treating the infections because of prolonged hospitalization. To improve the understanding of Staphylococcus aureus and Staphylococcus epidermidis infections, we have developed a series of improved techniques that allow the genetic manipulation of strains that were previously refractory to transformation. These developments will speed up the process of mutant construction and increase our understanding of these species as a whole, rather than just a small subset of strains that could previously be manipulated. PMID:22434850

Monk, Ian R.; Shah, Ishita M.; Xu, Min; Tan, Man-Wah; Foster, Timothy J.

2012-01-01

416

Genetic algorithm based adaptive neural network ensemble and its application in predicting carbon flux  

USGS Publications Warehouse

To improve the accuracy in prediction, Genetic Algorithm based Adaptive Neural Network Ensemble (GA-ANNE) is presented. Intersections are allowed between different training sets based on the fuzzy clustering analysis, which ensures the diversity as well as the accuracy of individual Neural Networks (NNs). Moreover, to improve the accuracy of the adaptive weights of individual NNs, GA is used to optimize the cluster centers. Empirical results in predicting carbon flux of Duke Forest reveal that GA-ANNE can predict the carbon flux more accurately than Radial Basis Function Neural Network (RBFNN), Bagging NN ensemble, and ANNE. ?? 2007 IEEE.

Xue, Y.; Liu, S.; Hu, Y.; Yang, J.; Chen, Q.

2007-01-01

417

Application of Genetic Algorithms in the New Air Ttraffic Management Simulation System  

NASA Astrophysics Data System (ADS)

The air traffic control systems are facing more and more serious congestions because of the increasing of air traffic flow in China. To solve the problem we have developed a New Air Traffic Management Simulation System that is according to the ideology of the New Air Traffic Management and the concept of Free Flight. First this paper analyses the mass design idea and the module functions, and then use the genetic algorithms to give the detail methods to solve the airline conflicts on airlines and aircraft sequence takeoff-landfall sorting schedule in the terminal airport area at last we has achieved anticipative effect by use stimulant data compute in the system

Guo, Hang

418

Representation of DNA sequences in genetic codon context with applications in exon and intron prediction.  

PubMed

To apply digital signal processing (DSP) methods to analyze DNA sequences, the sequences first must be specially mapped into numerical sequences. Thus, effective numerical mappings of DNA sequences play key roles in the effectiveness of DSP-based methods such as exon prediction. Despite numerous mappings of symbolic DNA sequences to numerical series, the existing mapping methods do not include the genetic coding features of DNA sequences. We present a novel numerical representation of DNA sequences using genetic codon context (GCC) in which the numerical values are optimized by simulation annealing to maximize the 3-periodicity signal to noise ratio (SNR). The optimized GCC representation is then applied in exon and intron prediction by Short-Time Fourier Transform (STFT) approach. The results show the GCC method enhances the SNR values of exon sequences and thus increases the accuracy of predicting protein coding regions in genomes compared with the commonly used 4D binary representation. In addition, this study offers a novel way to reveal specific features of DNA sequences by optimizing numerical mappings of symbolic DNA sequences. PMID:25491390

Yin, Changchuan

2014-11-12

419

Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases  

PubMed Central

The function of genes is often evolutionarily conserved, and comparing the annotation of ortholog genes in different model organisms has proved to be a powerful predictive tool to identify the function of human genes. Here, we describe Manteia, a resource available online at http://manteia.igbmc.fr. Manteia allows the comparison of embryological, expression, molecular and etiological data from human, mouse, chicken and zebrafish simultaneously to identify new functional and structural correlations and gene-disease associations. Manteia is particularly useful for the analysis of gene lists produced by high-throughput techniques such as microarrays or proteomics. Data can be easily analyzed statistically to characterize the function of groups of genes and to correlate the different aspects of their annotation. Sophisticated querying tools provide unlimited ways to merge the information contained in Manteia along with the possibility of introducing custom user-designed biological questions into the system. This allows for example to connect all the animal experimental results and annotations to the human genome, and take advantage of data not available for human to look for candidate genes responsible for genetic disorders. Here, we demonstrate the predictive and analytical power of the system to predict candidate genes responsible for human genetic diseases. PMID:24038354

Tassy, Olivier; Pourquié, Olivier

2014-01-01

420

[Application of molecular genetic methods during Legionnaires' disease outbreak in town Verkhnyaya Pyshma].  

PubMed

The aim of the study was to perform molecular genetic analysis based on multi-locus sequence typing in order to identify source of Legionnaires' disease outbreak in town Verkhnyaya Pyshma in July 2007 and genetic profile of the causative agent. Sequence-based typing protocol recommended by European Working Group on Legionella infection (EWGLI) was used. It was not possible to obtain satisfactory results of Fla gene sequencing for all samples. Obtained allelic profiles of other genes were typical for L. pneumophila. Allelic profiles of L. pneumophila isolated from patients were identical and matched with L. pneumophila DNA detected in water from hot water supply of domestic building, but differed from cooling tower's isolates and isolates from showerhead in apartment of one patient. Identity of 5 genes of L. pneumophila isolated from autopsy samples and from hot water of central hot water supply of domestic building confirms aspiration route of infection through hot water contaminated by the microorganism. L. pneumophila detected in water from cooling tower, showerhead in apartment of one patient, and from drainage canal of hot water supply station belonged to other allelic variants and, therefore, are not related with the outbreak. PMID:18464536

Iatsyshina, S B; Astakhova, T S; Romanenko, V V; Platonov, A E; Zhukova, Iu V; Braslavskaia, S I; Tartakovski?, I S; Shipulin, G A

2008-01-01

421

Addressing Genetics Delivering Health  

E-print Network

Addressing Genetics Delivering Health A strategy for advancing the dissemination and application of genetics knowledge throughout our health professions Funded by Hilary Burton September 2003 Executive Summary #12;Summary of Recommendations Establishment of a national Steering Group for Genetics Education q

Rambaut, Andrew

422

Genetic Counseling Program Information  

E-print Network

Genetic Counseling Program Information for Potential Applicants #12;Page 2 of 12 8.24.11 Program Overview "Genetic counseling is the process of helping people understand and adapt to the medical, psychological, and familial implications of genetic contributions to disease. The process integrates

Finley Jr., Russell L.

423

Dynamics of the Genetic Diversity of Subsurface Microbial Communities and Their Applications to Contaminated Site Cleanups  

EPA Science Inventory

When compared to traditional approaches, the utilization of molecular and genomic techniques to soil and groundwater cleanup investigations can reduce inherent parameter variability when conducting bench and pilot-scale investigations or carrying out full-scale field applications...

424

HIV-1 Reverse Transcription  

PubMed Central

Reverse transcription and integration are the defining features of the Retroviridae; the common name “retrovirus” derives from the fact that these viruses use a virally encoded enzyme, reverse transcriptase (RT), to convert their RNA genomes into DNA. Reverse transcription is an essential step in retroviral replication. This article presents an overview of reverse transcription, briefly describes the structure and function of RT, provides an introduction to some of the cellular and viral factors that can affect reverse transcription, and discusses fidelity and recombination, two processes in which reverse transcription plays an important role. In keeping with the theme of the collection, the emphasis is on HIV-1 and HIV-1 RT. PMID:23028129

Hu, Wei-Shau; Hughes, Stephen H.

2012-01-01

425

Application of genetic algorithm in quasi-static fiber grating wavelength demodulation technology  

NASA Astrophysics Data System (ADS)

A modified genetic algorithm (GA) has been proposed, which was used to wavelength demodulation in quasi-static fiber grating sensing system. The modification method of GA has been introduced and the relevant mathematical model has been established. The objective function and individual fitness evaluation strategy interrelated with GA are also established. The influence of population size, chromosome size, generations, crossover probability and mutation probability on the GA has been analyzed, and the optimal parameters of modified GA have been obtained. The simulations and experiments, show that the modified GA can be applied to quasi-static fiber grating sensing system, and the wavelength demodulation precision is equal to or less than 3 pm.

Teng, Feng-Cheng; Yin, Wen-Wen; Wu, Fei; Li, Zhi-Quang; Wu, Ti-Hua

2007-07-01

426

Calibration of neural networks using genetic algorithms, with application to optimal path planning  

NASA Technical Reports Server (NTRS)

Genetic algorithms (GA) are used to search the synaptic weight space of artificial neural systems (ANS) for weight vectors that optimize some network performance function. GAs do not suffer from some of the architectural constraints involved with other techniques and it is straightforward to incorporate terms into the performance function concerning the metastructure of the ANS. Hence GAs offer a remarkably general approach to calibrating ANS. GAs are applied to the problem of calibrating an ANS that finds optimal paths over a given surface. This problem involves training an ANS on a relatively small set of paths and then examining whether the calibrated ANS is able to find good paths between arbitrary start and end points on the surface.

Smith, Terence R.; Pitney, Gilbert A.; Greenwood, Daniel

1987-01-01

427

Application of carrier testing to genetic counseling for X-linked agammaglobulinemia  

SciTech Connect

Bruton X-linked agammaglobulinemia (XLA) is a phenotypically recessive genetic disorder of B lymphocyte development. Female carriers of XLA, although asymptomatic, have a characteristic B cell lineage-specific skewing of the pattern of X inactivation. Skewing apparently results from defective growth and maturation of B cell precursors bearing a mutant active X chromosome. In this study, carrier status was tested in 58 women from 22 families referred with a history of agammaglobulinemia. Primary carrier analysis to examine patterns of X inactivation in CD19[sup +] peripheral blood cells (B lymphocytes) was conducted using quantitative PCR at the androgen-receptor locus. Obligate carriers of XLA demonstrated >95% skewing of X inactivation in peripheral blood CD19[sup +] cells but not in CD19[sup [minus

Allen, R.C.; Nachtman, R.G.; Belmont, J.W.; Rosenblatt, H.M.

1994-01-01

428

Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system (E2FyDPytwo-step selectionynegative selectionyURA3ymarked box)  

Microsoft Academic Search

Manybiologicalprocessesrelyuponprotein- protein interactions. Hence, detailed analysis of these inter- actions is critical for their understanding. Due to the com- plexities involved, genetic approaches are often needed. In yeast and phage, genetic characterizations of protein com- plexesarepossible.However,inmulticellularorganisms,such characterizationsarelimitedbythelackofpowerfulselection systems. Herein we describe genetic selections that allow single amino acid changes that disrupt protein-protein inter- actions to be selected from large libraries

P ASCALBRAUN; JEFD. BOEKE

1996-01-01

429

Properly apply reverse osmosis  

SciTech Connect

Reverse osmosis (RO) is a water purification technique used to reduce the loading of dissolved solids in solution. The popularity of RO for treating boiler feedwater is growing because of the rising cost of ion-exchange-based demineralization as well as safety concerns associated with handling acid and caustic. A properly designed and operated RO-based boiler-feedwater-treatment system can reduce the load to, and costs associated with, ion exchange demineralization. This article discusses RO feedwater quality recommendations, pretreatment techniques, and system monitoring necessary to achieve optimum RO system performance in the most cost-effective manner. Regardless of the application--whether it is the treatment of boiler feedwater, industrial wastewater, or process water--the approach to pretreatment and the other design and operating guidance offered here remains the same.

Kucera, J.

1997-02-01

430

On Derivations Of Genetic Algebras  

NASA Astrophysics Data System (ADS)

A genetic algebra is a (possibly non-associative) algebra used to model inheritance in genetics. In application of genetics this algebra often has a basis corresponding to genetically different gametes, and the structure constant of the algebra encode the probabilities of producing offspring of various types. In this paper, we find the connection between the genetic algebras and evolution algebras. Moreover, we prove the existence of nontrivial derivations of genetic algebras in dimension two.

Mukhamedov, Farrukh; Qaralleh, Izzat

2014-11-01

431

Application of genotyping-by-sequencing on semiconductor sequencing platforms: A comparison of genetic and reference-based marker ordering in barley  

Technology Transfer Automated Retrieval System (TEKTRAN)

The rapid development of next generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach fo...

432

A Hierarchical and Distributed Approach for Mapping Large Applications to Heterogeneous Grids using Genetic Algorithms  

NASA Technical Reports Server (NTRS)

In this paper, we propose a distributed approach for mapping a single large application to a heterogeneous grid environment. To minimize the execution time of the parallel application, we distribute the mapping overhead to the available nodes of the grid. This approach not only provides a fast mapping of tasks to resources but is also scalable. We adopt a hierarchical grid model and accomplish the job of mapping tasks to this topology using a scheduler tree. Results show that our three-phase algorithm provides high quality mappings, and is fast and scalable.

Sanyal, Soumya; Jain, Amit; Das, Sajal K.; Biswas, Rupak

2003-01-01

433

Application of reversal electron attachment for ultrasensitive detection of thermal electron-attaching molecules - CCl4 and C6H5O2  

NASA Technical Reports Server (NTRS)

A standard gas-dilution method was used to determine the selective response of the reversal electron attachment detector to carbon tetrachloride concentrations in nitrogen. Data are provided that determine the lowest concentration of sample detectable with the present instrumental configuration as being below 1.0 part per trillion by volume. The incorporation of a 90-deg electrostatic deflector with the quadrupole mass spectrometer is shown to be vital, and with it, negative-ion quadrupole mass spectrometry is used to characterize the ionization process. Observations are also made of the reversal electron attachment response to nitrobenzene. The analytical potential of reversal electron capture negative-ion mass spectrometry is examined, and areas for future development are discussed.

Bernius, Mark T.; Chutjian, Ara

1990-01-01

434

Morphological evolution of protective works by Genetic Algorithms: An application to Mt Etna  

NASA Astrophysics Data System (ADS)

The hazard induced by dangerous flow-type phenomena - e.g. lava flows, earth flows, debris flows, and debris avalanches - has increased in recent years due to continuous urbanization. In many cases, the numerical simulation of hypothetical events can help to forecast the flow path in advance and therefore give indications about the areas that can be considered for the construction of protective works - e.g. earth barriers or channels. In this way, urbanized areas, as well as cultural heritage sites or even important infrastructures, can be protected by diverting the flow towards lower interest regions. Here, we have considered the numerical Cellular Automata model Sciara-fv2 for simulating lava flows at Mt Etna and Genetic Algorithms for optimizing the position, orientation and extension of an earth barrier built to protect the Rifugio Sapienza, a well-known touristic facility located near the summit of the volcano. The Rifugio Sapienza area was in fact interested by a lava flow in 2003, which destroyed a Service Center, a parking area and a Cafeteria. In this study, a perimeter was devised around the Rifugio (i.e., security perimeter), which delimitates the area that has to be protected by the flow. Furthermore, another perimeter was devised (i.e., work perimeter), specifying the area in which the earth barrier can be located. The barrier is specified by three parameters, namely the two geographic coordinates of the vertex and the height. In fact, in this preliminary analysis the barrier was modeled as a segment (in plant) having a constant height. Though preliminary, the study has produced extremely positive results. Among different alternatives generated by the genetic algorithm, an interesting scenario consists of a 35 meters barrier high solution, which completely deviates the flow avoiding that the lava reaches the inhabited area. The relative elevated height of the barrier is high due to the fact that the crater is located close to the area to be protected and, consequently, the lava rate is very high.

Marocco, Davide; Spataro, William; D'Ambrosio, Donato; Filippone, Giuseppe; Rongo, Rocco; Iovine, Giulio; Neri, Marco

2013-04-01

435

Industrial-hygiene characterization of commercial applications of genetic engineering and biotechnology  

Microsoft Academic Search

Walkthrough surveys of six companies involved in research and development of recombinant DNA techniques applicable to fermentation processes (SIC-7391) were conducted. Engineering controls at the sites included general and local ventilation systems, gas filtration, waste-products control, biological safety cabinets, access barriers, and room surfaces that met National Institutes of Health guidelines for working with contaminants. Five companies regularly tested and

L. J. Elliott; G. Carson; S. Pauker; K. Wallingford

1983-01-01

436

Reversible logic for supercomputing  

Microsoft Academic Search

This paper is about making reversible logic a reality for supercomputing. Reversible logic offers a way to exceed certain basic limits on the performance of computers, yet a powerful case will have to be made to justify its substantial development expense. This paper explores the limits of current, irreversible logic for supercomputers, thus forming a threshold above which reversible logic

Erik P. DeBenedictis; Erik P

2005-01-01

437

Application of genetic programming and Landsat multi-date imagery for urban growth monitoring  

NASA Astrophysics Data System (ADS)

Monitoring of earth surface changes from space by using multi-date satellite imagery was always a main concern to researchers in the field of remotely sensed image processing. Thus, several techniques have been proposed to saving technicians from interpreting and digitizing hundreds of areas by hand. The exploiting of simple, easy to memorize and often comprehensible mathematical models such band-ratios and indices are one of the widely used techniques in remote sensing for the extraction of particular land-cover/land-use like urban and vegetation areas. The results of these models generally only need the definition of adequate threshold or using simple unsupervised classification algorithms to discriminate between the class of interest and the background. In our work a genetic programming based approach has been adopted to evolve simple mathematical expression to extract urban areas from image series. The model is built from a single image by using a basic set of operators between spectral bands and maximizing a fitness function, which is based on the using of the M-statistic criterion. The model was constructed from the Landsat 5 TM image acquired in 2006 by using training samples extracted with the help of a Quick-bird high spatial resolution satellite image acquired the same day as the Landsat image over the city of Oran, Algeria. The model has been tested to extract urban areas from multi-date series of Landsat TM imagery

Djerriri, Khelifa; Malki, Mimoun

2013-10-01