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1

Reverse Genetics of Measles Virus and Resulting Multivalent Recombinant Vaccines: Applications of Recombinant Measles Viruses  

Microsoft Academic Search

An overview is given on the development of technologies to allow reverse genetics of RNA viruses, i.e., the rescue of viruses\\u000a from cDNA, with emphasis on nonsegmented negative-strand RNA viruses ( Mononegavirales ), as exemplified for measles virus\\u000a (MV). Primarily, these technologies allowed site-directed mutagenesis, enabling important insights into a variety of aspects\\u000a of the biology of these viruses. Concomitantly,

M. A. Billeter; H. Y. Naim; S. A. Udem

2

Reverse genetics for mammalian reovirus.  

PubMed

Mammalian orthoreoviruses (reoviruses) are highly tractable models for studies of viral replication and pathogenesis. The versatility of reovirus as an experimental model has been enhanced by development of a plasmid-based reverse genetics system. Infectious reovirus can be recovered from cells transfected with plasmids encoding cDNAs of each reovirus gene segment using a strategy that does not require helper virus and is independent of selection. In this system, transcription of each gene segment is driven by bacteriophage T7 RNA polymerase, which can be supplied transiently by recombinant vaccinia virus (rDIs-T7pol) or by cells that constitutively express the enzyme. Reverse genetics systems have been developed for two prototype reovirus strains, type 1 Lang (T1L) and type 3 Dearing (T3D). Each reovirus cDNA was encoded on an independent plasmid for the first-generation rescue system. The efficiency of virus recovery was enhanced in a second-generation system by combining the cDNAs for multiple reovirus gene segments onto single plasmids to reduce the number of plasmids from 10 to 4. The reduction in plasmid number and the use of baby hamster kidney cells that express T7 RNA polymerase increased the efficiency of viral rescue, reduced the incubation time required to recover infectious virus, and eliminated potential biosafety concerns associated with the use of recombinant vaccinia virus. Reovirus reverse genetics has been used to introduce mutations into viral capsid and nonstructural components to study viral protein-structure activity relationships and can be exploited to engineer recombinant reoviruses for vaccine and oncolytic applications. PMID:21798351

Boehme, Karl W; Ikizler, Miné; Kobayashi, Takeshi; Dermody, Terence S

2011-07-21

3

Reverse genetics of measles virus and resulting multivalent recombinant vaccines: applications of recombinant measles viruses.  

PubMed

An overview is given on the development of technologies to allow reverse genetics of RNA viruses, i.e., the rescue of viruses from cDNA, with emphasis on nonsegmented negative-strand RNA viruses (Mononegavirales), as exemplified for measles virus (MV). Primarily, these technologies allowed site-directed mutagenesis, enabling important insights into a variety of aspects of the biology of these viruses. Concomitantly, foreign coding sequences were inserted to (a) allow localization of virus replication in vivo through marker gene expression, (b) develop candidate multivalent vaccines against measles and other pathogens, and (c) create candidate oncolytic viruses. The vector use of these viruses was experimentally encouraged by the pronounced genetic stability of the recombinants unexpected for RNA viruses, and by the high load of insertable genetic material, in excess of 6 kb. The known assets, such as the small genome size of the vector in comparison to DNA viruses proposed as vectors, the extensive clinical experience of attenuated MV as vaccine with a proven record of high safety and efficacy, and the low production cost per vaccination dose are thus favorably complemented. PMID:19198565

Billeter, M A; Naim, H Y; Udem, S A

2009-01-01

4

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

PubMed Central

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

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

2007-01-01

5

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 ...

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.

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

2008-01-01

7

Reverse Osmosis Application Studies.  

National Technical Information Service (NTIS)

To assess the feasibility of applying reverse osmosis (RO) and ultrafiltration (UF) for effective treatment of process and waste streams from operations at Ontario Hydro's thermal and nuclear stations, an extensive literature survey has been carried out. ...

A. Golomb

1982-01-01

8

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

Microsoft Academic Search

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

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

2006-01-01

9

Reverse genetics in complex multigene operons by co-transformation of the plastid genome and its application to the open reading frame previously designated psbN.  

PubMed

Reverse genetics approaches have contributed enormously to the elucidation of gene functions in plastid genomes and the determination of structure-function relationships in chloroplast multiprotein complexes. Gene knock-outs are usually performed by disrupting the reading frame of interest with a selectable marker cassette. Site-directed mutagenesis is done by placing the marker into the adjacent intergenic spacer and relying on co-integration of the desired mutation by homologous recombination. These strategies are not applicable to genes residing in large multigene operons or other gene-dense genomic regions, because insertion of the marker cassette into an operon-internal gene or into the nearest intergenic spacer is likely to interfere with expression of adjacent genes in the operon or disrupt cis-elements for the expression of neighboring genes and operons. Here we have explored the possibility of using a co-transformation strategy to mutate a small gene of unknown function (psbN) that is embedded in a complex multigene operon. Although inactivation of psbN resulted in strong impairment of photosynthesis, homoplasmic knock-out lines were readily recovered by co-transformation with a selectable marker integrating >38 kb away from the targeted psbN. Our results suggest co-transformation as a suitable strategy for the functional analysis of plastid genes and operons, which allows the recovery of unselected homoplasmic mutants even if the introduced mutations entail a significant selective disadvantage. Moreover, our data provide evidence for involvement of the psbN gene product in the biogenesis of both photosystem I and photosystem II. We therefore propose to rename the gene product 'photosystem biogenesis factor 1' and the gene pbf1. PMID:23738654

Krech, Katharina; Fu, Han-Yi; Thiele, Wolfram; Ruf, Stephanie; Schöttler, Mark A; Bock, Ralph

2013-06-26

10

Reverse genetics in rice using Tos17.  

PubMed

Transposon of Oryza sativa 17 (Tos17), a Ty1-Copia Class I retroelement, is one of the few active retroelements identified in rice, the main cereal crop of human consumption and the model genome for cereals. Tos17 exists in two copies in the standard Nipponbare japonica genome (n = 12 and 379 Mb). Tos17 copies are inactive in the plant grown under normal conditions. However, the copy located on chromosome 7 can be activated upon tissue culture. Plants regenerated from 3- and 5-month-old tissue cultures harbor, respectively, an average of 3.5 and 8 newly transposed copies that are stably inserted at new positions in the genome. Due to its favorable features, Tos17 has been extensively used for insertion mutagenesis of the model genome and 31,403 sequence indexed inserts harbored by regenerants/T-DNA plants are available in the databases. The corresponding seed stocks can be ordered from the laboratories which generated them. Both forward genetics and reverse genetics approaches using these lines have allowed the deciphering of gene function in rice. We report here two protocols for ascertaining the presence of a Tos17 insertion in a gene of interest among R2/T2 seeds received from Tos17 mutant stock centers: The first protocol is PCR-based and allows the identification of azygous, heterozygous and homozygous plants among progenies segregating the insertion. The second protocol is based on DNA blot analysis and can be used to identify homozygous plants carrying the Tos17 copy responsible for gene disruption while cleaning the mutant background from other unwitting mutagen inserts. PMID:23918431

Mieulet, Delphine; Diévart, Anne; Droc, Gaëtan; Lanau, Nadège; Guiderdoni, Emmanuel

2013-01-01

11

Reversible gelation of genetically engineered macromolecules  

NASA Astrophysics Data System (ADS)

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

Petka, Wendy Ann

12

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

Microsoft Academic Search

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

Stephen T. Reeders

1987-01-01

13

Revolution, Revision or Reversal: Genetics - Ethics Curriculum.  

ERIC Educational Resources Information Center

Reviews three pioneer programs that attempt to integrate genetic science and ethics in the classroom. Concludes by suggesting that the basic goal of integrating science and ethics is undermined in each program by a lack of correspondence between the articulated pedagogical goals and the unarticulated theoretical framework. (LZ)

Blake, Deborah D.

1994-01-01

14

Genetic Dissection of Behavioral Flexibility: Reversal Learning in Mice  

PubMed Central

Background Behavioral inflexibility is a feature of schizophrenia, attention deficit-hyperactivity disorder, and behavior addictions that likely results from heritable deficits in the inhibitory control over behavior. Here, we investigate the genetic basis of individual differences in flexibility, measured using an operant reversal learning task. Methods We quantified discrimination acquisition and subsequent reversal learning in a cohort of 51 BXD strains of mice (2–5 mice/strain, N = 176) for which we have matched data on sequence, gene expression in key CNS regions, and neuroreceptor levels. Results Strain variation in trials to criterion on acquisition and reversal was high, with moderate heritability (~0.3). Acquisition and reversal learning phenotypes did not covary at the strain level, suggesting that these traits are effectively under independent genetic control. Reversal performance did covary with dopamine D2 receptor levels in the ventral midbrain, consistent with a similar observed relationship between impulsivity and D2 receptors in humans. Reversal, but not acquisition, is linked to a locus on mouse chromosome 10 with a peak LRS at 86.2Mb (p <.05 genome-wide). Variance in mRNA levels of select transcripts expressed in neocortex, hippocampus, and striatum correlated with the reversal learning phenotype, including Syn3, Nt5dc3 and Hcfc2. Conclusions This work demonstrates the clear trait independence between, and genetic control of, discrimination acquisition and reversal and illustrates how globally coherent data sets for a single panel of highly-related strains can be interrogated and integrated to uncover genetic sources and molecular and neuropharmacological candidates of complex behavioral traits relevant to human psychopathology.

Laughlin, Rick E.; Grant, Tara L.; Williams, Robert W.; Jentsch, J. David

2011-01-01

15

Revolution, revision or reversal: Genetics — Ethics curriculum  

NASA Astrophysics Data System (ADS)

This paper reviews three pioneer programs that attempt to integrate genetic science and ethics in the classroom. The critical discussion focuses on what counts for ethics in each of these programs, on the corresponding theoretical framework represented in each, and on the success of each program in integrating science and ethics. It concludes by suggesting that the basic goal of integrating science and ethics is undermined in each program by a lack of correspondence between the articulated pedagogical goals and the unarticulated theoretical framework. In each case the unexamined framework gives epistemological privilege to science and undercuts the veracity of ethics. The constructive discussion suggests a theoretical framework that corresponds with the pedagogical goal of integrating ethics and genetic science in the classroom.

Blake, Deborah D.

1994-10-01

16

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.

Lyons, Leslie A.

2010-01-01

17

Forward and reverse genetics of rapid-cycling Brassica oleracea.  

PubMed

Seeds of rapid-cycling Brassica oleracea were mutagenized with the chemical mutagen, ethylmethane sulfonate. The reverse genetics technique, TILLING, was used on a sample population of 1,000 plants, to determine the mutation profile. The spectrum and frequency of mutations induced by ethylmethane sulfonate was similar to that seen in other diploid species such as Arabidopsis thaliana. These data indicate that the mutagenesis was effective and demonstrate that TILLING represents an efficient reverse genetic technique in B. oleracea that will become more valuable as increasing genomic sequence data become available for this species. The extensive duplication in the B. oleracea genome is believed to result in the genetic redundancy that has been important for the evolution of morphological diversity seen in today's B. oleracea crops (broccoli, Brussels sprouts, cauliflower, cabbage, kale and kohlrabi). However, our forward genetic screens identified 120 mutants in which some aspect of development was affected. Some of these lines have been characterized genetically and in the majority of these, the mutant trait segregates as a recessive allele affecting a single locus. One dominant mutation (curly leaves) and one semi-dominant mutation (dwarf-like) were also identified. Allelism tests of two groups of mutants (glossy and dwarf) revealed that for some loci, multiple independent alleles have been identified. These data indicate that, despite genetic redundancy, mutation of many individual loci in B. oleracea results in distinct phenotypes. PMID:19132334

Himelblau, Edward; Gilchrist, Erin J; Buono, Kelly; Bizzell, Colleen; Mentzer, Laurie; Vogelzang, Robert; Osborn, Thomas; Amasino, Richard M; Parkin, Isobel A P; Haughn, George W

2009-01-09

18

[Using reverse genetics method for developing recombinant strains of influenza viruses acceptable for use as live attenuated vaccines].  

PubMed

Perspectives of using reverse genetics methods for constructing of recombinant influenza virus strains acceptable for use as live attenuated vaccines are discussed. Using of attenuated NS-vectors of influenza virus opens possibilities for the development of recombinant vaccines with optimal ratio of immunogenicity and safety. Reverse genetics is applicable for development of effective vaccines against new pathogens such as highly pathogenic avian influenza A/H5N1. PMID:19462520

Merkulov, V A; Lebedev, V N; Plekhanova, T M; Maksimov, V A; Korovkin, S A; Mironov, A N

19

Retrotransposons, reverse transcriptase and the genesis of new genetic information.  

PubMed

Spermatozoa of virtually all species can take up exogenous DNA or RNA molecules and internalize them into nuclei. A sperm endogenous reverse transcriptase activity can reverse-transcribe the internalized molecules in cDNA copies: exogenous RNA is reverse-transcribed in a one-step reaction, whereas DNA is first transcribed into RNA and subsequently reverse-transcribed. In either case, the newly synthesized cDNAs are delivered from sperm cells to oocytes at fertilization and are further propagated throughout embryogenesis and in tissues of adult animals. The reverse-transcribed sequences are underrepresented (below 1 copy/genome), mosaic distributed in tissues of adult individuals, transmitted in a non-Mendelian fashion from founders to F1 progeny, transcriptionally competent, variably expressed in different tissues and temporally transient, as they progressively disappear in aged animals. Based on these features, the reverse-transcribed sequences behave as extrachromosomal, biologically active retrogenes and induce novel phenotypic traits in animals. This RT-dependent mechanism, presumably originating from LINE-1 retroelements, generates transcriptionally competent retrogenes in sperm cells. These data strengthen the emerging view of a novel transgenerational genetics as the source of a continuous flow of novel epigenetic and phenotypic traits, independent from those associated to chromosomes. The distinctive features of this retrotransposon-based phenomenon share analogies with a recently discovered form of RNA-mediated inheritance, compatible with a Lamarckian-type adaptation. PMID:19631262

Sciamanna, Ilaria; Vitullo, Patrizia; Curatolo, Angela; Spadafora, Corrado

2009-07-21

20

Optimization of a Reverse Osmosis System Using Genetic Algorithm  

Microsoft Academic Search

Reverse Osmosis (RO) has found extensive application in industry as a highly efficient separation process. In most cases, it is required to select the optimum set of operating variables such that the performance of the system is maximized. In this work, an attempt has been made to optimize the performance of RO system with a cellulose acetate membrane to separate

Z. V. P. Murthy; Jiju Cherian Vengal

2006-01-01

21

A simple reverse genetics approach to elucidating the biosynthetic pathway of nocathiacin  

Microsoft Academic Search

\\u000a Abstract  Genomic library screening and genome mining are currently employed to identify biosynthetic gene clusters of thiopeptides.\\u000a To elucidate the biosynthetic pathway of nocathiacin, we present a new approach with the application of simple reverse genetics.\\u000a A relationship between structural features of thiopeptides and their biosynthetic pathways is established and is a starting\\u000a point for speedily elucidating biosynthetic genes of various

Maochen WeiJing; Jing Deng; Shuzhen Wang; Nan Liu; Yijun Chen

2011-01-01

22

A reverse genetics approach to study feline infectious peritonitis.  

PubMed

Feline infectious peritonitis (FIP) is a lethal immunopathological disease caused by feline coronaviruses (FCoVs). Here, we describe a reverse genetics approach to study FIP by assessing the pathogenicity of recombinant type I and type II and chimeric type I/type II FCoVs. All recombinant FCoVs established productive infection in cats, and recombinant type II FCoV (strain 79-1146) induced FIP. Virus sequence analyses from FIP-diseased cats revealed that the 3c gene stop codon of strain 79-1146 has changed to restore a full-length open reading frame (ORF). PMID:22491466

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

2012-04-04

23

A Reverse Genetics Approach To Study Feline Infectious Peritonitis  

PubMed Central

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

Tekes, Gergely; Spies, Danica; Bank-Wolf, Barbara

2012-01-01

24

Application of Reverse Osmosis Technology to Hawaiian Low Quality Waters.  

National Technical Information Service (NTIS)

A study of the application of reverse osmosis technology to the treatment of Hawaiian low quality waters was conducted. The purpose was to investigate the technical and economical feasibility of utilizing reverse osmosis technology to renovate waste water...

B. J. Chang R. H. F. Young J. C. S. Chou

1973-01-01

25

Improved and simplified recombineering approach for influenza virus reverse genetics  

PubMed Central

Typical reverse genetics systems for generating influenza viruses require the insertion of each genome segments by DNA ligation into vectors for genome synthesis and expression. Herein is described the construction and use of a novel pair of plasmid vectors for cloning all eight genome segments of influenza A virus by homologous recombination for influenza virus reverse genetics. Plasmids, pLLBA and pLLBG, were constructed to possess opposing RNA polymerase I and RNA polymerase II transcription units for generating influenza genomic and messenger RNAs, respectively. In addition these promoters flanked a recombination cassette which comprised the conserved 5' (13bp) and 3' (12bp) terminal promoters of influenza virus. These vectors differed due to the presence of an A or a G (plus sense) to correspond to differences at nucleotide position 4 among negative-sense influenza virus promoters. The cloning approach involved homologous recombination of each influenza gene segment and the appropriate linearized pLLBA or pLLBG vectors in E. coli. Direct cloning by recombination was simpler and faster than conventional restriction digestion and ligation methods. This new vector system was successfully used to clone and rescue various influenza viruses and thus has the potential to promote the rapid analysis and vaccine development of novel influenza strains.

Liu, Qinfang; Wang, Shuai; Ma, Guangpeng; Pu, Juan; Forbes, Nicole E; Brown, Earl G; Liu, Jin-Hua

2009-01-01

26

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.

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

27

THE APPLICATION OF HABIT REVERSAL IN TREATING TRICHOTILLOMANIA  

Microsoft Academic Search

Habit reversal is a multicomponent approach of behavioral therapy shown to be effective in treating trichotillomania. This article reviews and outlines the application of habit reversal, drawing upon research, training, and clinical experience in treating this disorder. Included are a case illustration and a 10-session treatment outline incorporating all the components of habit reversal.

Patricia A. Kraemer

1999-01-01

28

Marker reconstitution mutagenesis: a simple and efficient reverse genetic approach.  

PubMed

A novel reverse genetic approach termed 'marker reconstitution mutagenesis' was designed to generate mutational allelic series in genes of interest. This approach consists of two simple steps which utilize two selective markers. First, using one selective marker, a partial fragment of another selective marker gene is inserted adjacently to a gene of interest by homologous recombination. Second, random mutations are introduced precisely into the gene of interest, together with the reconstitution of the latter selective marker by homologous recombination. This approach was successfully tested for several genes in the fission yeast Schizosaccharomyces pombe. It circumvents the problems encountered with other methods and should be adaptable to any organism that incorporates exogenous DNA by homologous recombination. PMID:21360732

Tang, Xie; Huang, Junqi; Padmanabhan, Anup; Bakka, Kavya; Bao, Yun; Tan, Brenda Yuelin; Cande, W Zacheus; Balasubramanian, Mohan K

2010-11-22

29

Optimizing TILLING populations for reverse genetics in Medicago truncatula.  

PubMed

Medicago truncatula has been widely adopted as a model plant for crop legume species of the Vicieae. Despite the availability of transformation and regeneration protocols, there are currently limited tools available in this species for the systematic investigation of gene function. Within the framework of the European Grain Legumes Integrated Project (http://www.eugrainlegumes.org), chemical mutagenesis was applied to M. truncatula to create two mutant populations that were used to establish a TILLING (targeting induced local lesions in genomes) platform and a phenotypic database, allowing both reverse and forward genetics screens. Both populations had the same M2 line number, but differed in their M1 population size: population 1 was derived from a small M1 population (one-tenth the size of the M2 generation), whereas population 2 was generated by single seed descent and therefore has M1 and M2 generations of equal size. Fifty-six targets were screened, 10 on both populations, and 546 point mutations were identified. Population 2 had a mutation frequency of 1/485 kb, twice that of population 1. The strategy used to generate population 2 is more efficient than that used to generate population 1, with regard to mutagenesis density and mutation recovery. However, the design of population 1 allowed us to estimate the genetically effective cell number to be three in M. truncatula. Phenotyping data to help forward screenings are publicly available, as well as a web tool for ordering seeds at http://www.inra.fr/legumbase. PMID:19490506

Le Signor, Christine; Savois, Vincent; Aubert, Grégoire; Verdier, Jérôme; Nicolas, Marie; Pagny, Gaelle; Moussy, Françoise; Sanchez, Myriam; Baker, Dave; Clarke, Jonathan; Thompson, Richard

2009-06-01

30

Reverse genetics plasmid for cloning unstable Influenza A virus gene segments  

Microsoft Academic Search

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

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

2011-01-01

31

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.

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

2012-01-01

32

Molecular studies of influenza B virus in the reverse genetics era.  

PubMed

Recovery of an infectious virus of defined genetic structure entirely from cDNA and the deduction of information about the virus resulting from phenotypic characterization of the mutant is the process of reverse genetics. This approach has been possible for a number of negative-strand RNA viruses since the recovery of rabies virus in 1994. However, the recovery of recombinant orthomyxoviruses posed a greater challenge due to the segmented nature of the genome. It was not until 1999 that such a system was reported for influenza A viruses, but since that time our knowledge of influenza A virus biology has grown dramatically. Annual influenza epidemics are caused not only by influenza A viruses but also by influenza B viruses. In 2002, two groups reported the successful recovery of influenza B virus entirely from cDNA. This has allowed greater depth of study into the biology of these viruses. This review will highlight the advances made in various areas of influenza B virus biology as a result of the development of reverse genetics techniques for these viruses, including (i) the importance of the non-coding regions of the influenza B virus genome; (ii) the generation of novel vaccine strains; (iii) studies into the mechanisms of drug resistance; (iv) the function(s) of viral proteins, both those analogous to influenza A virus proteins and those unique to influenza B viruses. The information generated by the application of influenza B virus reverse genetics systems will continue to contribute to our improved surveillance and control of human influenza. PMID:20926635

Jackson, David; Elderfield, Ruth A; Barclay, Wendy S

2010-10-06

33

Reversibility conditions for quantum channels and their applications  

NASA Astrophysics Data System (ADS)

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

Shirokov, M. E.

2013-08-01

34

Deletion-Based Reverse Genetics in Medicago truncatula1[W][OA  

PubMed Central

The primary goal of reverse genetics, the identification of null mutations in targeted genes, is achieved through screening large populations of randomly mutagenized plants. T-DNA and transposon-based mutagenesis has been widely employed but is limited to species in which transformation and tissue culture are efficient. In other species, TILLING (for Targeting Induced Local Lesions IN Genomes), based on chemical mutagenesis, has provided an efficient method for the identification of single base pair mutations, only 5% of which will be null mutations. Furthermore, the efficiency of inducing point mutations, like insertion-based mutations, is dependent on target size. Here, we describe an alternative reverse genetic strategy based on physically induced genomic deletions that, independent of target size, exclusively recovers knockout mutants. Deletion TILLING (De-TILLING) employs fast neutron mutagenesis and a sensitive polymerase chain reaction-based detection. A population of 156,000 Medicago truncatula plants has been structured as 13 towers each representing 12,000 M2 plants. The De-TILLING strategy allows a single tower to be screened using just four polymerase chain reaction reactions. Dual screening and three-dimensional pooling allows efficient location of mutants from within the towers. With this method, we have demonstrated the detection of mutants from this population at a rate of 29% using five targets per gene. This De-TILLING reverse genetic strategy is independent of tissue culture and efficient plant transformation and therefore applicable to any plant species. De-TILLING mutants offer advantages for crop improvement as they possess relatively few background mutations and no exogenous DNA.

Rogers, Christian; Wen, Jiangqi; Chen, Rujin; Oldroyd, Giles

2009-01-01

35

Applications of behavioural genetics: outpacing the science?  

Microsoft Academic Search

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

Mark A. Rothstein

2005-01-01

36

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

37

Combination of reverse and chemical genetic screens reveals angiogenesis inhibitors and targets.  

PubMed

We combined reverse and chemical genetics to identify targets and compounds modulating blood vessel development. Through transcript profiling in mice, we identified 150 potentially druggable microvessel-enriched gene products. Orthologs of 50 of these were knocked down in a reverse genetic screen in zebrafish, demonstrating that 16 were necessary for developmental angiogenesis. In parallel, 1280 pharmacologically active compounds were screened in a human cell-based assay, identifying 28 compounds selectively inhibiting endothelial sprouting. Several links were revealed between the results of the reverse and chemical genetic screens, including the serine/threonine (S/T) phosphatases ppp1ca, ppp1cc, and ppp4c and an inhibitor of this gene family; Endothall. Our results suggest that the combination of reverse and chemical genetic screens, in vertebrates, is an efficient strategy for the identification of drug targets and compounds that modulate complex biological systems, such as angiogenesis. PMID:19389629

Kalén, Mattias; Wallgard, Elisabet; Asker, Noomi; Nasevicius, Aidas; Athley, Elisabet; Billgren, Erik; Larson, Jon D; Wadman, Shannon A; Norseng, Elizabeth; Clark, Karl J; He, Liqun; Karlsson-Lindahl, Linda; Häger, Ann-Katrin; Weber, Holger; Augustin, Hellmut; Samuelsson, Tore; Kemmet, Chelsy K; Utesch, Carly M; Essner, Jeffrey J; Hackett, Perry B; Hellström, Mats

2009-04-24

38

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.

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

2013-01-01

39

Experimental implementation of reverse time migration for nondestructive evaluation applications  

NASA Astrophysics Data System (ADS)

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

Le Bas, P.; Anderson, B. E.; Griffa, M.; Ulrich, T. J.; Johnson, P. A.

2011-12-01

40

Experimental implementation of reverse time migration for nondestructive evaluation applications.  

PubMed

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

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

2011-01-01

41

Genetically modified industrial yeast ready for application.  

PubMed

Tremendous progress in the genetic engineering of yeast had been achieved at the end of 20th century, including the complete genome sequence, genome-wide gene expression profiling, and whole gene disruption strains. Nevertheless, genetically modified (GM) baking, brewing, wine, and sake yeasts have not, as yet, been used commercially, although numerous industrial recombinant yeasts have been constructed. The recent progress of genetic engineering for the construction of GM yeast is reviewed and possible requirements for their application are discussed. 'Self-cloning' yeast will be the most likely candidate for the first commercial application of GM microorganisms in food and beverage industries. PMID:16233347

Akada, Rinji

2002-01-01

42

Reverse genetics-generated elastase-dependent swine influenza viruses are attenuated in pigs.  

PubMed

Influenza A virus causes significant morbidity in swine, resulting in a substantial economic burden. Swine influenza virus (SIV) infection also poses important human public health concerns. It has been shown that conversion of the haemagglutinin (HA) cleavage site from a trypsin-sensitive motif to an elastase-sensitive motif resulted in attenuated viruses in mouse models. However, application of this attenuation approach in a natural host has not been achieved yet. Here, we report that using reverse genetics, we generated two mutant SIVs derived from strain A/SW/SK/18789/02 (H1N1). Mutant A/SW/SK-R345V carries a mutation from arginine to valine at aa 345 of HA. Similarly, mutant A/SW/SK-R345A encodes alanine instead of arginine at aa 345 of HA. Our data showed that both mutants are solely dependent on neutrophil elastase cleavage in tissue culture. These tissue culture-grown mutant SIVs showed similar growth properties in terms of plaque size and growth kinetics to the wild-type virus. In addition, SIV mutants were able to maintain their genetic information after multiple passaging on MDCK cells. Furthermore, mutant SIVs were highly attenuated in pigs. Thus, these mutants may have the potential to serve as live attenuated vaccines. PMID:19141446

Masic, Aleksandar; Babiuk, Lorne A; Zhou, Yan

2009-02-01

43

Transgenesis and reverse genetics of mosquito innate immunity  

Microsoft Academic Search

genetically stable, dominant-negative and overexpression phenotypes. Using the blood-meal-activated vitellogenin gene (Vg) promoter, we have generated transgenic mosquitoes with blood-meal-activated, overexpressed antimicrobial peptides, Defensin A and Cecropin A. Moreover, we have recently generated a transgenic dominant-negative Relish mosquito strain, which after taking a blood meal, becomes immune-deficient to infection by Gram-negative bacteria. The latter accomplishment has opened the door to

Sang Woon Shin; Vladimir A. Kokoza; Alexander S. Raikhel

2003-01-01

44

Integrative Genetic Element That Reverses the Usual Target Gene Orientation  

Microsoft Academic Search

Prokaryotic genetic elements often encode integrases that allow site-specific integration into the host chromosome. When the host integration site (attB) lies within a gene, the element usually carries at its integration site (attP) the same segment of the gene as that displaced; integration disrupts yet smoothly restores the active gene (Fig. 1A). This strategy allows the use of host sequences

Sihui Zhao; Kelly P. Williams

2002-01-01

45

A fast neutron deletion mutagenesis-based reverse genetics system for plants  

Microsoft Academic Search

Summary A new reverse genetics method has been developed to identify and isolate deletion mutants for targeted plant genes. Deletion mutant libraries are generated using fast neutron bombardment. DNA samples extracted from the deletion libraries are used to screen for deletion mutants by polymerase chain reaction (PCR) using specific primers flanking the targeted genes. By adjusting PCR conditions to preferentially

Xin Li; Yujuan Song; Shelly Straight; Pamela Ronald; Xinnian Dong; Michael Lassner; Yuelin Zhang

2001-01-01

46

Inheritance Studies Implicate a Genetic Mechanism for Apparent Sex Reversal in Chinook Salmon  

Microsoft Academic Search

The apparent increase in altered sexual differentiation in Pacific salmon Oncorhynchus spp. is a growing concern. Previous studies suggest that incongruence between genetic and phenotypic sex in Chinook salmon O. tshawytscha may be a result of altered sexual differentiation through exposure to endocrine-disrupting chemicals (EDCs). Artificial crosses between genotypically normal Chinook salmon, or between genotypically normal males and apparent sex-reversed

Kevin S. Williamson; Bernie May

2005-01-01

47

A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING  

Microsoft Academic Search

We report the use of TILLING (targeting induced local lesions in genomes), a reverse genetic, nontransgenic method, to improve a quality trait in a polyploid crop plant. Waxy starches, composed mostly of amylopectin, have unique physiochemical properties. Wheat with only one or two functional waxy genes (granule-bound starch synthase I, or GBSSI) produces starch with intermediate levels of amylopectin. We

Susan I Fuerstenberg; Dayna Loeffler; Michael N Steine; Daniel Facciotti; Ann J Slade

2004-01-01

48

Plant genetics for forensic applications.  

PubMed

An emerging application for plant DNA fingerprinting and barcoding involves forensic investigations. Examples of DNA analysis of botanical evidence include crime scene analysis, identifying the source of commercial plant products, and investigation of trade in illicit drugs. Here, we review real and potential applications of DNA-based forensic botany and provide a protocol for microsatellite genotyping of leaf material, a protocol that could be used to link a suspect to a victim or to a crime scene. PMID:22419487

Zaya, David N; Ashley, Mary V

2012-01-01

49

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

PubMed

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

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

2013-07-24

50

A reverse genetic screen in Drosophila using a deletion-inducing mutagen  

PubMed Central

We report the use of the cross-linking drug hexamethylphosphoramide (HMPA), which introduces small deletions, as a mutagen suitable for reverse genetics in the model organism Drosophila melanogaster. A compatible mutation-detection method based on resolution of PCR fragment-length polymorphisms on standard DNA sequencers is implemented. As the spectrum of HMPA-induced mutations is similar in a variety of organisms, it should be possible to transfer this mutagenesis and detection procedure to other model systems.

Nairz, Knud; Zipperlen, Peder; Dearolf, Charles; Basler, Konrad; Hafen, Ernst

2004-01-01

51

A reverse genetic screen in Drosophila using a deletion-inducing mutagen.  

PubMed

We report the use of the cross-linking drug hexamethylphosphoramide (HMPA), which introduces small deletions, as a mutagen suitable for reverse genetics in the model organism Drosophila melanogaster. A compatible mutation-detection method based on resolution of PCR fragment-length polymorphisms on standard DNA sequencers is implemented. As the spectrum of HMPA-induced mutations is similar in a variety of organisms, it should be possible to transfer this mutagenesis and detection procedure to other model systems. PMID:15461801

Nairz, Knud; Zipperlen, Peder; Dearolf, Charles; Basler, Konrad; Hafen, Ernst

2004-09-28

52

Genome Organization and Reverse Genetic Analysis of a Type I Feline Coronavirus  

Microsoft Academic Search

In this study we report the complete sequence and genome organization of the serotype I feline coronavirus (FCoV) strain Black. Furthermore, a reverse genetic system was established for this FCoV strain by cloning a full-length cDNA copy into vaccinia virus. This clone served as basis for the generation of recombinant FCoV (recFCoV) that was shown to bear the same features

Gergely Tekes; Regina Hofmann-Lehmann; Iris Stallkamp; Volker Thiel; Heinz-Jurgen Thiel

2008-01-01

53

[Applications of gene therapy in medical genetics].  

PubMed

Over the past three decades, an increasing proportion of genetic research has consisted of molecular studies in medicine. It has resulted in a profound change in the understanding of the pathophysiology of diverse genetic diseases. Gene therapy is the use of nucleic acids as therapeutically useful molecules. Although many genetic discoveries have resulted in better diagnostic tests, the application of molecular technologies to the treatment of genetic diseases is natural and logical. Gene therapy is in a phase of its youth, nevertheless it holds very real promise. In the first 9 years, 396 clinical protocols have been approved worldwide and over 3,000 patients from 22 different countries have carried genetically engineered cells in their body. The conclusion from these trials are that gene therapy has the potential for treating a broad array of human diseases and the procedure appears to carry a very low risk of adverse reactions, but the efficiency of gene transfer and expression in human patients is low. No formal phase III studies to establish clinical efficacy have been completed. Gene therapy is potentially a powerful clinical approach, but it has been restricted by the limited knowledge of vectors and pathophysiology of the diseases to be treated. Better understanding of the disease processes, improvements in vector design, and a great attention to the pharmacological aspects should permit the development of more effective gene therapy. PMID:10835697

Turyk, S

2000-01-01

54

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

55

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

PubMed Central

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

Luna, Ana P.; Bejarano, Eduardo R.

2011-01-01

56

Genetic switchboard for synthetic biology applications  

PubMed Central

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

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

2012-01-01

57

The regenerative capacity of zebrafish reverses cardiac failure caused by genetic cardiomyocyte depletion  

PubMed Central

Natural models of heart regeneration in lower vertebrates such as zebrafish are based on invasive surgeries causing mechanical injuries that are limited in size. Here, we created a genetic cell ablation model in zebrafish that facilitates inducible destruction of a high percentage of cardiomyocytes. Cell-specific depletion of over 60% of the ventricular myocardium triggered signs of cardiac failure that were not observed after partial ventricular resection, including reduced animal exercise tolerance and sudden death in the setting of stressors. Massive myocardial loss activated robust cellular and molecular responses by endocardial, immune, epicardial and vascular cells. Destroyed cardiomyocytes fully regenerated within several days, restoring cardiac anatomy, physiology and performance. Regenerated muscle originated from spared cardiomyocytes that acquired ultrastructural and electrophysiological characteristics of de-differentiation and underwent vigorous proliferation. Our study indicates that genetic depletion of cardiomyocytes, even at levels so extreme as to elicit signs of cardiac failure, can be reversed by natural regenerative capacity in lower vertebrates such as zebrafish.

Wang, Jinhu; Panakova, Daniela; Kikuchi, Kazu; Holdway, Jennifer E.; Gemberling, Matthew; Burris, James S.; Singh, Sumeet Pal; Dickson, Amy L.; Lin, Yi-Fan; Sabeh, M. Khaled; Werdich, Andreas A.; Yelon, Deborah; MacRae, Calum A.; Poss, Kenneth D.

2011-01-01

58

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

59

The Application of Reverse Genetics to Polyploid Plant Species  

Microsoft Academic Search

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

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

2012-01-01

60

Application of time reversal acoustics focusing for nonlinear imaging ms  

NASA Astrophysics Data System (ADS)

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

Sarvazyan, Armen; Sutin, Alexander

2001-05-01

61

Establishment of a reverse genetics system for Schmallenberg virus, a newly emerged orthobunyavirus in Europe.  

PubMed

Schmallenberg virus (SBV) is a newly emerged orthobunyavirus that has caused widespread disease in cattle, sheep and goats in Europe. Like other orthobunyaviruses, SBV is characterized by a tripartite negative-sense RNA genome that encodes four structural and two non-structural proteins. This study showed that SBV has a wide in vitro host range, and that BHK-21 cells are a convenient host for both SBV propagation and assay by plaque titration. The SBV genome segments were cloned as cDNA and a three-plasmid rescue system was established to recover infectious virus. Recombinant virus behaved similarly in cell culture to authentic virus. The ORF for the non-structural NSs protein, encoded on the smallest genome segment, was disrupted by introduction of translation stop codons in the appropriate cDNA, and when this plasmid was used in reverse genetics, a recombinant virus that lacked NSs expression was recovered. This virus had reduced capacity to shut-off host-cell protein synthesis compared with the wild-type virus. In addition, the NSs-deleted virus induced interferon (IFN) in cells, indicating that, like other orthobunyaviruses, NSs functions as an IFN antagonist, most probably by globally inhibiting host-cell metabolism. The development of a robust reverse genetics system for SBV will facilitate investigation of its pathogenic mechanisms as well as the creation of attenuated strains that could be candidate vaccines. PMID:23255627

Elliott, Richard M; Blakqori, Gjon; van Knippenberg, Ingeborg C; Koudriakova, Elina; Li, Ping; McLees, Angela; Shi, Xiaohong; Szemiel, Agnieszka M

2012-12-19

62

Establishment of a reverse genetics system for Schmallenberg virus, a newly emerged orthobunyavirus in Europe  

PubMed Central

Schmallenberg virus (SBV) is a newly emerged orthobunyavirus that has caused widespread disease in cattle, sheep and goats in Europe. Like other orthobunyaviruses, SBV is characterized by a tripartite negative-sense RNA genome that encodes four structural and two non-structural proteins. This study showed that SBV has a wide in vitro host range, and that BHK-21 cells are a convenient host for both SBV propagation and assay by plaque titration. The SBV genome segments were cloned as cDNA and a three-plasmid rescue system was established to recover infectious virus. Recombinant virus behaved similarly in cell culture to authentic virus. The ORF for the non-structural NSs protein, encoded on the smallest genome segment, was disrupted by introduction of translation stop codons in the appropriate cDNA, and when this plasmid was used in reverse genetics, a recombinant virus that lacked NSs expression was recovered. This virus had reduced capacity to shut-off host-cell protein synthesis compared with the wild-type virus. In addition, the NSs-deleted virus induced interferon (IFN) in cells, indicating that, like other orthobunyaviruses, NSs functions as an IFN antagonist, most probably by globally inhibiting host-cell metabolism. The development of a robust reverse genetics system for SBV will facilitate investigation of its pathogenic mechanisms as well as the creation of attenuated strains that could be candidate vaccines.

Blakqori, Gjon; van Knippenberg, Ingeborg C.; Koudriakova, Elina; Li, Ping; McLees, Angela; Shi, Xiaohong; Szemiel, Agnieszka M.

2013-01-01

63

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

PubMed Central

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

2012-01-01

64

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

PubMed

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

2013-06-17

65

Identification of genetic changes associated with drug resistance by reverse in situ hybridization.  

PubMed Central

The molecular cytogenetic techniques of comparative genomic hybridization (CGH) and reverse in situ hybridization (REVISH) allow the entire genomes of tumours to be screened for genetic changes without the requirement for specific probes or markers. In order to define the ability of REVISH to detect and map regions of amplification associated with drug resistance, we investigated a panel of cell lines selected for resistance to doxorubicin and intrinsic sensitivity to topoisomerase II-inhibitory drugs. We have defined a modified REVISH protocol, which involves double hybridizations with genomic DNA from the test cell lines and chromosome-specific whole chromosome paints to identify the chromosomes to which the amplicons localize. Sites of amplification are then mapped by fractional length measurements (Flpter), using published genome databases. Our findings show that amplification of the topoisomerase II alpha gene is readily detected and mapped, as is amplification of the MDR and MRP loci. Interestingly, REVISH detected a new amplicon in the doxorubicin-resistant lung cancer cell line, GLC4-ADR, which mapped to chromosome 1q. REVISH is therefore ideally suited to characterize genetic changes specific for drug resistance within a background of genetic anomalies associated with tumour progression. Images Figure 1 Figure 2 Figure 3

Hoare, S. F.; Freeman, C. A.; Coutts, J. C.; Varley, J. M.; James, L.; Keith, W. N.

1997-01-01

66

APPLICATIONS OF MIXED LINEAR MODEL APPROACHES ON COTTON QUANTITATIVE GENETICS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Many practical genetic models have been developed based on the idea of analysis of variance (ANOVA) proposed by Fisher (1925). These genetic models include NC I, NC II designs, and diallele crossed models. The application of the ANOVA approach in quantitative genetic analyses greatly facilitated the...

67

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

68

Application of Genetic Algorithms to Tuning Fuzzy Control Systems.  

National Technical Information Service (NTIS)

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 a...

T. Espy E. Vombrack J. Aldridge

1993-01-01

69

Reversible quantum operations and their application to teleportation  

Microsoft Academic Search

Quantum operations provide a general description of the state changes allowed\\u000aby quantum mechanics. Simple necessary and sufficient conditions for an ideal\\u000aquantum operation to be reversible by a unitary operation are derived in this\\u000apaper. These results generalize recent work on reversible measurements by\\u000aMabuchi and Zoller [Phys. Rev. Lett. {\\\\bf 76}, 3108 (1996)]. Quantum\\u000ateleportation can be understood

M. A. Nielsen; Carlton M. Caves

1997-01-01

70

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

PubMed

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 shows that FMRP interacts with the transcript encoding striatal-enriched protein tyrosine phosphatase (STEP; Ptpn5). STEP opposes synaptic strengthening and promotes synaptic weakening by dephosphorylating its substrates, including ERK1/2, p38, Fyn and Pyk2, and subunits of N-methyl-d-aspartate (NMDA) and AMPA receptors. Here, we show that basal levels of STEP are elevated and mGluR-dependent STEP synthesis is absent in Fmr1(KO) mice. 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 Fmr1(KO) mice and assessed mice in a battery of behavioral tests. In addition to attenuating audiogenic seizures and seizure-induced c-Fos activation in the periaqueductal gray, genetically reducing STEP in Fmr1(KO) mice reversed characteristic social abnormalities, including approach, investigation and anxiety. Loss of STEP also corrected select nonsocial anxiety-related behaviors in Fmr1(KO) mice, such as light-side exploration in the light/dark box. Our findings indicate that genetically reducing STEP significantly diminishes seizures and restores select social and nonsocial anxiety-related behaviors in Fmr1(KO) mice, suggesting that strategies to inhibit STEP activity may be effective for treating patients with FXS. PMID:22405502

Goebel-Goody, S M; Wilson-Wallis, E D; Royston, S; Tagliatela, S M; Naegele, J R; Lombroso, P J

2012-04-06

71

Arenavirus Reverse Genetics: New Approaches for the Investigation of Arenavirus Biology and Development of Antiviral Strategies  

PubMed Central

Several arenaviruses, chiefly Lassa virus, cause hemorrhagic fever disease in humans and pose a significant public health problem in their endemic regions. On the other hand the prototypic arenavirus LCMV is a superb workhorse for the investigation of virus-host interactions and associated disease. The development of novel antiviral strategies to combat pathogenic arenaviruses would be facilitated by a detailed understanding of the arenavirus molecular and cell biology. To this end, the development of reverse genetics systems for several arenaviruses has provided investigators with novel and powerful approaches to dissect the functions of arenavirus proteins and their interactions with host factors required to complete each of the steps of the virus life cycle, as well as to cause disease.

Emonet, Sebastien E.; Urata, Shuzo; de la Torre, Juan C.

2011-01-01

72

Reverse genetic studies of mitochondrial DNA-based diseases using a mouse model  

PubMed Central

In the situation that it would not be able to produce model animals for mitochondrial diseases caused by mitochondrial DNA (mtDNA) with pathogenic mutations, we succeeded in generating mice with pathogenic deletion mutant mtDNA (?mtDNA), named “mito-mice”, by direct introduction of mitochondria with ?mtDNA into mouse zygotes. In the mito-mice, accumulation of ?mtDNA induced mitochondrial respiration defects in various tissues, resulting in mitochondrial disease phenotypes, such as low body weight, lactic acidosis, ischemia, myopathy, heart block, deafness, male infertility, and renal failure. Thus, mito-mice are the first model animal for mtDNA-based diseases, and the mice could be valuable for understanding precise pathogeneses and testing therapies of mitochondrial diseases. In the present review, we summarized reverse genetic studies using the mito-mice.

NAKADA, Kazuto; SATO, Akitsugu; HAYASHI, Jun-Ichi

2008-01-01

73

Development of a reverse genetics system to generate recombinant Marburg virus derived from a bat isolate.  

PubMed

Recent investigations have shown the Egyptian fruit bat (Rousettus aegyptiacus) to be a natural reservoir for marburgviruses. To better understand the life cycle of these viruses in the natural host, a new reverse genetics system was developed for the reliable rescue of a Marburg virus (MARV) originally isolated directly from a R. aegyptiacus bat (371Bat). To develop this system, the exact terminal sequences were first determined by 5' and 3' RACE, followed by the cloning of viral proteins NP, VP35, VP30 and L into expression plasmids. Novel conditions were then developed to efficiently replicate virus mini-genomes followed by the construction of full-length genomic clones from which recombinant wild type and GFP-containing MARVs were rescued. Surprisingly, when these recombinant MARVs were propagated in primary human macrophages, a dramatic difference was found in their ability to grow and to elicit anti-viral cytokine responses. PMID:24074586

Albariño, César G; Uebelhoer, Luke S; Vincent, Joel P; Khristova, Marina L; Chakrabarti, Ayan K; McElroy, Anita; Nichol, Stuart T; Towner, Jonathan S

2013-09-05

74

Multiobjective Genetic Algorithms with Application to Control Engineering Problems  

Microsoft Academic Search

Constraint handling with genetic algorithms is then developed from a decision making perspective and characterized, with application to control system design in mind. Related genetic algorithm issues, such as the ability to maintain diverse solutions along the trade-off surface and responsiveness to on-line changes in decision policy, are also considered. The application of the multiobjective GA to three realistic problems

Carlos Manuel Mira Da Fonseca

1995-01-01

75

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

Microsoft Academic Search

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.

Yaliang Sun; Jianli Guo

2001-01-01

76

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

PubMed

Options for the control of emerging and reemerging H5N1 influenza viruses include improvements in biosecurity and the use of inactivated vaccines. Commercially available H5N2 influenza vaccine prevents disease signs and reduces virus load but does not completely prevent virus shedding after challenge with H5N1 virus. By using reverse genetics, we prepared an H5N3 vaccine whose hemagglutinin is 99.6% homologous to that of A/CK/HK/86.3/02 (H5N1). We used the internal genes of A/PR/8/34 and the H5 of A/Goose/HK/437.4/99 (H5N1) after deletion of basic amino acids from its connecting peptide region. The resulting virus was not lethal to chicken embryos and grew to high HA titers in eggs, allowing preparation of HA protein-standardized vaccine in unconcentrated allantoic fluid. The N3 neuraminidase, derived from A/Duck/Germany/1215/73 (H2N3), permitted discrimination between vaccinated and naturally infected birds. The virus construct failed to replicate in quail and chickens. Similar to parental A/PR/8/34 (H1N1), it replicated in mice and ferrets and spread to the brains of mice; therefore, it should not be used as a live-attenuated vaccine. The H5N3 vaccine, at doses of 1.2 microg HA, induced HI antibodies in chickens and prevented death, signs of disease, and markedly reduced virus shedding after challenge with A/CK/HK/86.3/02 (H5N1) but did not provide sterilizing immunity. Thus, reverse genetics allows the inexpensive preparation of standardized, efficacious H5N3 poultry vaccines that may also reduce the reemergence of H5N1 genotypes. PMID:14554086

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

2003-09-30

77

Detection of infectious bursal disease virus isolates with unknown antigenic properties by reverse genetics.  

PubMed

Infectious bursal disease virus (IBDV) serotype 1 is the causative agent of a highly contagious immunosuppressive disease of young chickens. In the past, a number of antigenic, as well as pathogenic, subtypes have been described. The determination of the antigenic makeup of circulating strains is of vital interest to the poultry industry because changes in the antigenicity of circulating field strains have an impact on the use of vaccines. To obtain a more comprehensive overview of the relationship between the nucleotide and amino acid sequence and the antigenic makeup of field isolates, a system based on reverse genetics of IBDV was established. Using this approach, a database for field isolates from three different states in the United States (Georgia, Alabama, and Louisiana), consisting of nucleotide sequence, amino acid sequence, and a reaction pattern based on a panel of monoclonal antibodies, was established. The obtained results showed that phylogenic analysis, which is based on the similarity of sequences, would lead to false conclusions regarding a possible antigenic makeup of the particular isolate. Sequences of field samples were divided into three groups: 1) those that grouped with variant strain E/Del sequences but were antigenically different, 2) those that did not group with sequences of E/Del but were similar in their antigenic makeup, and 3) those that did not group with E/Del sequences and were antigenically different. In addition, using the reverse-genetics approach, a number of field isolates showed no reactivity with any of the used monoclonal antibodies, indicating that an unknown, antigenic subtype of IBDV serotype 1 is circulating in the field. PMID:19166049

Icard, Alan H; Sellers, Holly S; Mundt, Egbert

2008-12-01

78

Applications of retrotransposons as genetic tools in plant biology  

Microsoft Academic Search

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

Amar Kumar; Hirohiko Hirochika

2001-01-01

79

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

Microsoft Academic Search

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

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

2011-01-01

80

Recycle of Papermill Waste Waters and Application of Reverse Osmosis.  

National Technical Information Service (NTIS)

Pilot plant reverse osmosis (R.O.) units were operated on weak waste waters from a pulp and paperboard mill to obtain further data on R.O. as an integral part of a closed water system within the mill. Of the many equipment types tested, the one selected w...

D. C. Morris W. R. Nelson G. O. Walraven

1972-01-01

81

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

82

Synthesis and Evaluation of New Membrane Candidates for Application in Reverse Osmosis.  

National Technical Information Service (NTIS)

The purpose of the program was to investigate the block and graft copolymer approach to synthetic polymer membrane materials which may be useful in reverse osmosis applications. Block copolymers have been sythesized from peroxycarbamate-terminated poly(et...

T. W. Brooks C. L. Daffin

1969-01-01

83

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

National Technical Information Service (NTIS)

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

J. Markind T. Van Tran

1979-01-01

84

Reverse osmosis application for butanol-acetone fermentation  

SciTech Connect

The problems of dilute solvent concentration in butanol-acetone fermentation can be solved by using reverse osmosis to dewater the fermentation liquor. Polyamide membranes exhibited butanol rejection rates as high as 85%. Optimum rejection of butanol occurs at a pressure of approximately 5.5 to 6.5 MPa and hydraulic recoveries of 50-70%. Flux ranged from 0.5 to 1.8 l.

Garcia, A.; Iannotti, E.L.; Fischer, J.R.

1984-01-01

85

Application of Ultrasound for Genetic Improvement  

Microsoft Academic Search

Genetic improvement programs for livestock would be enhanced by the ability to accurately and easily measure body composition of live animals or to make measurements at anatomical reference points that can be used to accurately predict body composition. Advances in ultrasonic technology, such as real-time imagery and portable ultrasound units, have renewed interest among animal scientists working with genetic improvement

Doyle E. Wilson

2010-01-01

86

Genetically modified industrial yeast ready for application  

Microsoft Academic Search

Tremendous progress in the genetic engineering of yeast had been achieved at the end of 20th century, including the complete genome sequence, genome-wide gene expression profiling, and whole gene disruption strains. Nevertheless, genetically modified (GM) baking, brewing, wine, and sake yeasts have not, as yet, been used commercially, although numerous industrial recombinant yeasts have been constructed. The recent progress of

Rinji Akada

2002-01-01

87

Current Applications of Transposons in Mouse Genetics  

Microsoft Academic Search

Transposable elements (TEs) have been used to study the genetics of a wide variety of species, including prokaryotes, plants, yeast, and Drosophila. The use of TEs to study mouse genetics has previously not been possible as mice do not have endogenous, highly active TEs like other organisms. Over the past decade, however, two retrotransposons (class I TEs) and four DNA

Adam J. Dupuy

2010-01-01

88

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

89

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

PubMed

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

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

2010-07-14

90

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

PubMed Central

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

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

2012-01-01

91

Application of genetic algorithm for optimization gasoline fractions blending compounding  

Microsoft Academic Search

The paper deals with the application of a genetic algorithm for the solution of the task of gasoline fraction blending compounding, keeping the given conditions on octane numbers and the amount of given types of commodity gasolines. The principle of coding solutions is described. Several results of experiments on the determination of the effective genetic algorithm configuration are given.

J. A. Burgher; V. S. Vyshemirskij; N. A. Sokolova

2002-01-01

92

Oyster Genetics: Research and Commercial Applications.  

National Technical Information Service (NTIS)

This report outlines the oyster genetics and breeding program at the Milford Biological Laboratory almost exclusively concerned presently with the commercial American oyster, Crassostrea virginica. At the same time is summarized the background information...

A. C. Longwell

1969-01-01

93

Development of a reverse genetics system for a human rabies virus vaccine strain employed in China.  

PubMed

The CTN rabies virus was isolated from a human in China in 1953 and subsequently attenuated by multiple passaging to a vaccine strain now approved by the WHO. In this study, we describe the development of a reverse genetics system for the CTN rabies virus strain. The recombinant full-length genomic cDNA was flanked by a hammerhead ribozyme (HamRz) and the hepatitis delta virus ribozyme (HdvRz) while the non-coding G-L region was replaced with a green fluorescent protein (GFP) gene. A set of helper plasmids encoding nucleoprotein (N), phosphoprotein (P), and large protein (L) were constructed and co-transfected with recombinant full-length genome plasmid into BHK-21 cells. Recombinant virus was successfully recovered from cloned cDNA under control of the CMV promoter driven by RNA polymerase II. The recombinant virus, CTN-GFP, stably expressed GFP as detected by fluorescence microscopy. A group of 1-day-old suckling mice was challenged with the CTN-GFP strain by intracerebral inoculation, resulting in 100% morbidity and GFP expression was detected in brain tissues. The recombinant virus CTN-GFP strain recovered from cloned cDNA will be useful as a viral vector to express other foreign genes. PMID:20080136

Huang, Ying; Tang, Qing; Nadin-Davis, Susan A; Zhang, Shoufeng; Hooper, Craig D; Ming, Pinggang; Du, Jialiang; Tao, Xiaoyan; Hu, Rongliang; Liang, Guodong

2010-01-18

94

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

PubMed Central

Human bocavirus 1 (HBoV1) has been identified as one of the etiological agents of wheezing in young children with acute respiratory-tract infections. In this study, we have obtained the sequence of a full-length HBoV1 genome (including both termini) using viral DNA extracted from a nasopharyngeal aspirate of an infected patient, cloned the full-length HBoV1 genome, and demonstrated DNA replication, encapsidation of the ssDNA genome, and release of the HBoV1 virions from human embryonic kidney 293 cells. The HBoV1 virions generated from this cell line-based production system exhibits a typical icosahedral structure of approximately 26 nm in diameter, and is capable of productively infecting polarized primary human airway epithelia (HAE) from the apical surface. Infected HAE showed hallmarks of lung airway-tract injury, including disruption of the tight junction barrier, loss of cilia and epithelial cell hypertrophy. Notably, polarized HAE cultured from an immortalized airway epithelial cell line, CuFi-8 (originally derived from a cystic fibrosis patient), also supported productive infection of HBoV1. Thus, we have established a reverse genetics system and generated the first cell line-based culture system for the study of HBoV1 infection, which will significantly advance the study of HBoV1 replication and pathogenesis.

Cheng, Fang; Luo, Yong; Shen, Weiran; Lei-Butters, Diana C. M.; Chen, Aaron Yun; Li, Yi; Tang, Liang; Soderlund-Venermo, Maria; Engelhardt, John F.; Qiu, Jianming

2012-01-01

95

Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses  

PubMed Central

Since 1999, plasmid-based reverse genetics (RG) systems have revolutionized the way influenza viruses are studied. However, it is not unusual to encounter cloning difficulties for one or more influenza genes while attempting to recover virus de novo. To overcome some of these shortcomings we sought to develop partial or full plasmid-free RG systems. The influenza gene of choice is assembled into a RG competent unit by virtue of overlapping PCR reactions containing a cDNA copy of the viral gene segment under the control of RNA polymerase I promoter (pol1) and termination (t1) signals – herein referred to as Flu PCR amplicons. Transfection of tissue culture cells with either HA or NA Flu PCR amplicons and 7 plasmids encoding the remaining influenza RG units, resulted in efficient virus rescue. Likewise, transfections including both HA and NA Flu PCR amplicons and 6 RG plasmids also resulted in efficient virus rescue. In addition, influenza viruses were recovered from a full set of Flu PCR amplicons without the use of plasmids.

Chen, Hongjun; Ye, Jianqiang; Xu, Kemin; Angel, Matthew; Shao, Hongxia; Ferrero, Andrea; Sutton, Troy; Perez, Daniel R.

2012-01-01

96

Studies on the paramyxovirus accessory genes by reverse genetics in the Sendai virus-mouse system  

PubMed Central

Nucleotide sequencing of the entire genomes was completed in the 1980s for most members of the Paramyxoviridae. It then became a new common task with challenge for researchers in the field to establish a system to recover the virus entirely from cDNA, thereby allowing reverse genetics (free manipulation of the viral genome). Using Sendai virus, we established a system of incomparable virus recovery efficiency early on. This technology was then fully exploited in answering a series of long-held questions. In particular, two accessory genes whose functions had remained enigmatic were demonstrated to encode special functions critical in viral in vivo pathogenesis producing fatal pneumonia in mice, although dispensable in virus replication at the in vitro cellular level. Their in vivo functions were found to counteract the two respective facets of the antiviral state induced by interferons and an interferon regulatory factor 3-dependent but yet unknown effector. These achievements appear to have facilitated a scientific trend where the accessory genes are a focus of active investigation in studies on other paramyxoviruses and opened up a new common ground shared between virology and immunology.

Sakaguchi, Takemasa; Kato, Atsushi; Kiyotani, Katsuhiro; Yoshida, Tetsuya; Nagai, Yoshiyuki

2008-01-01

97

Reverse genetics system for porcine enteric calicivirus, a prototype sapovirus in the Caliciviridae.  

PubMed

A porcine enteric calicivirus (PEC), strain Cowden in the genus Sapovirus of the Caliciviridae family, can be propagated in a porcine kidney continuous cell line (LLC-PK) in the presence of bile acids in the cell culture medium. A full-length cDNA copy of the Cowden PEC genome was cloned into a plasmid vector directly downstream from the T7 RNA polymerase promoter, and capped RNA transcripts derived from this clone were infectious when transfected into LLC-PK cells. The recovery of PEC after transfection of RNA transcripts was dependent on the presence of bile acids, consistent with our recent identification of a bile acid-mediated signaling pathway required for PEC replication (Chang et al., Proc. Natl. Acad. Sci. USA 101:8733-8788, 2004). Recovery of virus was verified by detection of PEC antigen in transfected cells by immunofluorescence and enzyme-linked immunosorbent assays, direct observation of recovered viral particles by electron microscopy, and partial sequence analysis of their genomes (first 1,070 nucleotides) to differentiate them from tissue culture-adapted parental virus. The recovered virus retained its ability to infect piglets when administered by the oral route and showed an attenuated phenotype similar to that of the tissue culture-adapted parental virus. This reverse genetics system for PEC provides a new tool to study the molecular basis of replication and pathogenesis for caliciviruses associated with diarrheal disease. PMID:15650167

Chang, Kyeong-Ok; Sosnovtsev, Stanislav V; Sosnovtsev, Stanislav S; Belliot, Gaël; Wang, Qiuhong; Saif, Linda J; Green, Kim Y

2005-02-01

98

Genetic Engineering Applications In Crop Improvement  

Microsoft Academic Search

Genetic engineering of crop plants is one of, or perhaps, the most influential technologies in agriculture for plant improvement\\u000a of the 21st century. The food and fiber requirements of approximately 10 billion people need to be met with existing resources\\u000a that are currently limited. Biotechnology, and specifically genetic engineering, can greatly expand those limits. The potential\\u000a of agricultural biotechnology and

M. E. John; J. Mc D. Stewart

99

Time reverse modeling of low-frequency microtremors: Application to hydrocarbon reservoir localization  

NASA Astrophysics Data System (ADS)

Time reverse modeling is applied to synthetic and real low-frequency microtremors measured at the Earth surface with synchronized seismometers. In contrast to previous time-reverse applications, no single event or first arrival time identification is applied for microtremor localization. Synthetic low-frequency microtremors are numerically generated within a small underground area and modeled with a finite-difference algorithm simulating two-dimensional elastic wave propagation. Time reverse modeling using synthetic microtremors shows that small underground source areas can be accurately located. Different source characteristics which emit mainly P-waves or S-waves vertically influence the localization accuracy. Time reverse modeling is applied to two real microtremor data sets acquired 16 months apart above known oil reservoirs nearby Voitsdorf, Austria, to investigate whether spectral anomalies observed above the reservoirs originate from the reservoirs. Time reverse modeling indicates that low-frequency microtremor signals originate from the reservoir locations and provides a possible method for reservoir localization.

Steiner, Brian; Saenger, Erik H.; Schmalholz, Stefan M.

2008-02-01

100

Applicability of yeast genetics to neurologic disease.  

PubMed

As advances in gene mapping technology reveal genes associated with neurologic diseases, the need to identify a gene's normal function arises often. Experimental genetics is very useful in identifying a gene's function. It relies on model organisms both because it is not appropriate in humans, and because many processes are remarkably similar among eukaryotes. Many cellular processes have evolved once, and species differences are variations on a theme. Molecular genetic tools available in the yeast Saccharomyces cerevisiae provide a means to more rapidly reach an understanding of gene function, yielding substantial insight into the same process in humans. Yeast will never complain of headache or "spells," but do have expansions of trinucleotide repeats, prions, and other processes very much analogous to those underlying many neurologic diseases. In spite of the absence of a nervous system in yeast, yeast genetics has contributed substantial insight into neurologic diseases mechanisms. The real strength of yeast in studying human disease is in genetic analysis of gene function and in providing genetically powerful functional assays. Arch Neurol. 2000;57:1129-1134 PMID:10927792

Walberg, M W

2000-08-01

101

Time reverse modeling of low-frequency microtremors: Application to hydrocarbon reservoir localization  

Microsoft Academic Search

Time reverse modeling is applied to synthetic and real low-frequency microtremors measured at the Earth surface with synchronized seismometers. In contrast to previous time-reverse applications, no single event or first arrival time identification is applied for microtremor localization. Synthetic low-frequency microtremors are numerically generated within a small underground area and modeled with a finite-difference algorithm simulating two-dimensional elastic wave propagation.

Brian Steiner; Erik H. Saenger; Stefan M. Schmalholz

2008-01-01

102

Methods for reverse genetic screening in zebrafish by resequencing and TILLING.  

PubMed

Animal models provide an in vivo system to study gene function by transgenic and knockout approaches. Targeted knockout approaches have been very successful in mice, but are currently not feasible in zebrafish due to the inability to grow embryonic stem cells. As an alternative, a reverse genetic approach that utilizes screening by resequencing and/or TILLING (Targeting Induced Local Lesions INGenomes) of mutagenized genomes has recently gained popularity in the zebrafish field. Spermatogonia of healthy males are mutagenized using ENU (N-ethyl-N-nitrosourea) and F1 progeny is collected by breeding treated males with healthy wild type females. Sperm and DNA banks are generated from F1 males. DNA is screened for ENU-induced mutations by sequencing or TILLING. These mutations can then be studied by in vitro fertilization (IVF) from the cryopreserved sperm of the corresponding F1 male followed by breeding to homozygosity. A high-throughput method of screening for rare heterozygotes and efficient recovery of mutant lines are important in identification of a large number of mutations using this approach. This article provides optimized protocols for resequencing and TILLING based on our experiences. We performed a pilot screen on 1235 F1 males by resequencing 54 exons from 17 genes and analyzed the sequencing data using multiple programs to maximize the mutation detection with minimal false positive detection. As an alternative to sequencing, we developed the protocols for TILLING by capillary electrophoresis using an ABI Genetic analyzer 3100 platform followed by fragment analysis using GeneScan and Genotyper softwares. PCR products generated by fluorescently labeled universal primers and tailed exon-specific primers were pooled 4-fold prior to heteroduplex formation. Overall, our pilot screen shows that a combination of TILLING and sequencing is optimal for achieving cost-effective, high-throughput screening of a large number of samples. Amplicons with fewer common SNPs are ideal for TILLING whereas amplicons with multiple SNPs and in/del polymorphisms are best suited for sequencing followed by analysis with SNPdetector. PMID:16828311

Sood, Raman; English, Milton A; Jones, MaryPat; Mullikin, James; Wang, Duen-Mei; Anderson, Maria; Wu, Dongying; Chandrasekharappa, Settara C; Yu, Jun; Zhang, Jinghui; Paul Liu, P

2006-07-01

103

Genetically modified plants for law enforcement applications  

Microsoft Academic Search

Plants are ubiquitous in the environment and have the unique ability to respond to their environment physiologically and through altered gene expression profiles (they cannot walk away). In addition, plant genetic transformation techniques and genomic information in plants are becoming increasingly advanced. We have been performing research to express the jellyfish green fluorescent protein (GFP) in plants. GFP emits green

C. Neal Stewart

2002-01-01

104

Genetically modified plants for tactical systems applications  

Microsoft Academic Search

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

C. Neal Stewart Jr.

2002-01-01

105

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

NASA Astrophysics Data System (ADS)

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

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

2008-02-01

106

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

Microsoft Academic Search

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

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

2005-01-01

107

Investigation of the antigenic evolution of field isolates using the reverse genetics system of infectious bursal disease virus (IBDV)  

Microsoft Academic Search

The antigenic profiles of over 300 infectious bursal disease virus (IBDV) isolates were analyzed using a panel of monoclonal\\u000a antibodies in a reverse genetics system. In addition, the sequences of a large portion of the neutralizing-antibody-inducing\\u000a VP2 of IBDV were determined. Phylogenetic analysis of nucleotide and amino acid sequences in combination with the antigenic\\u000a profiles obtained using the monoclonal antibody

Vijay Durairaj; Holly S. Sellers; Erich G. Linnemann; Alan H. Icard; Egbert Mundt

108

Generation of an external guide sequence library for a reverse genetic screen in Caenorhabditis elegans  

PubMed Central

Background A method for inhibiting the expression of particular genes using external guide sequences (EGSs) has been developed in bacteria, mammalian cells and maize cells. Results To examine whether EGS technology can be used to down-regulate gene expression in Caenorhabditis elegans (C. elegans), we generated EGS-Ngfp-lacZ and EGS-Mtgfp that are targeted against Ngfp-lacZ and Mtgfp mRNA, respectively. These EGSs were introduced, both separately and together, into the C. elegans strain PD4251, which contains Ngfp-lacZ and Mtgfp. Consequently, the expression levels of Ngfp-lacZ and Mtgfp were affected by EGS-Ngfp-lacZ and EGS-Mtgfp, respectively. We further generated an EGS library that contains a randomized antisense domain of tRNA-derived EGS ("3/4 EGS"). Examination of the composition of the EGS library showed that there was no obvious bias in the cloning of certain EGSs. A subset of EGSs was randomly chosen for screening in the C. elegans strain N2. About 6% of these EGSs induced abnormal phenotypes such as P0 slow postembryonic growth, P0 larval arrest, P0 larval lethality and P0 sterility. Of these, EGS-35 and EGS-83 caused the greatest phenotype changes, and their target mRNAs were identified as ZK858.7 mRNA and Lin-13 mRNA, respectively. Conclusion EGS technology can be used to down-regulate gene expression in C. elegans. The EGS library is a research tool for reverse genetic screening in C. elegans. These observations are potentially of great importance to further our understanding and use of C. elegans genomics.

Yan, Qitao; Zhao, Rui; Zheng, Wenlin; Yin, Changxin; Zhang, Bao; Ma, Wenli

2009-01-01

109

Clinical application of multiple displacement amplification in preimplantation genetic diagnosis  

Microsoft Academic Search

Multiple displacement amplification (MDA) is a technique used in the amplification of very small amounts of DNA. MDA is reported to yield large quantities of high-quality DNA. The applicability of MDA to single cells was recently demonstrated as a potential technique for preimplantation genetic diagnosis (PGD). This paper shows the first clinical application of MDA in PGD. Two cycles of

Ali Hellani; Serdar Coskun; Abdelghhani Tbakhi; Saad Al-Hassan

2005-01-01

110

Applications of Genetic Programming in Cancer Research  

PubMed Central

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

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

2012-01-01

111

Environmental Optimization: Applications of Genetic Algorithms  

Microsoft Academic Search

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

Sue Ellen Haupt

112

Reverse engineering the genotype-phenotype map with natural genetic variation  

Microsoft Academic Search

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

Matthew V. Rockman

2008-01-01

113

Applicability of One-factor Mean-reversion Equation to Electricity Price in Deregulated Markets  

NASA Astrophysics Data System (ADS)

One-factor mean-reversion equation (OFMRE) having three parameters of reversion speed, mean-reversion level, and volatility is a mathematical model to simulate a characteristic of electricity price which tends to revert to the mean-reversion level with a random walk. An applicability of OFMRE to 1 year, 3 months, and 2 months-periods of electricity price at three foreign deregulated day-ahead spot markets (Nord Pool, National Electricity Market of Australia, and PJM day-ahead market) at year 2000-2001 was studied. 1 year-period of electricity price at all the markets could not be applied to OFMRE, but several 3 months-period or 2 months-period of the electricity price at Nord Pool and PJM day-ahead market could be applied, which was related with price spike appearances and/or normal distribution of the electricity price.

Kumagai, Seiji; Sato, Masashi; Yoshimura, Noboru

114

Degree of sex reversal as related to plasma steroid levels in genetic female chickens (Gallus domesticus) treated with Fadrozole.  

PubMed

The objectives of this work were to determine whether or not plasma levels of testosterone and estradiol reflect the various grades of sex reversal in genetic female chickens treated with Fadrozole (CGS 16949 A), a nonsteroidal aromatase inhibitor, and whether gonadal aromatase activity and plasma levels of testosterone and estradiol in treated females can or not be modified by post-hatch treatments with Fadrozole or Fadrozole + testosterone. Eggs were injected with 1 mg Fadrozole on day 4 of incubation. In females having developed sex-reversed gonads, endocrine parameters (estradiol and testosterone) at and after 13 weeks of age were indicative of the degree of sex reversal, with, for example, sex-reversed females with two testes having the highest levels of testosterone and the lowest levels of estradiol. Among these females, eight (from a total of 13) produced ejaculates with scarce and abnormal spermatozoa. Some motility was observable in the ejaculates from five of them. None of the post-hatch treatments had a significant effect on plasma levels of testosterone or estradiol (measured at 3-week intervals from week 4 to week 28 post-hatch) or on gonadal aromatase activity (measured at 12 and 28 weeks). In conclusion, these results indicate that plasma levels of testosterone and estradiol at and after 13 weeks of age are valuable indicators of the degree of sex reversal in female chickens treated with Fadrozole prior to gonadal sex differentiation. In pre-cited conditions, post-natal treatments with either Fadrozole or Fadrozole + testosterone had no apparent effect on the degree of sex reversal in these birds. Finally, the occurrence of ejaculates with motile although scarce and abnormal spermatozoa, revealed that epididymes and ducti deferens can develop and become functional in sex-reversed female chickens. PMID:12840815

Vaillant, S; Guémené, D; Dorizzi, M; Pieau, C; Richard-Mercier, N; Brillard, J-P

2003-08-01

115

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

PubMed Central

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

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

2012-01-01

116

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

117

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

118

Application of genetic based fuzzy systems to hydroelectric generation scheduling  

SciTech Connect

An application of genetic based fuzzy systems to hydroelectric generation scheduling is presented in this paper. In the proposed approach, the system was fuzzified with respect to objectives and constraints. A genetic algorithm was included to further enhance the process of tuning membership functions. By this way, membership mappings for those important parameters can be optimally adjusted. The computation performance is thus improved. The proposed approach has been tested on Taiwan Power System (Taipower) through the utility data. Test results have demonstrated are feasibility and effectiveness of the proposed approach for the applications.

Huang, S.J.

1999-09-01

119

An Automated Approach in Reverse Engineering Java Applications Using Petri Nets  

Microsoft Academic Search

In this paper, we propose a new approach for reverse engineering Java applications into Petri Net structures. Our approach rests on utilizing the foundations of Petri Nets as a means of uncovering certain attributes of interests. Petri Nets offers techniques of predicting path execution, flow complexity, dead paths, and resource utilization. The conclusion of this work will provide the strengths

Jared Fuhs; James Cannady

2004-01-01

120

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

Microsoft Academic Search

This dissertation describes a model for acoustic propagation in inhomogeneous fluids, and explores the focusing by arrays onto targets under various conditions. The work explores the use of arrays, in particular the time reversal array, for underwater and biomedical applications. Aspects of propagation and phasing which can lead to reduced focusing effectiveness are described. An acoustic wave equation was derived

Ibrahim M. Hallaj

1999-01-01

121

Hybrid Stirling \\/ Reverse Brayton and Multistage Brayton Cryocoolers for Space Applications  

Microsoft Academic Search

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

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

2006-01-01

122

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

123

Genetic diagnosis in pediatric cardiomyopathy: clinical application and research perspectives  

PubMed Central

There has been tremendous growth in the application of genetics to the clinical practice of pediatric cardiomyopathy. The identification of the genetic basis for cardiomyopathies is important for establishing a causal diagnosis, providing definitive identification of at risk family members, and providing cost-effective screening and surveillance. Additional research is needed to better understand the genetic heterogeneity of cardiomyopathy in children, the implications of specific genotypes, the best approach to cardiac surveillance and genetic testing, and the utility of genotyping for individual risk stratification. As the technology for evaluation of the human genome continues to improve, there is an increasing need for assessment of clinical relevance and utility. This is coupled with an ongoing need for education and training of professionals to interpret and implement genomics in a clinical setting.

Ware, Stephanie M.

2011-01-01

124

Using medical genetics applications to educate for computer competence.  

PubMed Central

This article proposes specific areas of computing competence and illustrates how these skills can be acquired as an integral part of the curriculum of medical genetics. Geneticists are at the forefront in the use of computers for medical care, because of the driving force of the Human Genome Project. Computer searching of international data bases is the most efficient method to keep current with the explosion in molecular genetics data and with its immediate relevance to clinical care. The use of computers in genetics education could go far beyond the use of computer-assisted instruction (CAI) to show how to use computer systems to assist with clinical decisions. The proposed basic computer skills can be obtained using genetics software. The six proposed skills include the use of (1) microcomputers, (2) productivity software, (3) CAI, patient simulations and specific application programs, (4) remote computers, (5) data bases and knowledge bases, and (6) computers to improve the clinical care of patients.

Mitchell, J A

1991-01-01

125

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

Microsoft Academic Search

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

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

2009-01-01

126

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

SciTech Connect

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

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

1999-11-01

127

Application of genetic algorithm to bridge construction management  

Microsoft Academic Search

Genetic algorithms (GA) have attracted attention in recent years as a method of solving combinatorial optimization problems. This research is an application of these algorithms to the problem of determining the laying sequence for a continuous girder reinforced concrete floor system. If the number of design variables and the number of combinations are large, it is often impossible to obtain

Y. Natsuaki; H. Furuta; S. Mukandai; K. Yasuda

1995-01-01

128

Imaging and Genetics: Future Applications in the Emergency Room  

Microsoft Academic Search

Developments in brain imaging and genetics are revolutionizing our understanding of behavior, particularly the role of neurobiology in aggression and violence. In the emergency room (ER), these develop- ments will have special application for the evaluation of patients who are assaultive and potentially homicidal. Though useful, traditional psychiatric diagnosis with its focus on categoric conditions such as personality disorders, schizophrenia,

Laurence R. Tancredi

2009-01-01

129

Genetic Algorithm Application to the Standard Arabic Phonemes Classification  

Microsoft Academic Search

The goal of this article is the application of genetic algorithms (GAs) to the automatic speech recognition (ASR) domain at the acoustic sequences classification level. Speech recognition has been cast as a pattern classification problem where we would like to classify an input acoustic signal into one of all possible phonemes. Also, the supervised classification has been formulated as a

M. Aissiou; M. Guerti

2008-01-01

130

Reverse Genetics Modification of Cytomegalovirus Antigenicity and Immunogenicity by CD8 T-Cell Epitope Deletion and Insertion  

PubMed Central

The advent of cloning herpesviral genomes as bacterial artificial chromosomes (BACs) has made herpesviruses accessible to bacterial genetics and has thus revolutionised their mutagenesis. This opened all possibilities of reverse genetics to ask scientific questions by introducing precisely accurate mutations into the viral genome for testing their influence on the phenotype under study or to create phenotypes of interest. Here, we report on our experience with using BAC technology for a designed modulation of viral antigenicity and immunogenicity with focus on the CD8 T-cell response. One approach is replacing an intrinsic antigenic peptide in a viral carrier protein with a foreign antigenic sequence, a strategy that we have termed “orthotopic peptide swap”. Another approach is the functional deletion of an antigenic peptide by point mutation of its C-terminal MHC class-I anchor residue. We discuss the concepts and summarize recently published major scientific results obtained with immunological mutants of murine cytomegalovirus.

Lemmermann, Niels A. W.; Kropp, Kai A.; Seckert, Christof K.; Grzimek, Natascha K. A.; Reddehase, Matthias J.

2011-01-01

131

Comparison between approximate entropy, correntropy and time reversibility: application to uterine electromyogram signals.  

PubMed

Detection of nonlinearity should be the first step before any analysis of nonlinearity or nonlinear behavior in biological signal. The question is which method should be used in each case and which one can best respect the different characteristics of the signals under investigation. In this paper we compare three methods widely used in nonlinearity detection: approximate entropy, correntropy and time reversibility. The false alarm rates with the numbers of surrogates for the three methods were computed on linear, nonlinear stationary and nonlinear nonstationary signals. The results indicate the superiority of time reversibility over the other methods for detecting linearity and nonlinearity in different signal types. The application of time reversibility on uterine electromyographic signal showed very good performance in classifying pregnancy and labor signals. PMID:21497127

Hassan, Mahmoud; Terrien, Jérémy; Marque, Catherine; Karlsson, Brynjar

2011-04-15

132

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

PubMed

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 2(9) 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, Nantawan; Lekcharoensuk, Chalermpol; Auewarakul, Prasert; Richt, Juergen A

2012-01-09

133

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.

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

2012-01-01

134

Physiology and genetic traits of reverse osmosis membrane biofilms: a case study with Pseudomonas aeruginosa  

Microsoft Academic Search

Biofilm formation of Pseudomonas aeruginosa on the surface of a reverse osmosis (RO) membrane was studied using a synthetic wastewater medium to simulate conditions relevant to reclamation of secondary wastewater effluent. P. aeruginosa biofilm physiology and spatial activity were analyzed following growth on the membrane using a short-life green fluorescent protein derivative expressed in a growth-dependent manner. As a consequence

Moshe Herzberg; Menachem Elimelech

2008-01-01

135

Frequent mutation reversion inversely correlates with clinical severity in a genetic liver disease, hereditary tyrosinemia.  

PubMed

Hereditary tyrosinemia type I (HTI), a severe disease affecting primarily the liver, is caused by a deficiency of fumarylacetoacetate hydrolase (FAH). HTI is clinically heterogeneous, with no correlation between genotype and phenotype. Reversion of FAH mutant alleles in livers of HTI patients was reported previously, but the clinical significance of this phenomenon has not been fully documented. In the present study, the mosaic expression of FAH was analyzed by immune cytochemistry in liver specimens from a cohort of 26 French-Canadian HTI patients who underwent liver transplantation and related to the histopathologic status of the liver and the clinical history. Reversion was observed in 88% of patients with reverted surfaces ranging from 0.1% to 85%. Patients with the chronic form had a much higher surface of reversion (average, 36%) than those with the acute form (average, 1.6%) and a lower incidence of liver dysplasia. Within reverted nodules, hepatocytes had a normal appearance and showed no dysplasia. Hepatocellular carcinoma was observed only in FAH-negative regions. In summary, the extent of mutation reversion of the FAH gene in the liver of HTI patients was inversely correlated with the clinical severity of the disease, suggesting that the corrected hepatocytes play a substantial protective role in liver function. PMID:14691918

Demers, Sylvie I; Russo, Pierre; Lettre, Francine; Tanguay, Robert M

2003-12-01

136

Expanding applications of chemical genetics in signal transduction  

PubMed Central

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

Carlson, Scott M.; White, Forest M.

2012-01-01

137

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

PubMed

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

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

2005-10-15

138

Network Model and Optimization of Medical Waste Reverse Logistics by Improved Genetic Algorithm  

Microsoft Academic Search

The medical waste management is of great importance because of the potential environmental hazards and public health risks.\\u000a Manufacturers have to collect the medical waste and control its recovery or disposal. Medical waste recovery, which encompasses\\u000a reusing, remanufacturing and materials recycling, requires a specially structured reverse logistics network in order to collect\\u000a the medical waste efficiently. This paper presents a

Lihong Shi; Houming Fan; Pingquan Gao; Hanyu Zhang

2009-01-01

139

Effect of Host Genetic Variation on the Pharmacokinetics and Clinical Response of Non-nucleoside Reverse Transcriptase Inhibitors  

PubMed Central

Non-nucleoside reverse transcriptase inhibitors (NNRTIs) have been used widely for treating human immunodeficiency virus type 1 (HIV-1) infected patients as a component of highly active antiretroviral therapy (HAART) and for the prevention of mother-to-child transmission (MTCT). Cytochrome P450 (CYP) 2B6 is an important hepatic isoenzyme responsible for the metabolism of NNRTIs including efavirenz and nevirapine. Recent pharmacogenetic studies have shown that CYP2B6 genetic variants alter hepatic CYP2B6 protein expression and function, and the pharmacokinetics of several CYP2B6 substrates. In particular, the CYP2B6-G516T polymorphism in exon 4 affects the pharmacokinetics of efavirenz. Other studies have shown associations of the CYP2B6-G516T genotype with nevirapine pharmacokinetics and central nervous system adverse effects related to efavirenz use. In total, CYP2B6 genetic variants are important determinants of efavirenz and nevirapine pharmacokinetics . Further studies are needed to identify the associations of CYP2B6 genetic variants with the development of NNRTI resistant viruses.

Saitoh, Akihiko; Spector, Stephen A.

2010-01-01

140

Reverse-genetic approaches to the study of Borna disease virus  

Microsoft Academic Search

Borna disease virus (BDV) is an enveloped virus that has a non-segmented, negative-strand RNA genome with the characteristic organization of the mononegaviruses. However, based on its unique genetic and biological features, BDV is considered to be the prototypic member of a new mononegavirus family, the Bornaviridae. BDV causes central nervous system (CNS) disease in a wide variety of mammals. This

Juan C. de la Torre

2006-01-01

141

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

2011-11-03

142

In situ reverse transcription, an approach to characterize genetic diversity and activities of prokaryotes.  

PubMed

Reverse transcription of RNA molecules inside intact bacterial cells was carried out by using reverse transcriptase with a single oligonucleotide complementary to specific 16S rRNA or mRNA sequences. Fluorescently labeled nucleotides were incorporated into each transcribed cDNA inside cells. This protocol is termed in situ reverse transcription (ISRT). In this study, by using species-specific primers targeting unique regions of the 16S rRNA sequences, ISRT was used successfully to detect and enumerate the two lignin-degrading bacteria Microbulbifer hydrolyticus IRE-31 and Sagittula stellata E-37 in culture mixtures and complex enrichment communities selected for lignin degradation. Image analysis revealed that M. hydrolyticus IRE-31 and S. stellata E-37 accounted for approximately 30 and 2%, respectively, of the total bacterial cells in lignin enrichment communities. Populations estimated by ISRT were comparable to those estimated by in situ hybridization (ISH) techniques and to those estimated by hybridization against extracted community DNA. ISRT was also successfully used to detect Pseudomonas putida F1 expressing the todC1 gene in seawater exposed to toluene vapor. ISRT provided a higher signal intensity than ISH, especially when targeting mRNA. The calculated pixel intensities resulting from ISRT were up to 4.2 times greater than those from ISH. This suggests that multiple incorporation of fluorescently labeled nucleotides into cDNA provides a high sensitivity for phylogenetic identification of bacterial populations as well as detection of cells expressing a specific functional gene within complex bacterial communities. PMID:16535753

Chen, F; Gonzalez, J M; Dustman, W A; Moran, M A; Hodson, R E

1997-12-01

143

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

PubMed Central

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

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

2010-01-01

144

Blue light- and genetically-reversed gravitropic response in protonemata of the moss Ceratodon purpureus.  

PubMed

In darkness, protonemal filaments of Ceratodon purpureus (Brid.) grow negatively gravitropically (upwards). Red light induces a positive phototropic response mediated by the photoreceptor phytochrome. A red light treatment also has an inhibitory effect on the gravitropic response, an effect also mediated by phytochrome. In this study the effects of blue light on phototropism and on gravitropism were analysed. Unilateral blue light resulted in only a weak phototropic response, but markedly randomised growth direction. Blue light given together with a gravitropic stimulus reversed the gravitropism, changing it from negative to positive (filaments grow downward). The effect of blue light was also analysed with the mutant ptr116, which is defective in the biosynthesis of the phytochrome chromophore, and in a newly isolated mutant wwr2, which is positively gravitropic in darkness. Blue light induced the same reversal of gravitropism in ptrll6 as in the wild type, indicating that phytochrome is not involved in this process. In wwr2 the direction of gravitropism was unaltered by the blue light treatment. Light also affects chlorophyll content and the size of plastids, potential statoliths for gravitropism. Red light induced an increase in plastid size and chlorophyll content in the wild type but not in ptr116. Blue light induced a similar change in wild type plastids. It seems as though light-induced alterations of gravitropism are not simply mediated by alterations in plastid properties, and that red light and blue light evoke fundamentally different responses. PMID:11536885

Lamparter, T; Hughes, J; Hartmann, E

1998-09-01

145

Reverse Genetics System for Uukuniemi Virus (Bunyaviridae): RNA Polymerase I-Catalyzed Expression of Chimeric Viral RNAs  

PubMed Central

We describe here the development of a reverse genetics system for the phlebovirus Uukuniemi virus, a member of the Bunyaviridae family, by using RNA polymerase I (pol I)-mediated transcription. Complementary DNAs containing the coding sequence for either chloramphenicol acetyltransferase (CAT) or green fluorescent protein (GFP) (both in antisense orientation) were flanked by the 5?- and 3?-terminal untranslated regions of the Uukuniemi virus sense or complementary RNA derived from the medium-sized (M) RNA segment. This chimeric cDNA (pol I expression cassette) was cloned between the murine pol I promoter and terminator and the plasmid transfected into BHK-21 cells. When such cells were either superinfected with Uukuniemi virus or cotransfected with expression plasmids encoding the L (RNA polymerase), N (nucleoprotein), and NSs (nonstructural protein) viral proteins, strong CAT activity or GFP expression was observed. CAT activity was consistently stronger in cells expressing L plus N than following superinfection. No activity was seen without superinfection, nor was activity detected when either the L or N expression plasmid was omitted. Omitting NSs expression had no effect on CAT activity or GFP expression, indicating that this protein is not needed for viral RNA replication or transcription. CAT activity could be serially passaged to fresh cultures by transferring medium from CAT-expressing cells, indicating that recombinant virus containing the reporter construct had been produced. In summary, we demonstrate that the RNA pol I system, originally developed for influenza virus, which replicates in the nucleus, has strong potential for the development of an efficient reverse genetics system also for Bunyaviridae members, which replicate in the cytoplasm.

Flick, Ramon; Pettersson, Ralf F.

2001-01-01

146

A unique series of reversibly switchable fluorescent proteins with beneficial properties for various applications  

PubMed Central

Reversibly switchable fluorescent proteins (RSFPs) have attracted widespread interest for emerging techniques including repeated tracking of protein behavior and superresolution microscopy. Among the limited number of RSFPs available, only Dronpa is widely employed for most cell biology applications due to its monomeric and other favorable photochemical properties. Here we developed a series of monomeric green RSFPs with beneficial optical characteristics such as high photon output per switch, high photostability, a broad range of switching rate, and pH-dependence, which make them potentially useful for various applications. One member of this series, mGeos-M, exhibits the highest photon budget and localization precision potential among all green RSFPs. We propose mGeos-M as a candidate to replace Dronpa for applications such as dynamic tracking, dual-color superresolution imaging, and optical lock-in detection.

Chang, Hao; Zhang, Mingshu; Ji, Wei; Chen, Juanjuan; Zhang, Yongdeng; Liu, Bei; Lu, Jingze; Zhang, Junlong; Xu, Pingyong; Xu, Tao

2012-01-01

147

Development of a highly effective T-DNA inserted mutant screening method in a Chinese cabbage ( Brassica rapa L. spp. pekinensis ) reverse genetics system  

Microsoft Academic Search

We present a highly effective T-DNA inserted gene screening method as part of a reverse genetics model system using the Chinese\\u000a cabbage (Brassica rapa L. spp. pekinensis). Three-step two-dimensional (2D) matrix strategies are potentially accurate and useful for the identification of specific\\u000a T-DNA inserted mutants from a large population. To construct our Chinese cabbage model, we utilized a forward genetics

Gi-Ho Lee; Yoon-Jee Kang; Seul-Ki Yi; Suk-Bin Lim; Young-Doo Park

2010-01-01

148

The Identification of Candidate Genes for a Reverse Genetic Analysis of Development and Function in the Arabidopsis Gynoecium1  

PubMed Central

The screening for mutants and their subsequent molecular analysis has permitted the identification of a number of genes of Arabidopsis involved in the development and functions of the gynoecium. However, these processes remain far from completely understood. It is clear that in many cases, genetic redundancy and other factors can limit the efficiency of classical mutant screening. We have taken the alternative approach of a reverse genetic analysis of gene function in the Arabidopsis gynoecium. A high-throughput fluorescent differential display screen performed between two Arabidopsis floral homeotic mutants has permitted the identification of a number of genes that are specifically or preferentially expressed in the gynoecium. Here, we present the results of this screen and a detailed characterization of the expression profiles of the genes identified. Our expression analysis makes novel use of several Arabidopsis floral homeotic mutants to provide floral organ-specific gene expression profiles. The results of these studies permit the efficient targeting of effort into a functional analysis of gynoecium-expressed genes.

Scutt, Charles P.; Vinauger-Douard, Marion; Fourquin, Chloe; Ailhas, Jerome; Kuno, Norihito; Uchida, Kenko; Gaude, Thierry; Furuya, Masaki; Dumas, Christian

2003-01-01

149

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.

2010-01-01

150

Time-reversal symmetry in nonstationary Markov processes with application to some fluctuation theorems.  

PubMed

Nonequilibrium processes require that the density operator of an interacting system with Hamiltonian H(t) = H(0)(t)+?V converges and produces entropy. Employing projection operators in the state space, the density operator is developed to all orders of perturbation and then resummed. In contrast to earlier treatments by Van Hove [Physica 21, 517 (1955)] and others [U. Fano, Rev. Mod. Phys. 29, 74 (1959); U. Fano, in Lectures on the Many-Body Problem, Vol 2, edited by E. R. Caniello (Academic Press, New York, 1964); R. Zwanzig, in Lectures in Theoretical Physics, Vol. III, edited by W. E. Britten, B. W. Downs, and J. Downs (Wiley Interscience, New York, 1961), pp. 116-141; K. M. Van Vliet, J. Math. Phys. 19, 1345 (1978); K. M. Van Vliet, Can. J. Phys. 56, 1206 (1978)], closed expressions are obtained. From these we establish the time-reversal symmetry property P(?,t|?',t') = P?',t'|?,t), where the tilde refers to the time-reversed protocol; also a nonstationary Markovian master equation is derived. Time-reversal symmetry is then applied to thermostatted systems yielding the Crooks-Tasaki fluctuation theorem (FT) and the quantum Jarzynski work-energy theorem, as well as the general entropy FT. The quantum mechanical concepts of work and entropy are discussed in detail. Finally, we present a nonequilibrium extension of Mazo's lemma of linear response theory, obtaining some applications via this alternate route. PMID:23214737

Van Vliet, Carolyne M

2012-11-06

151

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

PubMed Central

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

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

2008-01-01

152

[Genetic biomarkers and personalized medicine: application in cardiovascular pharmacology].  

PubMed

Not all patients respond to drug therapy in a uniform and beneficial fashion. The goal of this article is to describe the contribution of genetic variation to drug response, with a focus on drugs used in cardiovascular therapy. The rapid development of techniques in the area of genome analysis has facilitated identification of new pharmacogenomic biomarkers that can provide predictive tools for improvement of drug response and fewer incidence of adverse drug reactions. Such biomarkers mainly originate from genes encoding drug-metabolizing enzymes, drug transporters, drug targets and human leukocyte antigens. However, despite significant progress in pharmacogenomic research, only a few drugs require a pharmacogenetic test before prescription. Among the several gaps that limit the application of pharmacogenetics, it deserves to be mentioned the complex nature of drug response, that makes difficult to disentangle the interplay between genetics and environment leading to pharmacological phenotype. We have to spare no effort in the identification of genetic biomarkers related to the pathogenesis of the diseases and therapeutic targets. It may help clinicians to individualize dosing drug regimen, maximize drug efficacy and enhance drug safety with certain drugs and populations at risk. PMID:23427736

Carrillo Norte, Juan Antonio

2013-01-01

153

Synchronized time-reversal focusing with application to remote imaging from a distant virtual source array.  

PubMed

Time-reversing the transfer function between a time-reversal mirror (TRM) and a distant probe source location generates an acoustic spatio-temporal focus at the location. It is shown that a TR focus behaves as a "virtual" source (in the far-field limit) in the outbound direction with respect to the TRM. By extension, a collection of TRM-to-probe source transfer functions constitutes a virtual source array (VSA) that can serve as a remote platform for active imaging methods such as beam-steering and other coherent wavefront techniques. As a demonstration, a set of a-priori sampled TRM-to-VSA transfer functions are steered to coherently focus at a selected location beyond the VSA for which the transfer function is not known a-priori. In this case the VSA acts as a lens that refocuses the TRM field to the target location. Under proper conditions, the resolution is comparable to that of standard TR. While the specific application of active focusing is presented as a validation of the concept, the relationship between coherent focusing and the transfer function implies that the virtual array concept may find use in a range of imaging methods, both active and passive. Possible applications are discussed, and simulation and experimental results are presented. PMID:19507965

Walker, S C; Roux, Philippe; Kuperman, W A

2009-06-01

154

Reversal of cognitive impairment in an elderly parkinsonian patient by transcranial application of picotesla electromagnetic fields.  

PubMed

A 74 year old retired building inspector with a 15 year history of Parkinson's disease (PD) presented with severe resting tremor in the right hand, generalized bradykinesia, difficulties with the initiation of gait with freezing, mental depression and generalized cognitive impairment despite being fully medicated. Testing of constructional abilities employing various drawing tasks demonstrated drawing impairment compatible with severe left hemispheric dysfunction. After receiving two successive transcranial applications, each of 20 minutes duration, with AC pulsed electromagnetic fields (EMFs) of 7.5 picotesla flux density and frequencies of 5Hz and 7Hz respectively, his tremor remitted and there was dramatic improvement in his drawing performance. Additional striking improvements in his drawing performance occurred over the following two days after he continued to receive daily treatments with EMFs. The patient's drawings were subjected to a Reliability Test in which 10 raters reported 100% correct assessment of pre- and post drawings with all possible comparisons (mean 2 = 5.0; p < .05). This case demonstrates in PD rapid reversal of drawing impairment related to left hemispheric dysfunction by brief transcranial applications of AC pulsed picotesla flux density EMFs and suggests that cognitive deficits associated with Parkinsonism, which usually are progressive and unaffected by dopamine replacement therapy, may be partly reversed by administration of these EMFs. Treatment with picotesla EMFs reflects a "cutting edge" approach to the management of cognitive impairment in Parkinsonism. PMID:9394215

Sandyk, R

1997-09-01

155

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.

2012-01-01

156

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

PubMed Central

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

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

2010-01-01

157

Evolution of a persistent aphthovirus in cytolytic infections: partial reversion of phenotypic traits accompanied by genetic diversification.  

PubMed

Foot-and-mouth disease virus (FMDV) shows a dual potential to be cytolytic or to establish persistent infections in cell culture. FMDV R100, a virus rescued after 100 passages of carrier BHK-21 cells persistently infected with FMDV clone C-S8c1, showed multiple genetic and phenotypic alterations relative to the parental clone C-S8c1. Several FMDV R100 populations have been subjected to 100 serial cytolytic infections in BHK-21 cells, and the reversion of phenotypic and genetic alterations has been analyzed. An extreme temperature sensitivity of R100 reverted totally or partially in some passage series but not in others. The small-plaque morphology reverted to normal size in all cases. The hypervirulence for BHK-21 cells did not revert, and even showed an increase, upon cytolytic passage. Most of the mutations that had been fixed in the R100 genome during persistence did not revert in the course of cytolytic passages, but the extended polyribocytidylate tract of R100 (about 460 residues, versus 290 in C-S8c1) decreased dramatically in length, to the range of 220 to 260 residues in all passage series examined. In passages involving very large viral populations, a variant with two amino acid substitutions (L-144-->V and A-145-->P) next to the highly conserved Arg-Gly-Asp (RGD motif; positions 141 to 143) within the G-H loop of capsid protein VP1 became dominant. A clonal analysis allowed isolation of a mutant with the single replacement A-145-->P. Viral production and growth competition experiments showed the two variants to have a fitness very close to that of the parental virus. The results provide evidence that the repertoire of variants that could potentially become dominant in viral quasispecies may be influenced by the population size of the evolving virus. The net results of a series of persistent-infection passages followed by a series of cytolytic passages was progressive genomic diversification despite reversion or stasis of phenotypic traits. Implications for the evolution of RNA viruses are discussed. PMID:8794296

Sevilla, N; Domingo, E

1996-10-01

158

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

Microsoft Academic Search

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

Jean-Louis Thomas; Mathias A. Fink

1996-01-01

159

Reverse genetics provides direct evidence for a correlation of hemagglutinin cleavability and virulence of an avian influenza A virus.  

PubMed

To obtain direct evidence for a relationship between hemagglutinin (HA) cleavability and the virulence of avian influenza A viruses, we generated a series of HA cleavage mutants from a virulent virus, A/turkey/Ontario/7732/66 (H5N9), by reverse genetics. A transfectant virus containing the wild-type HA with R-R-R-K-K-R at the cleavage site, which was readily cleaved by endogenous proteases in chicken embryo fibroblasts (CEF), was highly virulent in intramuscularly or intranasally/orally inoculated chickens. By contrast, a mutant containing the HA with an avirulent-like sequence (R-E-T-R) at the cleavage site, which was not cleaved by the proteases in CEF, was avirulent in chickens, indicating that a genetic alteration confined to the HA cleavage site can affect cleavability and virulence. Mutant viruses with HA cleavage site sequences of T-R-R-K-K-R or T-T-R-K-K-R were as virulent as viruses with the wild-type HA, whereas a mutant with a two-amino-acid deletion but retention of four consecutive basic residues (R-K-K-R) was as avirulent as a virus with the avirulent-type HA. Interestingly, although a mutant containing an HA with R-R-R-K-T-R, which has reduced cleavability in CEF, was as virulent as viruses with high HA cleavability when given intramuscularly, it was less virulent when given intranasally/orally. We conclude that the degree of HA cleavability in CEF predicts the virulence of avian influenza viruses. PMID:8151777

Horimoto, T; Kawaoka, Y

1994-05-01

160

Time-reversal symmetry in nonstationary Markov processes with application to some fluctuation theorems  

NASA Astrophysics Data System (ADS)

Nonequilibrium processes require that the density operator of an interacting system with Hamiltonian H(t)=H0(t)+?V converges and produces entropy. Employing projection operators in the state space, the density operator is developed to all orders of perturbation and then resummed. In contrast to earlier treatments by Van Hove [Physica0031-891410.1016/S0031-8914(54)92646-4 21, 517 (1955)] and others [U. Fano, Rev. Mod. Phys.0034-686110.1103/RevModPhys.29.74 29, 74 (1959); U. Fano, in Lectures on the Many-Body Problem, Vol 2, edited by E. R. Caniello (Academic Press, New York, 1964); R. Zwanzig, in Lectures in Theoretical Physics, Vol. III, edited by W. E. Britten, B. W. Downs, and J. Downs (Wiley Interscience, New York, 1961), pp. 116-141; K. M. Van Vliet, J. Math. Phys.0022-248810.1063/1.523833 19, 1345 (1978); K. M. Van Vliet, Can. J. Phys. 56, 1206 (1978)], closed expressions are obtained. From these we establish the time-reversal symmetry property P(?,t|?',t')=P˜(?',t'|?,t), where the tilde refers to the time-reversed protocol; also a nonstationary Markovian master equation is derived. Time-reversal symmetry is then applied to thermostatted systems yielding the Crooks-Tasaki fluctuation theorem (FT) and the quantum Jarzynski work-energy theorem, as well as the general entropy FT. The quantum mechanical concepts of work and entropy are discussed in detail. Finally, we present a nonequilibrium extension of Mazo's lemma of linear response theory, obtaining some applications via this alternate route.

Van Vliet, Carolyne M.

2012-11-01

161

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

NASA Astrophysics Data System (ADS)

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

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

2012-02-01

162

Roles of interferon-gamma and its target genes in schizophrenia: Proteomics-based reverse genetics from mouse to human.  

PubMed

A decreased production of interferon gamma (IFNG) has been observed in acute schizophrenia. In order to explore the possible relationship between IFNG and schizophrenia, we attempted to analyze the differentially expressed proteins in the brains of interferon-gamma knockout (Ifng-KO) mice. Five upregulated and five downregulated proteins were identified with 2D gels and MALDI-TOF/TOF MS analyses in Ifng-KO mouse brain. Of the identified proteins, we focused on creatine kinase brain (CKB) and triose phosphate isomerase 1 (TPI1). Consistent with the proteomic data, reverse transcriptase-mediated PCR, immunoblotting, and immunohistochemistry analyses confirmed that the levels of gene expressions of Ckb and Tpi1 were downregulated and upregulated, respectively. When we analyzed the genetic polymorphisms of the single nucleotide polymorphisms (SNPs) of their human orthologous genes in a Korean population, the promoter SNPs of CKB and TPI1 were weakly associated with schizophrenia. In addition, IFNG polymorphisms were associated with schizophrenia. These results suggest that IFNG and proteins affected by IFNG may play a role in the pathogenesis of schizophrenia. PMID:22623148

Kim, Hak-Jae; Eom, Chi-Yong; Kwon, Joseph; Joo, Jaesoon; Lee, Sujeong; Nah, Seong-Su; Kim, Il-Chul; Jang, Ik-Soon; Chung, Young-Ho; Kim, Seung Il; Chung, Joo-Ho; Choi, Jong-Soon

2012-06-01

163

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

164

Genetically engineered mesenchymal stem cells: applications in spine therapy.  

PubMed

Spine disorders and intervertebral disc degeneration are considered the main causes for the clinical condition commonly known as back pain. Spinal fusion by implanting autologous bone to produce bony bridging between the two vertebrae flanking the degenerated-intervertebral disc is currently the most efficient treatment for relieving the symptoms of back pain. However, donor-site morbidity, complications and the long healing time limit the success of this approach. Novel developments undertaken by regenerative medicine might bring more efficient and available treatments. Here we discuss the pros and cons of utilizing genetically engineered mesenchymal stem cells for inducing spinal fusion. The combination of the stem cells, gene and carrier are crucial elements for achieving optimal spinal fusion in both small and large animal models, which hopefully will lead to the development of clinical applications. PMID:19105619

Aslan, Hadi; Sheyn, Dima; Gazit, Dan

2009-01-01

165

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

Microsoft Academic Search

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

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

2012-01-01

166

The pros and cons of using nanofiltration in lieu of reverse osmosis for indirect potable reuse applications  

Microsoft Academic Search

In recent years, considerable interest has been given to using nanofiltration (NF) in lieu of reverse osmosis (RO) for water reclamation applications. This work first examined the operational and rejection performance of several NF membranes compared to a commonly employed RO (ESPA2) membrane at a water reclamation facility. Rejection performance of the NF membranes mainly differed for monovalent ions, however,

Christopher Bellona; Dean Heil; Christopher Yu; Paul Fu; Jörg E. Drewes

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

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

169

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

170

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

171

Interactions of biomacromolecules with reverse hexagonal liquid crystals: drug delivery and crystallization applications.  

PubMed

Recently, self-assembled lyotropic liquid crystals (LLCs) of lipids and water have attracted the attention of both scientific and applied research communities, due to their remarkable structural complexity and practical potential in diverse applications. The phase behavior of mixtures of glycerol monooleate (monoolein, GMO) was particularly well studied due to the potential utilization of these systems in drug delivery systems, food products, and encapsulation and crystallization of proteins. Among the studied lyotropic mesophases, reverse hexagonal LLC (H(II)) of monoolein/water were not widely subjected to practical applications since these were stable only at elevated temperatures. Lately, we obtained stable H(II) mesophases at room temperature by incorporating triacylglycerol (TAG) molecules into the GMO/water mixtures and explored the physical properties of these structures. The present feature article summarizes recent systematic efforts in our laboratory to utilize the H(II) mesophases for solubilization, and potential release and crystallization of biomacromolecules. Such a concept was demonstrated in the case of two therapeutic peptides-cyclosporin A (CSA) and desmopressin, as well as RALA peptide, which is a model skin penetration enhancer, and eventually a larger macromolecule-lysozyme (LSZ). In the course of the study we tried to elucidate relationships between the different levels of organization of LLCs (from the microstructural level, through mesoscale, to macroscopic level) and find feasible correlations between them. Since the structural properties of the mesophase systems are a key factor in drug release applications, we investigated the effects of these guest molecules on their conformations and the way these molecules partition within the domains of the mesophases. The examined H(II) mesophases exhibited great potential as transdermal delivery vehicles for bioactive peptides, enabling tuning the release properties according to their chemical composition and physical properties. Furthermore, we showed a promising opportunity for crystallization of CSA and LSZ in single crystal form as model biomacromolecules for crystallographic structure determination. The main outcomes of our research demonstrated that control of the physical properties of hexagonal LLC on different length scales is key for rational design of these systems as delivery vehicles and crystallization medium for biomacromolecules. PMID:21315366

Libster, Dima; Aserin, Abraham; Garti, Nissim

2011-01-21

172

Barriers to application of genetically modified lactic acid bacteria  

Microsoft Academic Search

To increase the acceptability of food products containing genetically modified microorganisms it is necessary to provide in an early stage to the consumers that the product is safe and that the product provide a clear benefit to the consumer. To comply with the first requirement a systematic approach to analyze the probability that genetically modified lactic acid bacteria will transform

C. T. Verrips; D. J. C. Berg

1996-01-01

173

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

Microsoft Academic Search

Summary Scientific and technological advances in our under- standing of the nature and consequences of human genetic variation are now allowing genetic determi- nants 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 dis- ease susceptibility loci, providing insights into dis- ease

J. C. Knight

2009-01-01

174

On the applicability of genetic algorithms to protein folding  

Microsoft Academic Search

Discusses the protein folding problem and suggests the use of genetic algorithms for protein folding simulations. The issues of protein energy functions, search algorithms, and folding pathways are discussed. The authors review the current approaches to the protein folding problem, point out the limitations of the approaches, and present the genetic algorithm method, which is based on viewing evolution as

Ron Unger; J. Moult

1993-01-01

175

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.

Alvarez-Castro, Jose M

2012-01-01

176

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

Microsoft Academic Search

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

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

2004-01-01

177

Reversible Suppression of Glutamatergic Neurotransmission of Cerebellar Granule Cells In Vivo by Genetically Manipulated Expression of Tetanus Neurotoxin Light Chain  

Microsoft Academic Search

We developed a novel technique that allowed reversible suppression of glutamatergic neurotransmission in the cerebellar network. We generated two lines of transgenic mice termed Tet and TeNT mice and crossed the two transgenic lines to produce the Tet\\/TeNT double transgenic mice. In the Tet mice, the tetracycline-controlled reverse activator (rtTA) was expressed selectively in cerebellar granule cells by the promoter

Mutsuya Yamamoto; Norio Wada; Yasuji Kitabatake; Dai Watanabe; Masayuki Anzai; Minesuke Yokoyama; Yutaka Teranishi; Shigetada Nakanishi

178

Finite element analysis/hydroburst test data correlation for reverse dome integrated stage application  

NASA Astrophysics Data System (ADS)

The U.S. Army's Missile Integrated Stage ('MIST') program has undertaken the development of an advanced strategic interceptor booster's solid-fueled rocket motor. The primary structural components of this booster are a composite case with full-diameter aft closure opening, a titanium reverse dome, and a forced-deflection nozzle plug housing. Attention is presently given to the correlation between the analytical models used in this program and the hydroburst test data obtained for the MIST reverse dome. It is found that the reverse dome exceeded the minimum required burst pressure of 2300 psig.

Burson, K. S.; Nowakowski, M.; Tiwari, S.

1993-02-01

179

Application of genetic algorithms to constrain shallow elastic parameters using in situ ground inclination measurements  

Microsoft Academic Search

Among the class of global optimization techniques, which includes Monte Carlo and simulated annealing methods, the Genetic Algorithms constitute a new class of methods to solve highly non-linear optimization problems. The issue has generated considerable interest in the field of artificial intelligence, and recently, in some multi-parameter optimization geophysical problems. In this study, we explore the applicability of genetic algorithms

R. Gaulon

1997-01-01

180

Application of fluorescence in situ hybridization (FISH) techniques to fish genetics: a review  

Microsoft Academic Search

The technology is now in place for major advances in the genetics and cytogenetics of fishes at the molecular level. One promising method with broad application is fluorescence in situ hybridization (FISH). Methodologies of FISH and the current and potential uses of these chromosomal techniques in fish genetics are reviewed. Highly repetitive ribosomal genes (rDNAs) and the multicopy genes for

Ruth B. Phillips; Kent M. Reed

1996-01-01

181

Application of Reversible Crosslinking and Co-Treatment in Stabilization and Viral Inactivation of Erythrocytes.  

National Technical Information Service (NTIS)

One aspect of the present invention is a method for storing tissues and cells (typically erythrocytes) having the step of: (1) stabilizing the cells with a reversible stabilizing agent. This method typically will have the additional steps of; (2) loading ...

I. B. Bakaltcheva A. S. Rudolph B. J. Spargo S. B. Leslie T. R. Groel

1998-01-01

182

Application of Reverse Osmosis to the Separation of Substances Derived from Acetonobutylic Fermentation (1983).  

National Technical Information Service (NTIS)

A bench-scale experimentation facility has been developed in order to study the reverse osmosis potential for the concentration process of fermented juices of Jerusalem artichokes. A special attention is given to the system pressure control and the outlet...

B. Roz T. Nenner

1983-01-01

183

Studies on the application of radiation for genetic transformation in higher plants.  

National Technical Information Service (NTIS)

Present research carried out to develop the radiation application on the mutation research of genetic engineering. Some variants selected in M1 generation derived from the plantlet by the nodal stem culture of three potato cultivars irradiated with gamma ...

Y. I. Lee H. S. Song J. S. Kim I. C. Shin S. J. Lee

1992-01-01

184

Application of Hybridized Genetic Algorithms to the Protein Folding Problem.  

National Technical Information Service (NTIS)

The protein folding problem consists of attempting to determine the native conformation of a protein given its primary structure. This study examines various methods of hybridizing a genetic algorithm implementation in order to minimize an energy function...

R. L. Gaulke

1995-01-01

185

Application of sucrose fatty acid ester to reverse micellar extraction of lysozyme  

Microsoft Academic Search

Reverse micellar extraction of lysozyme has been carried out using an organic solution containing a mixture of monoester and polyester of sucrose fatty acid ester. The forward extraction of lysozyme from the feed aqueous phase to the reverse micellar organic phase of the mixture of monoester and polyester of sucrose fatty acid ester at pH 7.2 was strongly dependent upon the

Hidetaka Noritomi; Hiroshi Kowata; Naoki Kojima; Satoru Kato; Kunio Nagahama

2006-01-01

186

Isolation of mtpim Proves Tnt1 a Useful Reverse Genetics Tool in Medicago truncatula and Uncovers New Aspects of AP1-Like Functions in Legumes1  

PubMed Central

Comparative studies help shed light on how the huge diversity in plant forms found in nature has been produced. We use legume species to study developmental differences in inflorescence architecture and flower ontogeny with classical models such as Arabidopsis thaliana or Antirrhinum majus. Whereas genetic control of these processes has been analyzed mostly in pea (Pisum sativum), Medicago truncatula is emerging as a promising alternative system for these studies due to the availability of a range of genetic tools. To assess the use of the retrotransposon Tnt1 for reverse genetics in M. truncatula, we screened a small Tnt1-mutagenized population using degenerate primers for MADS-box genes, known controllers of plant development. We describe here the characterization of mtpim, a new mutant caused by the insertion of Tnt1 in a homolog to the PROLIFERATING INFLORESCENCE MERISTEM (PIM)/APETALA1 (AP1)/SQUAMOSA genes. mtpim shows flower-to-inflorescence conversion and altered flowers with sepals transformed into leaves, indicating that MtPIM controls floral meristem identity and flower development. Although more extreme, this phenotype resembles the pea pim mutants, supporting the idea that M. truncatula could be used to complement analysis of reproductive development already initiated in pea. In fact, our study reveals aspects not shown by analysis of pea mutants: that the mutation in the AP1 homolog interferes with the specification of floral organs from common primordia and causes conversion of sepals into leaves, in addition to true conversion of flowers into inflorescences. The isolation of mtpim represents a proof of concept demonstrating that Tnt1 populations can be efficiently used in reverse genetics screenings in M. truncatula.

Benlloch, Reyes; d'Erfurth, Isabelle; Ferrandiz, Cristina; Cosson, Viviane; Beltran, Jose Pio; Canas, Luis Antonio; Kondorosi, Adam; Madueno, Francisco; Ratet, Pascal

2006-01-01

187

Experimental demonstration of time-reversed reverberation focusing in a rough waveguide. Application to target detection  

NASA Astrophysics Data System (ADS)

For most shallow-water waveguides, the backscattered energy measured in a monostatic configuration is dominated by ocean bottom reverberation. A selected time-gated portion of the measured reverberation signals is used to provide a transfer function between a time-reversing array and a corresponding range interval on the bottom. Ultrasonic and at-sea experiments demonstrate focusing capabilities along the rough bottom interface of a time-reversing array using these reverberation signals only. The iterative time-reversal technique facilitates robust focusing along the ocean bottom, with little signal-processing effort involved and a priori information on the environment, and the enhancement of detection and localization of proud or buried targets in complex shallow-water environments. A passive implementation of the iterative time-reversal processing is used to construct reflectivity maps, similar to a sonar map, but with an enhanced contrast for the strongest reflectors (or scatterers), at the water-bottom interface. Ultrasonic and at-sea experiments show that targets lying on the seafloor located up to 400 wavelengths from the time-reversing array were detected over the bottom reverberation.

Sabra, Karim G.; Roux, Philippe; Song, Hee-Chun; Hodgkiss, William; Kuperman, William A.; Akal, Tuncay; Stevenson, Mark R.

2005-09-01

188

[Preparation and application of internal surface reversed-phase restricted-access material].  

PubMed

A new convenient synthetic method was developed for the preparation of restricted-access material belonging to the group of the internal surface reversed-phase supports, which can be used for the direct injection and analysis of complex biological samples such as plasma samples. The supports, owning the function of reversed-phase chromatography, have an alkyl-chain only to the internal surfaces of the porous silica. Polyvinyl alcoholic groups chemically bound to the external surfaces of the porous silica that has the ability of hydrophilicity. Its structure was characterized by elemental analysis and electron microscope observation. The reversed-phase chromatographic performance was evaluated by using different solute probes, including propranolol, atenolol, phenobarbital and carbamazepine. Meanwhile, the comparative study with Merck Company' s ADS columns was carried out to prove capability of removing protein. At the same time, the plasma sample of propranolol was applied for the determination by direct injections. The results showed that the new internal surface reversed-phase restricted-access material owned the capabilities of protein exclusion and reversed-phase stationary, which could come true the double functions of excluding biomacromolecules and enriching micromolecule analysis. It can be used as a pretreatment column, which has the ability of online and fast analyzing biological specimen by direct probe inlet. PMID:23256384

Wu, Xiaoyu; Wang, Rong; Xie, Hua; Wang, Jianfeng; Yang, Pei; Jia, Zhengping; Zhang, Qiang; Wang, Xianhua

2012-08-01

189

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

PubMed

Contrary to other genetic disorders, the genetic study of sex determination anomalies in humans stumbles over the difficulty in observing large pedigrees. In goats, abnormalities in sex determination are intimately linked to a dominant Mendelian gene coding for the "polled" (hornless) character, which could render this species an interesting animal model for the rare human cases of SRY-negative XX males. In this report, we describe genetic linkage between the polled/intersex synchome (PIS) and four microsatellite markers of the distal region of goat Chromosome 1 (CHI1), quite distinct from the bovine "polled" region. According to comparative mapping data, no sex-determining gene has been described so far in homologous regions in the human. This genetic localization constitutes a first step towards identifying a new autosomal sex-determining gene in mammals. PMID:8835530

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

1996-02-01

190

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

Microsoft Academic Search

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

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

2001-01-01

191

High-Frequency Genetic Reversion Mediated by a DNA Duplication: The Mouse PinkEyed Unstable Mutation  

Microsoft Academic Search

The mouse pink-eyed unstable (pun) mutation, affecting coat color, exhibits one of the highest reported reversion frequencies of any mammalian mutation and is associated with a duplication of genomic DNA at the p locus. In this study, genomic clones containing the boundaries of the pun duplication were isolated and characterized. The structure of these sequences and their wild-type and revertant

Yoichi Gondo; John M. Gardner; Yoshimichi Nakatsu; Donna Durham-Pierre; Susan A. Deveau; Cynthia Kuper; Murray H. Brilliant

1993-01-01

192

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

Microsoft Academic Search

Summary  The luminous intensity of dark variant (S1) separated from photobacterium phosphoreum (A2) was 1\\/10 000 less than that of\\u000a wild-type. Ethidium bromide (EB) (0.6 mg\\/L), Mytomycin C (MC, 0.05 mg\\/L), 2-amino fluorene (2-AF, 1.0 mg\\/L) all could strongly\\u000a induce reversion mutation for S1 within 24 h and increase reversion ratio significantly. The results of experiments indicated\\u000a that these revertants had

Guo Jianli; Sun Yaliang

2002-01-01

193

Hairy Root and Its Application in Plant Genetic Engineering  

Microsoft Academic Search

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

Zhi-Bi Hu

194

QTL x Genetic Background Interaction: Application to Predicting Progeny Value  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

195

An application of the genetic programming technique to strategy development  

Microsoft Academic Search

In this paper, we will apply genetic programming (GP) and co-evolution techniques to develop two strategies: the ghost (attacker) and players (survivors) in the Traffic Light Game (a popular game among children). These two strategies compete against each other. By applying the co-evolution technique alongside GP, each strategy is used as an “imaginary enemy” from which evolves (is trained in)

Koun-tem Sun; Yi-chun Lin; Cheng-yen Wu; Yueh-min Huang

2009-01-01

196

Genetic algorithms and their statistical applications: an introduction  

Microsoft Academic Search

Genetic algorithms (GA) are stochastic optimization tools that work on “Darwinian” models of population biology and are capable of solving for near-optimal solution for multivariable functions without the usual mathematical requirements of strict continuity, differentiability, convexity and other properties. The algorithm begins by choosing a large number of candidate solutions which propagate themselves through a “selection criteria” and are changed

Sangit Chatterjee; Matthew Laudato; Lucy A. Lynch

1996-01-01

197

[The application of genetic engineering to the petroleum biodesulfurization].  

PubMed

The developed course and reaction mechanisms of petroleum biodesulfurization were introduced. The recent development of genetic engineering technology, which used in desulfuration strain's construction, reconstruction and other fields, was summarized emphatically. Its current research situation internal and overseas and the developing prospect were simply analyzed, and our research designs were submitted. PMID:11910751

Tong, M Y; Fang, X C; Ma, T; Zhang, Q

2001-11-01

198

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

199

Molecular genetics applications in fisheries: snake oil or restorative?  

Microsoft Academic Search

Life was once much simpler for Pacific salmon fishery managers. They could aggregate genetic stocks from a region for the convenience of spawning escapement goals and scheduling fisheries, and also designate some regions as hatchery management areas where wild stocks could be overfished to take full advantage of hatchery production capacities. These management tasks could be accomplished without facing an

Rich Lincoln

1994-01-01

200

Applications of Genetic Algorithm in Polymer Science and Engineering  

Microsoft Academic Search

In the last several years, genetic algorithm (GA) has gained wide acceptance as a robust optimization algorithm in almost all areas of science and engineering. Polymer science and engineering is no exception. Researchers in this field have devoted considerable attention to the optimization of polymer productionusing objective functions and constraints that lead to products having desired material properties. Multiple-objective functions

Rahul B. Kasat; Ajay K. Ray; Santosh K. Gupta

2003-01-01

201

Genetic studies in chronic kidney disease: interpretation and clinical applicability.  

PubMed

The tools of modern molecular biology are evolving rapidly, resulting in vastly more efficient approaches to illuminating human genetic variations and their effects on common multifactorial disorders such as chronic kidney disease (CKD). Indeed, candidate gene association studies and genome-wide association studies (GWASs) have generated novel genetic variants in previously unrecognized biological pathways, highlighting disease mechanisms with a potential role in CKD etiology, morbidity and mortality. Nephrologists now need to find ways to make use of these advancements and meet the increasingly stringent requirements for valid study design, data handling and interpretation of genetic studies. Adding to our prior article in this journal, which introduced the basics of genotype-phenotype association studies in CKD, this second article focuses on how to ascertain robust and reproducible findings by applying adequate methodological and statistical approaches to genotype-phenotype studies in CKD populations. Moreover, this review will briefly discuss genotype-based risk prediction, pharmacotherapy, drug target identification and individualized treatment solutions, specifically highlighting potentially important findings in CKD patients. This increased knowledge will hopefully facilitate the exciting transition from conventional clinical medicine to gene-based medicine. However, before this can be accomplished, unsolved issues regarding the complex human genetic architecture as well technical and clinically oriented obstacles will have to be overcome. Additionally, new policies and standardized risk evaluations for genetic testing in the clinical setting will have to be established to guarantee that CKD patients are provided with high-quality genotype-guided counseling that will help to improve their poor outcomes. PMID:23042432

Witasp, Anna; Nordfors, Louise; Carrero, Juan Jesus; Luttropp, Karin; Lindholm, Bengt; Schalling, Martin; Stenvinkel, Peter

202

Some applications of reversal theory to the explanation of gambling and gambling addictions  

Microsoft Academic Search

Reversal theory (Apter, 1982) provides a conceptual framework for the study of homeostatic psychological systems with multiple points of stability. This theory is applied to the explanation of normal and pathological gambling with special attention given to Apter's distinction between Telic (goal oriented) and Paratelic (playful) States. The entry of an individual to an episode of gambling is interpreted as

G. Anderson; R. I. F. Brown

1987-01-01

203

Change in membrane performance due to organic fouling in nanofiltration (NF)\\/reverse osmosis (RO) applications  

Microsoft Academic Search

The effect of fouling by organics on rejection was observed for the removal of 36 neutral trace plastic additives, endocrine disruptors and other organic contaminants. Two membranes (a reverse osmosis membrane and a nanofiltration membrane) with very different volume fluxes and chloride rejections characteristics were used. Membranes were fouled by activated sludge and landfill leachate to simulate long-term membrane condition

Kenneth O. Agenson; Taro Urase

2007-01-01

204

Reversible assembly of magnetized particles: Application to water-borne pathogen enumeration  

NASA Astrophysics Data System (ADS)

Reversible assembly of magnetized particles and cells has been proposed and implemented. The approach is based on magnetized particles or magnetically labeled cell immobilization in an array of individual particle/cell for optical counting. The device has been tested for few types of magnetic particles and one water-borne pathogen: Giardia Lamblia. An individual particle immobilization efficiency of 92% was achieved.

Ramadan, Qasem

2009-12-01

205

A field-reversed magnetic configuration and applications of high-temperature FRC plasma  

SciTech Connect

As applied to a tokomak, a magnetic trap for confinement of a plasma with an inverted field or a magnetic field reversed configuration (FRC) is one of the most promising alternatives of the systems with high {beta}. A brief review of the latest data on FRC and potential directions of using such configurations in addition to energy generation in thermonuclear reactors (TNRs) is proposed.

Ryzhkov, S. V., E-mail: ryzhkov@power.bmstu.ru [Bauman Moscow State Technical University (Russian Federation)

2011-12-15

206

Approximation for the enhancement factor applicable to reversible reactions of finite rate in chemically loaded solutions  

Microsoft Academic Search

A new explicit relation is proposed for the prediction of the enhancement factor for reversible reactions of finite rate in chemically loaded solutions which also allows for unequal diffusivities. The relation for the enhancement factor is not based on an approximation of the absorption process, but is derived from a similarity which can be observed between the results of the

J. A. Hogendoorn; R. D. Vas Bhat; J. A. M. Kuipers; W. P. M. van Swaaij; G. F. Versteeg

1997-01-01

207

Metamotivational characteristics of eating-disordered and exercise-dependent triathletes: an application of reversal theory  

Microsoft Academic Search

Objectives: To compare triathletes with exercise dependence and\\/or eating disorders on their metamotivational characteristics using the framework of Reversal Theory.Design: Participants were classified according to their scores on an eating disorder and an exercise dependence questionnaire into a primary, a secondary, an eating disorder, and a no dependence or disorder group. These groups were contrasted on measures derived from the

Michelle J. Blaydon; Koenraad J. Lindner; John H. Kerr

2002-01-01

208

Some moment properties and limit theorems of the reversed generalized logistic distribution with applications  

Microsoft Academic Search

In this paper we discuss an extended form of the logistic distribution and refer to it as the reversed generalized logistic distribution. We study some moment properties, and derive exact and explicit formulas for the mean, median, mode, variance, coefficients of skewness and kurtosis, and percentage points of this distribution. In addition, we study its limiting distributions as the shape

Mohammed A. El-Saidi; Boyan Dimitrov; Stefanka Chukova

1996-01-01

209

Fourth derivative UV-spectroscopy of proteins under high pressure II. Application to reversible structural changes  

Microsoft Academic Search

The structural basis and the thermodynamics of pressure induced reversible spectral transitions in the fourth derivative ultraviolet absorbance spectra of proteins were analysed as described in the preceding paper. Three proteins were studied: adrenodoxin (a small iron-sulphur protein that serves as an electron donor for cytochrome P450scc), ribonuclease A, and methanol dehydrogenase (a tetrameric protein). Fourth derivative spectroscopy is used

R. Lange; N. Bec; V. V. Mozhaev; J. Frank

1996-01-01

210

Application of Reverse Osmosis to the Separation of Substances Derived from Acetonobutylic Fermentation (1986).  

National Technical Information Service (NTIS)

The main objective of the study was to verify on a large scale prototype plant the concentration process of reverse osmosis applied to fermented juices of Jerusalem artichoke (acetone, n-butanol, ethanol (ABE)) and of beets (isopropanol, n-butanol, ethano...

A. Driancourt R. Dick

1986-01-01

211

Development of a reverse-genetics system for murine norovirus 3: long-term persistence occurs in the caecum and colon  

PubMed Central

Human noroviruses (HuNoV) are a major cause of viral gastroenteritis worldwide, yet, due to the inability to propagate HuNoV in cell culture, murine norovirus (MNV) is typically used as a surrogate to study norovirus biology. MNV-3 represents an attractive strain to study norovirus infections in vivo because it establishes persistence in wild-type mice, yet causes symptoms resembling gastroenteritis in immune-compromised STAT1?/? mice. The lack of reverse-genetics approaches to recover genetically defined MNV-3 has limited further studies on the identification of viral sequences that contribute to persistence. Here we report the establishment of a combined DNA-based reverse-genetics and mouse-model system to study persistent MNV-3 infections in wild-type (C57BL/6) mice. Viral RNA and infectious virus were detected in faeces for at least 56 days after inoculation. Strikingly, the highest concentrations of viral RNA during persistence were detected in the caecum and colon, suggesting that viral persistence is maintained in these tissues. Possible adaptive changes arising during persistence in vivo appeared to accumulate in the minor capsid protein (VP2) and the viral polymerase (NS7), in contrast with adaptive mutations selected during cell-culture passages in RAW264.7 cells that appeared in the major capsid protein (VP1) and non-structural protein NS4. This system provides an attractive model that can be readily used to identify viral sequences that contribute to persistence in an immunocompetent host and to more acute infection in an immunocompromised host, providing new insights into the biology of norovirus infections.

Bailey, Dalan; Chaudhry, Yasmin

2012-01-01

212

Speciation in reverse: morphological and genetic evidence of the collapse of a three-spined stickleback (Gasterosteus aculeatus) species pair.  

PubMed

Historically, six small lakes in southwestern British Columbia each contained a sympatric species pair of three-spined sticklebacks (Gasterosteus aculeatus). These pairs consisted of a 'benthic' and 'limnetic' species that had arisen postglacially and, in four of the lakes, independently. Sympatric sticklebacks are considered biological species because they are morphologically, ecologically and genetically distinct and because they are strongly reproductively isolated from one another. The restricted range of the species pairs places them at risk of extinction, and one of the pairs has gone extinct after the introduction of an exotic catfish. In another lake, Enos Lake, southeastern Vancouver Island, an earlier report suggested that its species pair is at risk from elevated levels of hybridization. We conducted a detailed morphological analysis, as well as genetic analysis of variation at five microsatellite loci for samples spanning a time frame of 1977 to 2002 to test the hypothesis that the pair in Enos Lake is collapsing into a hybrid swarm. Our morphological analysis showed a clear breakdown between benthics and limnetics. Bayesian model-based clustering indicated that two morphological clusters were evident in 1977 and 1988, which were replaced by 1997 by a single highly variable cluster. The most recent 2000 and 2002 samples confirm the breakdown. Microsatellite analysis corroborated the morphological results. Bayesian analyses of population structure in a sample collected in 1994 indicated two genetically distinct populations in Enos Lake, but only a single genetic population was evident in 1997, 2000, and 2002. In addition, genetic analyses of samples collected in 1997, 2000, and 2002 showed strong signals of 'hybrids'; they were genetically intermediate to parental genotypes. Our results support the idea that the Enos Lake species pair is collapsing into a hybrid swarm. Although the precise mechanism(s) responsible for elevated hybridization in the lake is unknown, the demise of the Enos Lake species pair follows the appearance of an exotic crayfish, Pascifasticus lenisculus, in the early 1990s. PMID:16448405

Taylor, E B; Boughman, J W; Groenenboom, M; Sniatynski, M; Schluter, D; Gow, J L

2006-02-01

213

Cassava genetic transformation and its application in breeding.  

PubMed

As a major source of food, cassava (Manihot esculenta Crantz) is an important root crop in the tropics and subtropics of Africa and Latin America, and serves as raw material for the production of starches and bioethanol in tropical Asia. Cassava improvement through genetic engineering not only overcomes the high heterozygosity and serious trait separation that occurs in its traditional breeding, but also quickly achieves improved target traits. Since the first report on genetic transformation in cassava in 1996, the technology has gradually matured over almost 15 years of development and has overcome cassava genotype constraints, changing from mode cultivars to farmer-preferred ones. Significant progress has been made in terms of an increased resistance to pests and diseases, biofortification, and improved starch quality, building on the fundamental knowledge and technologies related to planting, nutrition, and the processing of this important food crop that has often been neglected. Therefore, cassava has great potential in food security and bioenergy development worldwide. PMID:21564542

Liu, Jia; Zheng, Qijie; Ma, Qiuxiang; Gadidasu, Kranthi Kumar; Zhang, Peng

2011-06-22

214

Genetic Algorithms And Its Application To Economic Load Dispatch  

NASA Astrophysics Data System (ADS)

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

Borana, Kavita

2010-11-01

215

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

216

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

217

Clinical application of exome sequencing in undiagnosed genetic conditions  

PubMed Central

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

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

2012-01-01

218

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.

Shirasawa, Kenta; Hirakawa, Hideki

2013-01-01

219

Reverse pharmacognosy: identifying biological properties for plants by means of their molecule constituents: application to meranzin.  

PubMed

Reverse pharmacognosy aims at finding biological targets for natural compounds by virtual or real screening and identifying natural resources that contain the active molecules. We report herein a study focused on the identification of biological properties of meranzin, a major component isolated from Limnocitrus littoralis (Miq.) Swingle. Selnergy, an IN SILICO biological profiling software, was used to identify putative binding targets of meranzin. Among the 400 screened proteins, 3 targets were selected: COX1, COX2 and PPARgamma. Binding tests were realised for these 3 protein candidates, as well as two negative controls. The predictions made by Selnergy were consistent with the experimental results, meaning that these 3 targets can be modulated by an extract containing this compound in a suitable concentration. These results demonstrate that reverse pharmacognosy and its inverse docking component is a powerful tool to identify biological properties for natural molecules and hence for plants containing these compounds. PMID:17853346

Do, Quoc-Tuan; Lamy, Cécile; Renimel, Isabelle; Sauvan, Nancy; André, Patrice; Himbert, Franck; Morin-Allory, Luc; Bernard, Philippe

2007-09-13

220

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

PubMed

This paper presents a protocol for quantitative analysis of microbial communities by reverse sample genome probing is presented in which (i) whole community DNA is isolated and labeled in the presence of a known amount of an added internal standard and (ii) the resulting spiked reverse genome probe is hybridized with a master filter on which denatured genomic DNAs from bacterial standards isolated from the target environment were spotted in large amounts (up to 1,500 ng) in order to improve detection sensitivity. This protocol allowed reproducible fingerprinting of the microbial community in oil field production waters at 19 sites from which water and biofilm samples were collected. It appeared that selected sulfate-reducing bacteria were significantly enhanced in biofilms covering the metal surfaces in contact with the production waters. PMID:16349111

Voordouw, G; Shen, Y; Harrington, C S; Telang, A J; Jack, T R; Westlake, D W

1993-12-01

221

Sequential application of major habit-reversal components to treat motor tics in children.  

PubMed Central

In this study, we sequentially administered up to four components of the habit-reversal treatment to 4 children with motor tics within a multiple baseline design. The habit-reversal components included (a) awareness training; (b) awareness training and self-monitoring; (c) awareness training, self-monitoring, and social support; and (d) awareness training, social support, and the use of a competing response. Results demonstrated that the combined use of awareness training, social support, and competing response training was effective in eliminating motor tics in 2 of 4 children, that awareness training alone was effective for 1 child, and that a combination of awareness training and self-monitoring was effective for the 4th child. The treatment and ensuing improvement were found to be socially valid. We discuss possible explanations for these results and recommend directions for future research.

Woods, D W; Miltenberger, R G; Lumley, V A

1996-01-01

222

Quantitative Reverse Sample Genome Probing of Microbial Communities and Its Application to Oil Field Production Waters  

PubMed Central

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

Voordouw, Gerrit; Shen, Yin; Harrington, Clare S.; Telang, Anita J.; Jack, Thomas R.; Westlake, Donald W. S.

1993-01-01

223

Harnessing reversible oxidative addition: application of diiodinated aromatic compounds in the carboiodination process.  

PubMed

An I for an I: Conditions for the intramolecular carboiodination and the simultaneous convergent intramolecular carboiodination/intermolecular Heck reaction of various diiodoarenes were developed. The ability of the Pd(0) /QPhos catalyst/ligand combination to undergo reversible oxidative addition allows these reactions to proceed well, thus increasing both the appeal and utility of this class of substrates in site-selective cross-coupling reactions. PMID:23939782

Petrone, David A; Lischka, Matthias; Lautens, Mark

2013-08-12

224

APPLICATION OF NANOFILTRATION AND REVERSE OSMOSIS MEMBRANES TO THE SALTY AND POLLUTED SURFACE WATER  

Microsoft Academic Search

Nanofiltration (NF) (TFC-S) and reverse osmosis (RO) (TFC-HR) membranes were evaluated for the treatment of salty and polluted Kucukcekmece Lake used as a drinking water reservoir for the Istanbul City. A thin film composite type of spiral wound membrane (2 m area) was used. Experiments were conducted at different pressures, pH ranges and temperatures. Flowrate was about 300 l\\/h. The

I. Koyuncu; M. Yazgan

2001-01-01

225

REVERSED PHASE LIQUID CHROMATOGRAPHIC DETERMINATION OF VINPOCETINE IN HUMAN PLASMA AND ITS PHARMACOKINETIC APPLICATION  

Microsoft Academic Search

A simple, rapid specific and reliable high performance liquid chromatographic assay of vinpocetine in human plasma has been developed. Reversed phase chromatography was conducted using a mobile phase of methanol : water (80 : 20 v\\/v), containing 0.1% triethylamine, pH 7, adjusted with glacial acetic acid. The flow rate was 2 mL\\/min, UV detection at 274 nm. The drug after extraction from plasma was chromatographed using a C18

A. Abd Elbary; N. Foda; O. El-Gazayerly; M. El Khatib

2002-01-01

226

Low-loss microelectrodes fabricated using reverse-side exposure for a tunable ferroelectric capacitor application  

Microsoft Academic Search

Narrowly spaced thick microelectrodes are fabricated using a self-aligned multiple reverse-side exposure scheme for an improved quality-factor tunable ferroelectric capacitor. The microelectrodes are fabricated on a functional substrate—a thin film ferroelectric (barium strontium titanate, BST; BaxSr1?xTiO3) coated sapphire substrate, which has an electric-field-dependent dielectric property providing tuning functionality, as well as UV transparency permitting an additional degree of freedom in

Yong-Kyu Yoon; J Stevenson Kenney; Andrew T Hunt; Mark G Allen

2006-01-01

227

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

PubMed

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

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

2005-09-01

228

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

229

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.

2011-01-01

230

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

PubMed

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

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

2012-01-01

231

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

232

Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.  

PubMed

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

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

2012-01-09

233

Inducible and Reversible Enhancement of Learning, Memory, and Long-Term Potentiation by Genetic Inhibition of Calcineurin  

Microsoft Academic Search

The threshold for hippocampal-dependent synaptic plasticity and memory storage is thought to be determined by the balance between protein phosphorylation and dephosphorylation mediated by the kinase PKA and the phosphatase calcineurin. To establish whether endogenous calcineurin acts as an inhibitory constraint in this balance, we examined the effect of genetically inhibiting calcineurin on plasticity and memory. Using the doxycycline-dependent rtTA

Gaël Malleret; Ursula Haditsch; David Genoux; Matthew W. Jones; Tim V. P. Bliss; Amanda M. Vanhoose; Carl Weitlauf; Eric R. Kandel; Danny G. Winder; Isabelle M. Mansuy

2001-01-01

234

Obesity: from animal models to human genetics to practical applications.  

PubMed

Although many animal models are used in genetic studies, the mouse is most common. Analysis of single-gene mutations, linkage analysis in crossbred strains, and gene targeting are the primary techniques used to associate obesity phenotypes with specific genes or alleles. The orthologous human gene can then be tested, either in linkage studies in families or in genome-wide association studies (GWAS), for effect on the phenotype. Frequent lack of concordance between mouse and human obesity genes may be due to the difference in phenotypes measured in humans (body mass index) versus mouse (fat mass or % body fat), lack of intermediate phenotypes, and the fact that identified genes account for only a small percentage of the heritability of common obesity, suggesting that many genes remain unknown. New technology allows analysis of individual genomes at a reasonable cost, making large-scale obesity genome projects in humans feasible. Such projects could identify common allelic variants that contribute to obesity and to variable individual response to obesity therapy. Currently, family history may be more predictive than genetics for risk of obesity, but individual testing could ultimately guide therapy and, in the aggregate, guide public health policy. The primary limitation to development of genotype-based diets is that successful randomized diet trials of widely ranging macronutrient content, adequately powered for finding rare Mendelian mutations, have not been performed. PMID:21036332

Warden, Craig H; Fisler, Janis S

2010-01-01

235

Lassa Virus Nucleoprotein Mutants Generated by Reverse Genetics Induce a Robust Type I Interferon Response in Human Dendritic Cells and Macrophages ?  

PubMed Central

Lassa virus (LASV; Arenaviridae) is responsible for severe hemorrhagic fevers in Africa. LASV nucleoprotein (NP) plays important roles in regulating viral transcription and replication and in inhibiting type I interferon (IFN) production. The NP C-terminal domain contains a 3?-to-5? exonuclease activity involved in suppressing IFN induction. We have established a murine polymerase (Pol) I reverse genetics system for LASV, showing that residues D389 and G392 of NP were critical for LASV viability, while the D389A/G392A and D389T/392A double mutants were severely altered in the ability to suppress IFN in macrophages and dendritic cells. Assessing their attenuation in vivo may open new perspectives in vaccinology.

Carnec, Xavier; Baize, Sylvain; Reynard, Stephanie; Diancourt, Laure; Caro, Valerie; Tordo, Noel; Bouloy, Michele

2011-01-01

236

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

237

Ultrasonic Time Reversal Mirrors  

Microsoft Academic Search

For more than ten years, time reversal techniques have been developed in many different fields of applications including detection of defects in solids, underwater acoustics, room acoustics and also ultrasound medical imaging and therapy. The essential property that makes time reversed acoustics possible is that the underlying physical process of wave propagation would be unchanged if time were reversed. In

Mathias Fink; Gabriel Montaldo; Mickael Tanter

2004-01-01

238

Reverse Correlation in Neurophysiology  

ERIC Educational Resources Information Center

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

Ringach, Dario; Shapley, Robert

2004-01-01

239

Application of genetic algorithm in atmospheric carbon dioxide concentration retrieval  

NASA Astrophysics Data System (ADS)

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

Li, Jingyao; Shi, Runhe; Gao, Wei

2013-09-01

240

GENETIC ALGORITHMS FOR WATER DISTRIBUTION NETWORK CALIBRATION: A REAL APPLICATION  

Microsoft Academic Search

This paper presents a method can be used in water network model calibration with a particular application to the Parma water distribution system. Parma is an important city in the north of Italy with about 160.000 inhabitants and about 87.000 water users. The water distribution network covers about 650 Km. The company that manages the water systems in Parma and

ANGELO BORZÌ; ELISA GERBINO; STEFANO BOVIS; MICHELE CORRADINI

241

Studies on the radiation application for development genetic resources.  

National Technical Information Service (NTIS)

For the development of nuclear application technique on the induction and selection of radiation mutation in in vitro and in vivo mutagenesis, several crops plants such as rice, soybean, perilla potato and sweet potato were irradiated with gamma rays of v...

Y. I. Lee H. S. Song J. S. Kim I. C. Shin S. J. Lee

1997-01-01

242

Reverse Transcriptase.  

National Technical Information Service (NTIS)

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

1982-01-01

243

Reverse genetic analysis of Caenorhabditis elegans presenilins reveals redundant but unequal roles for sel-12 and hop-1 in Notch-pathway signaling  

PubMed Central

Mutations in the human presenilin genes PS1 and PS2 cause early-onset Alzheimer’s disease. Studies in Caenorhabditis elegans and in mice indicate that one function of presenilin genes is to facilitate Notch-pathway signaling. Notably, mutations in the C. elegans presenilin gene sel-12 reduce signaling through an activated version of the Notch receptor LIN-12. To investigate the function of a second C. elegans presenilin gene hop-1 and to examine possible genetic interactions between hop-1 and sel-12, we used a reverse genetic strategy to isolate deletion alleles of both loci. Animals bearing both hop-1 and sel-12 deletions displayed new phenotypes not observed in animals bearing either single deletion. These new phenotypes—germ-line proliferation defects, maternal-effect embryonic lethality, and somatic gonad defects—resemble those resulting from a reduction in signaling through the C. elegans Notch receptors GLP-1 and LIN-12. Thus SEL-12 and HOP-1 appear to function redundantly in promoting Notch-pathway signaling. Phenotypic analyses of hop-1 and sel-12 single and double mutant animals suggest that sel-12 provides more presenilin function than does hop-1.

Westlund, Bethany; Parry, Dianne; Clover, Ralph; Basson, Michael; Johnson, Carl D.

1999-01-01

244

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.

245

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

PubMed Central

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

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

2011-01-01

246

Application of resistance gene analog markers to analyses of genetic structure and diversity in rice.  

PubMed

Plant disease resistance gene analog (RGA) markers were designed according to the conserved sequence of known RGAs and used to map resistance genes. We used genome-wide RGA markers for genetic analyses of structure and diversity in a global rice germplasm collection. Of the 472 RGA markers, 138 were polymorphic and these were applied to 178 entries selected from the USDA rice core collection. Results from the RGA markers were similar between two methods, UPGMA and STRUCTURE. Additionally, the results from RGA markers in our study were agreeable with those previously reported from SSR markers, including cluster of ancestral classification, genetic diversity estimates, genetic relatedness, and cluster of geographic origins. These results suggest that RGA markers are applicable for analyses of genetic structure and diversity in rice. However, unlike SSR markers, the RGA markers failed to differentiate temperate japonica, tropical japonica, and aromatic subgroups. The restricted way for developing RGA markers from the cDNA sequence might limit the polymorphism of RGA markers in the genome, thus limiting the discriminatory power in comparison with SSR markers. Genetic differentiation obtained using RGA markers may be useful for defining genetic diversity of a suite of random R genes in plants, as many studies show a differentiation of resistance to a wide array of pathogens. They could also help to characterize the genetic structure and geographic distribution in crops, including rice, wheat, barley, and banana. PMID:24099390

Ren, Juansheng; Yu, Yuchao; Gao, Fangyuan; Zeng, Lihua; Lu, Xianjun; Wu, Xianting; Yan, Wengui; Ren, Guangjun

2013-09-06

247

Genetic transformation and biotechnological application of the yeast Arxula adeninivorans.  

PubMed

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

Wartmann, T; Kunze, G

2000-11-01

248

Application of anti-listerial bacteriocins: monitoring enterocin expression by multiplex relative reverse transcription-PCR.  

PubMed

Listeriosis is a deadly food-borne disease, and its incidence may be limited through the biotechnological exploitation of a number of anti-listerial biocontrol agents. The most widely used of these agents are bacteriocins and the Class II enterocins are characterized by their activity against Listeria. Enterocins are primarily produced by enterococci, particularly Enterococcus faecium and many strains have been described, often encoding multiple bacteriocins. The use of these strains in food will require that they are free of virulence functions and that they exhibit a high level expression of anti-listerial enterocins in fermentation conditions. Multiplex relative RT (reverse transcription)-PCR is a technique that is useful in the discovery of advantageous expression characteristics among enterocin-producing strains. It allows the levels of individual enterocin gene expression to be monitored and determination of how expression is altered under different growth conditions. PMID:23176514

Williams, D Ross; Chanos, Panagiotis

2012-12-01

249

Analytical construct of reversible desensitization of pituitary-testicular signaling: illustrative application in aging  

PubMed Central

Luteinizing hormone (LH) administered in pharmacological amounts downregulates Leydig cell steroidogenesis. Whether reversible downregulation of physiological gonadotropin drive operates in vivo is unknown. Most of the analytical models of dose-response functions that have been constructed are biased by the assumption that no downregulation exists. The present study employs a new analytical platform to quantify potential (but not required) pulsatile cycles of LH-testosterone (T) dose-response stimulation, desensitization, and recovery (pulse-by-pulse hysteresis) in 26 healthy men sampled every 10 min for 24 h. A sensitivity-downregulation hysteresis construct predicted marked hysteresis with a median time delay to LH dose-response inflection within individual T pulses of 23 min and with median T pulse onset and recovery LH sensitivities of 1.1 and 0.10 slope unit, respectively (P < 0.001). A potency-downregulation model yielded median estimates of one-half maximally stimulatory LH concentrations (EC50 values) of 0.66 and 7.5 IU/l for onset and recovery, respectively (P < 0.001). An efficacy-downregulation formulation of hysteresis forecasts median LH efficacies of 20 and 8.3 ng·dl?1·min?1 for onset and offset of T secretory burst, respectively (P = 0.002). Segmentation of the LH-T data by age suggested greater sensitivity, higher EC50 (increased LH potency), and markedly (2.7-fold) attenuated LH efficacy in older individuals. Each of the three hysteresis models yielded a marked (P < 0.005) reduction in estimated model residual error compared with no hysteresis. In summary, model-based analyses allowing for (but not requiring) reversible pituitary-gonadal effector-response downregulation are consistent with a hypothesis of recurrent, brief cycles of LH-dependent stimulation, desensitization, and recovery of pulsatile T secretion in vivo and an age-associated reduction of LH efficacy. Prospective studies would be required to prove this aging effect.

Keenan, Daniel M.; Iranmanesh, Ali

2011-01-01

250

Genetics.  

PubMed

The present state of knowledge on the genetics of anxiety disorders, in particular panic disorder, comprising clinical and molecular genetic studies, interaction analyses, as well as meta-analyses of single association studies will be presented in detail. A particular focus will be on the most robust findings in panic disorder to date in the serotonergic, noradrenergic, and dopaminergic system, such as the catechol-O-methyltransferase (COMT) gene. Additionally, findings on the adenosine receptor 2A (A2A) gene, which has been reported to be associated with panic disorder and also with anxiety levels after caffeine administration in a gene--environment interactional model, will be discussed. Furthermore, the first imaging genetic findings in panic disorder, social phobia, and anxiety-related traits using fMRI and PET techniques in combination with molecular genetic association analyses are reviewed, taking into account the present intermediate phenotype discussion in the investigation of complex genetic disorders. Finally, the first exemplary pharmacogenetic studies in panic disorder and generalized social phobia will be presented. The pathomechanism of anxiety disorders and in particular panic disorder is considered to be multifactorial with converging evidence for a pivotal role of genetic factors in particular, which will be presented in detail in this chapter. PMID:21309106

Domschke, Katharina; Deckert, Jürgen

2010-01-01

251

Tailoring harmonic radiation to different applications using a genetic algorithm  

NASA Astrophysics Data System (ADS)

We use a genetic algorithm to theoretically optimize several properties of extreme ultraviolet (XUV) radiation, generated as high-order harmonics in xenon and argon. We maximize the harmonic pulse energy, minimize the pulse duration or optimize the temporal coherence by varying at the same time two or three parameters that are easily accessible in experiments, related to the characteristics of the laser beam and the nonlinear medium. For the 15th and 29th harmonics in argon, we find up to 109 photons per pulse, and pulse durations as short as 6 fs generated by a 50 fs laser pulse. We can also tailor the phase matching conditions to spectrally select the transform-limited part of the harmonic radiation. This allows us to identify conditions when the time structure of the XUV radiation presents a train of attosecond pulses. We find that the optimum conditions for the different properties are in general not the same. They depend in particular on whether the harmonic belongs to the plateau or the cutoff region of the harmonic spectrum. This reflects the unavoidable interplay between the microscopic intensity-dependent harmonic phase and the macroscopic phase matching conditions imposed by a nonlinear medium interacting with an intense, focused laser beam.

Roos, L.; Gaarde, M. B.; L'Huillier, A.

2001-12-01

252

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

253

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

254

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

Microsoft Academic Search

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

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

2006-01-01

255

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

Microsoft Academic Search

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

Ruth B. Phillips

2001-01-01

256

An application of artificial neural networks and genetic algorithms to personnel selection in the financial industry  

Microsoft Academic Search

Personnel selection in the financial industry can improve the performance of this critical corporate resource when done properly. This paper introduces a neural net classifier to aid this selection process. A novel application of a genetic algorithm to speed up the neural learning process is presented

M. L. Gargano; R. A. Marose; L. von Kleeck

1991-01-01

257

Studies on the application of radiation for genetic transformation in higher plants.  

National Technical Information Service (NTIS)

Present research carried out to develop the radiation application on the mutation research of genetic engineering for increasing productivity. Some variants were selected in M2 generation of Namzack and M3 generation of Sumi derived from the plantlet by t...

Y. I. Lee H. S. Song J. S. Kim I. C. Shin S. J. Lee

1993-01-01

258

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

Microsoft Academic Search

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

Jochen Reiss; David N. Cooper

1990-01-01

259

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

Microsoft Academic Search

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

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

2011-01-01

260

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

261

VHDL-AMS Based Genetic Optimization of Mixed-Physical-Domain Systems in Automotive Applications  

Microsoft Academic Search

This paper presents a VHDL-AMS based genetic optimization methodology suitable for performance improvement of hardware systems in automotive applications. Models of such systems are mixed- signal (analog and digital) in which the analog parts cover mixed physical domains. A case study applying this novel method to the fuzzy logic controller (FLC) optimization in an automotive active suspension system (AASS) has

Leran Wang; Tom J. Kazmierski

2009-01-01

262

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

2012-02-28

263

Public concerns about general and specific applications of genetic engineering: a comparative study between the UK and Italy  

Microsoft Academic Search

Public opinion regarding the application and development of genetic engineering is likely to be an important factor influencing the future development of the technology, and its subsequent application within the commercial sector. Recent studies have been carried out which have assessed public attitudes to biotechnology, and in particular genetic engineering, but there is little empirical work to understand cross-cultural differences

Anna Saba; Anna Moles; Lynn J. Frewer

1998-01-01

264

On thermodynamic and microscopic reversibility  

SciTech Connect

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

Crooks, Gavin E.

2011-07-12

265

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

USGS Publications Warehouse

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

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

1975-01-01

266

Applications of Differential-Display Reverse Transcription-PCR to Molecular Pathogenesis and Medical Mycology  

PubMed Central

The host-fungus interaction is characterized by changes in gene expression in both host and pathogen. Differential-display reverse transcription PCR (DDRT-PCR) is a PCR-based method that allows extensive analysis of gene expression among several cell populations. Several limitations and drawbacks to this procedure have now been addressed, including the large number of false-positive results and the difficulty in confirming differential expression. Modifications that simplify the reaction time, allow the use of minute quantities of RNA, or address unusual species- or gene-specific sequences have been reported. DDRT-PCR has been used to address biological questions in mammalian systems, including cell differentiation, cell activation, cell stress, and identification of drug targets. In microbial pathogenesis and plant pathogenesis, DDRT-PCR has allowed the identification of virulence factors, genes involved in cell death, and signaling genes. In Candida albicans, DDRT-PCR studies identified TIF-2, which may play a role in the upregulation of phospholipases, and the stress-related genes, CIP1 and CIP2. In Histoplasma capsulatum and C. albicans, genes involved in the host-pathogen interaction, including a member of the 100-kDa family in Histoplasma and an ALS and 14-3-3 gene in Candida, were potentially identified by DDRT-PCR. Although very few reports have been published in medical mycology, studies in mammalian, nonfungal microbial, and plant pathogen systems are easily applied to basic questions in fungal pathogenesis and antifungal therapeutics.

Sturtevant, Joy

2000-01-01

267

Equilibrium paradigm for field-reversed configurations and application to experiments  

SciTech Connect

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-{beta}' 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 m{sup 2}/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. [Redmond Plasma Physics Laboratory, University of Washington, Redmond, Washington 98052 (United States); Intrator, T. P. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2009-07-15

268

Bootstrap current in enhanced reversed shear tokamaks for volume neutron source applications  

SciTech Connect

The bootstrap current is evaluated for two reference tokamak designs for a Volume Neutron Source (VNS). One is a larger aspect ratio design using superconducting coils (VNS-SC) and the other is a small aspect ratio design using a solid core with normal conducting toroidal field coils (VNS-ST). The target plasma profiles are taken as representative of the recently observed enhanced reverse shear plasmas with hollow magnetic safety factor (q) profiles in the core and corresponding peaked density profiles. The higher q in the plasma center in combination with peaked density is shown to move the peak in the bootstrap current toward the plasma center. This reduces the current drive requirements to a very small axial seed current and a source localized around the location of the desired minimum in the q profile. Very high bootstrap current fractions can be attained in the VNS-SC design with normalized betas (defined in terms of the vacuum toroidal magnetic field at the geometric center of the plasma) of {beta}{sub N} {le} 3.5. The bootstrap current is lower in the VNS-ST design because of its lower aspect ratio; the highest bootstrap fraction found in these limited cases is 50% at {beta}{sub N} = 5.

Houlberg, W.A.

1995-12-31

269

Probing the Early Temporal and Spatial Interaction of the Sindbis Virus Capsid and E2 Proteins with Reverse Genetics  

PubMed Central

A 7-Å cryoelectron microscopy-based reconstruction of Sindbis virus (SINV) was recently generated. Fitting the crystal structure of the SINV capsid protein (Cp) into the density map revealed that the F2-G2 loop of the Cp was shifted away from cytoplasmic domain of E2 (cdE2) in the 7-Å reconstruction relative to its position in the Cp crystal structure. Furthermore, the reconstruction demonstrated that residue E395 in region I of the cytoplasmic domain of the E2 envelope protein (cdE2-RI) and K252 of Cp, part of the Cp F2-G2 loop, formed a putative salt bridge in the virion. We generated amino acid substitutions at residues K250 and K252 of the SINV Cp and explored the resulting phenotypes. In the context of cells infected with wild-type or mutant virus, reversing the charge of these two residues resulted in the appearance of Cp aggregates around cytopathic vacuole type I (CPV-I) structures, the absence of nucleocapsid (NC) formation, and a lack of virus particle release in the infected mammalian cell. However, expressing the same Cp mutants in the cell without the envelope proteins or expressing and purifying the mutants from an Escherichia coli expression system and assembling in vitro yielded NC assembly in all cases. In addition, second-site mutations within cdE2 restored NC assembly but not release of infectious particles. Our data suggest an early temporal and spatial interaction between cdE2-RI and the Cp F2-G2 loop that, when ablated, leads to the absence of NC assembly. This interaction also appears to be important for budding of virus particles.

Snyder, Jonathan E.; Berrios, Christian J.; Edwards, Thomas J.; Jose, Joyce; Perera, Rushika

2012-01-01

270

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

PubMed Central

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

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

2001-01-01

271

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

272

The design and application of genetically encodable biosensors based on fluorescent proteins.  

PubMed

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

273

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

PubMed

Severe acute respiratory syndrome with high mortality rates (?50%) is associated with a novel group 2c betacoronavirus designated Middle East respiratory syndrome coronavirus (MERS-CoV). We synthesized a panel of contiguous cDNAs that spanned the entire genome. Following contig assembly into genome-length cDNA, transfected full-length transcripts recovered several recombinant viruses (rMERS-CoV) that contained the expected marker mutations inserted into the component clones. Because the wild-type MERS-CoV contains a tissue culture-adapted T1015N mutation in the S glycoprotein, rMERS-CoV replicated ?0.5 log less efficiently than wild-type virus. In addition, we ablated expression of the accessory protein ORF5 (rMERS•ORF5) and replaced it with tomato red fluorescent protein (rMERS-RFP) or deleted the entire ORF3, 4, and 5 accessory cluster (rMERS-?ORF3-5). Recombinant rMERS-CoV, rMERS-CoV•ORF5, and MERS-CoV-RFP replicated to high titers, whereas MERS-?ORF3-5 showed 1-1.5 logs reduced titer compared with rMERS-CoV. Northern blot analyses confirmed the associated molecular changes in the recombinant viruses, and sequence analysis demonstrated that RFP was expressed from the appropriate consensus sequence AACGAA. We further show dipeptidyl peptidase 4 expression, MERS-CoV replication, and RNA and protein synthesis in human airway epithelial cell cultures, primary lung fibroblasts, primary lung microvascular endothelial cells, and primary alveolar type II pneumocytes, demonstrating a much broader tissue tropism than severe acute respiratory syndrome coronavirus. The availability of a MERS-CoV molecular clone, as well as recombinant viruses expressing indicator proteins, will allow for high-throughput testing of therapeutic compounds and provide a genetic platform for studying gene function and the rational design of live virus vaccines. PMID:24043791

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

2013-09-16

274

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

PubMed Central

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

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

2013-01-01

275

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

276

Rapid reversal of hyperpigmentation in pityriasis versicolor upon short-term topical cycloserine application.  

PubMed

The clinical phenomena of pityriasis versicolor (PV), a common Malassezia-associated skin disease, such as hyperpigmentation, depigmentation and fluorescence of the lesions may at least partly be explained by the generation of Trp-derived indole pigments through the action of transaminase 1 (TAM 1). Cycloserine, a TAM inhibitor, was able to completely inhibit pigment production in M. furfur in vitro in a dose-dependent manner. Application of a 0.2-mol l(-1) aqueous cycloserine solution b.i.d. for 5 days in three patients with hyperpigmented PV resulted in complete healing within 3-5 days without side-effects. Topically applied TAM inhibitors may therefore represent a new therapeutic principle for prophylaxis and therapy of PV, thus underlining the importance of the TAM pathway for the pathogenesis of the disease. PMID:19780976

Mayser, Peter; Rieche, Inga

2009-09-22

277

Molecular Identification and Genetic Analysis of Norovirus Genogroups I and II in Water Environments: Comparative Analysis of Different Reverse Transcription-PCR Assays?  

PubMed Central

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

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

2007-01-01

278

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.

279

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

Microsoft Academic Search

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

Tang Wei

2001-01-01

280

Neutrophil Reverse Migration Becomes Transparent with Zebrafish  

PubMed Central

The precise control of neutrophil-mediated inflammation is critical for both host defense and the prevention of immunopathology. In vivo imaging studies in zebrafish, and more recently in mice, have made the novel observation that neutrophils leave a site of inflammation through a process called neutrophil reverse migration. The application of advanced imaging techniques to the genetically tractable, optically transparent zebrafish larvae was critical for these advances. Still, the mechanisms underlying neutrophil reverse migration and its effects on the resolution or priming of immune responses remain unclear. Here, we review the current knowledge of neutrophil reverse migration, its potential roles in host immunity, and the live imaging tools that make zebrafish a valuable model for increasing our knowledge of neutrophil behavior in vivo.

Starnes, Taylor W.; Huttenlocher, Anna

2012-01-01

281

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

Microsoft Academic Search

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

Ricardo Scrosati

2002-01-01

282

Estimating rate constants of heterogeneous catalytic reactions without supposition of rate determining surface steps — an application of a genetic algorithm  

Microsoft Academic Search

A method providing initial estimates for rate constants of nonlinear chemical kinetics is proposed. This method is based on a genetic algorithm. The particular structure of the genetic algorithm adapted to the problem of estimating rate constants is introduced. The rate and certainty of convergence of the estimation procedure is analysed illustrating the proposed strategy by example of its application

Dorit Wolf; Ralf Moros

1997-01-01

283

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

PubMed Central

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

Anderson, Karen E

2013-01-01

284

Reverse-Micelle Synthesis of Electrochemically Encoded Quantum Dot Barcodes: Application to Electronic Coding of a Cancer Marker  

PubMed Central

Reproducible electrochemically encoded quantum dot (QD) barcodes were prepared by using the reverse-micelle synthetic approach. The encoding elements, Zn2+, Cd2+, Pb2+ were confined within a single QD, which eliminates the cumbersome encapsulation process used by other common nanoparticle-based barcode preparation schemes. The distinct voltammetric stripping patterns of Zn2+, Cd2+, Pb2+ at distinguishable potentials with controllable current intensities offer excellent encoding capability for the prepared electrochemical (EC) QDs. Additionally, the simultaneous modification of the QD barcode surface with organic ligands during the preparation process make them potentially useful in biomedical research. For proof of concept of their application in bioassays, the EC QD barcodes were further employed as tags for an immunoassay of a cancer marker, carcinoembryonic antigen (CEA). The voltammetric stripping response of the dissolved bardcode tags was proportional to log[CEA] in the range from 0.01 ng mL?1 to 80 ng mL?1, with a detection limit of 3.3 pg mL?1. The synthesized EC QD barcodes hold considerable potentials in biodetection, encrypted information and product tracking.

Xiang, Yun; Zhang, Yuyong; Chang, Yue; Chai, Yaqin; Wang, Joseph; Yuan, Ruo

2010-01-01

285

Reverse-micelle synthesis of electrochemically encoded quantum dot barcodes: application to electronic coding of a cancer marker.  

PubMed

Reproducible electrochemically encoded quantum dot (QD) barcodes were prepared using the reverse-micelle synthetic approach. The encoding elements, Zn(2+), Cd(2+), and Pb(2+), were confined within a single QD, which eliminates the cumbersome encapsulation process used by other common nanoparticle-based barcode preparation schemes. The distinct voltammetric stripping patterns of Zn(2+), Cd(2+) and Pb(2+) at distinguishable potentials with controllable current intensities offer excellent encoding capability for the prepared electrochemical (EC) QDs. Additionally, the simultaneous modification of the QD barcode surface with organic ligands during the preparation process make them potentially useful in biomedical research. For proof of concept of their application in bioassays, the EC QD barcodes were further employed as tags for an immunoassay of a cancer marker, carcinoembryonic antigen (CEA). The voltammetric stripping response of the dissolved bardcode tags was proportional to log[CEA] in the range from 0.01 to 80 ng mL(-1), with a detection limit of 3.3 pg mL(-1). The synthesized EC QD barcodes hold considerable potential in biodetection, encrypted information, and product tracking. PMID:20067269

Xiang, Yun; Zhang, Yuyong; Chang, Yue; Chai, Yaqin; Wang, Joseph; Yuan, Ruo

2010-02-01

286

Improvement of Influenza A\\/Fujian\\/411\\/02 (H3N2) Virus Growth in Embryonated Chicken Eggs by Balancing the Hemagglutinin and Neuraminidase Activities, Using Reverse Genetics  

Microsoft Academic Search

The H3N2 influenza A\\/Fujian\\/411\\/02-like virus strains that circulated during the 2003-2004 influenza season caused influenza epidemics. Most of the A\\/Fujian\\/411\\/02 virus lineages did not replicate well in embryonated chicken eggs and had to be isolated originally by cell culture. The molecular basis for the poor replication of A\\/Fujian\\/411\\/02 virus was examined in this study by the reverse genetics technology. Two

Bin Lu; Helen Zhou; Dan Ye; George Kemble; Hong Jin

2005-01-01

287

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

PubMed Central

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

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

2008-01-01

288

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

PubMed Central

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

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

2013-01-01

289

Experimental pathways towards developing a rotavirus reverse genetics system: synthetic full length rotavirus ssRNAs are neither infectious nor translated in permissive cells.  

PubMed

At present the ability to create rationally engineered mutant rotaviruses is limited because of the lack of a tractable helper virus-free reverse genetics system. Using the cell culture adapted bovine RV RF strain (G6P6 [1]), we have attempted to recover infectious RV by co-transfecting in vitro transcribed ssRNAs which are identical in sequence to the positive sense strand of each of the 11 dsRNA genomic segments of the RF strain. The RNAs were produced either from cDNAs cloned by a target sequence-independent procedure, or from purified double layered RV particles (DLPs). We have validated their translational function by in vitro synthesis of (35)S-labelled proteins in rabbit reticulocyte lysates; all 11 proteins encoded by the RV genome were expressed. Transfection experiments with DLP- or cDNA-derived ssRNAs suggested that the RNAs do not act independently as mRNAs for protein synthesis, once delivered into various mammalian cell lines, and exhibit cytotoxicity. Transfected RNAs were not infectious since a viral cytopathic effect was not observed after infection of MA104 cells with lysates from transfected cells. By contrast, an engineered mRNA encoding eGFP was expressed when transfected under identical conditions into the same cell lines. Co-expression of plasmids encoding NSP2 and NSP5 using a fowlpox T7 polymerase recombinant virus revealed viroplasm-like structure formation, but this did not enable the translation of transfected RV ssRNAs. Attempts to recover RV from ssRNAs transcribed intracellularly from transfected cDNAs were also unsuccessful and suggested that these RNAs were also not translated, in contrast to successful translation from a transfected cDNA encoding an eGFP mRNA. PMID:24019962

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

2013-09-03

290

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

PubMed Central

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

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

2012-01-01

291

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

PubMed

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

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

2011-08-01

292

Genetic Algorithms Application for the Photoacoustic Signal Temporal Shape Analysis and Energy Density Spatial Distribution Calculation  

NASA Astrophysics Data System (ADS)

Recently, a few numerical methods based on the photoacoustic (PA) signal temporal shape analysis and energy density spatial distribution calculation, which is directly related to the laser beam spatial profile, have been presented. It has been shown that these methods allow a precise reproduction of the spatial profile and the radius of the laser beam, determining the vibrational-to-translational (V-T) relaxation time with good accuracy. Their applicability has been shown and confirmed for the analysis of an arbitrary symmetric laser beam spatial profile in cylindrical geometry. Here, the application of genetic optimization for solving the problem of a simultaneous laser beam spatial profile and V-T relaxation time determination by pulsed PAs is presented. Real-coded genetic algorithms are used to calculate the mentioned relaxation time by fitting the experimental signal {? }{p}({{r} }, t) with the theoretical one. The aim is to find combinations of PA signal parameters, namely, the radius of the laser beam and the V-T relaxation time that provide the best match with the given signal. A calculated PA signal with a known profile is used to simulate an experimental signal, and the sum of the square deviations representing deviations of the given and fitted signals is minimized by means of genetic optimization. In that way, the genetic algorithms are used to simultaneously estimate the radius of the laser beam and the V-T relaxation time efficiently and with high accuracy. Compared to previous methods, the presented method is much simpler and requires less time to compute.

Luki?, M.; ?ojbaši?, Ž.; Rabasovi?, M. D.; Markushev, D. D.; Todorovi?, D. M.

2013-10-01

293

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

NASA Astrophysics Data System (ADS)

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

Wu, Chih-Hung; Su, Wei-Han

2013-03-01

294

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

295

A Phosphate-Regulated Promoter for Fine-Tuned and Reversible Overexpression in Ostreococcus: Application to Circadian Clock Functional Analysis  

PubMed Central

Background The green picoalga Ostreococcus tauri (Prasinophyceae), which has been described as the smallest free-living eukaryotic organism, has minimal cellular ultra-structure and a very small genome. In recent years, O. tauri has emerged as a novel model organism for systems biology approaches that combine functional genomics and mathematical modeling, with a strong emphasis on light regulated processes and circadian clock. These approaches were made possible through the implementation of a minimal molecular toolbox for gene functional analysis including overexpression and knockdown strategies. We have previously shown that the promoter of the High Affinity Phosphate Transporter (HAPT) gene drives the expression of a luciferase reporter at high and constitutive levels under constant light. Methodology/Principal Findings Here we report, using a luciferase reporter construct, that the HAPT promoter can be finely and reversibly tuned by modulating the level and nature of phosphate in culture medium. This HAPT regulation was additionally used to analyze the circadian clock gene Time of Cab expression 1 (TOC1). The phenotype of a TOC1ox/CCA1:Luc line was reverted from arrhythmic to rhythmic simply by adding phosphate to the culture medium. Furthermore, since the time of phosphate injection had no effect on the phase of CCA1:Luc expression, this study suggests further that TOC1 is a central clock gene in Ostreococcus. Conclusions/Perspectives We have developed a phosphate-regulated expression system that allows fine gene function analysis in Ostreococcus. Recently, there has been a growing interest in microalgae as cell factories. This non-toxic phosphate-regulated system may prove useful in tuning protein expression levels quantitatively and temporally for biotechnological applications.

Lozano, Jean-Claude; Bouget, Francois-Yves

2011-01-01

296

Applications of genetic algorithms to optimization problems in the solvent extraction process for spent nuclear fuel  

SciTech Connect

Applications of genetic algorithms (GAs) to optimization problems in the solvent extraction process for spent nuclear fuel are described. Genetic algorithms have been considered a promising tool for use in solving optimization problems in complicated and nonlinear systems because they require no derivatives of the objective function. In addition, they have the ability to treat a set of many possible solutions and consider multiple objectives simultaneously, so they can calculate many pareto optimal points on the trade-off curve between the competing objectives in a single iteration, which leads to small computing time. Genetic algorithms were applied to two optimization problems. First, process variables in the partitioning process were optimized using a weighted objective function. It was observed that the average fitness of a generation increased steadily as the generation proceeded and satisfactory solutions were obtained in all cases, which means that GAs are an appropriate method to obtain such an optimization. Secondly, GAs were applied to a multiobjective optimization problem in the co-decontamination process, and the trade-off curve between the loss of uranium and the solvent flow rate was successfully obtained. For both optimization problems, CPU time with the present method was estimated to be several tens of times smaller than with the random search method.

Omori, Ryota, Sakakibara, Yasushi; Suzuki, Atsuyuki [Univ. of Tokyo (Japan). Dept. of Quantum Engineering and Systems Science

1997-04-01

297

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

SciTech Connect

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

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

1998-11-01

298

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

Microsoft Academic Search

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

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

2006-01-01

299

[Endogenous cellular reverse transcriptase in the rat brain. A comparative analysis of the authentic enzyme and recombinant reverse transcriptase coded by a mobile genetic element of the LINE class].  

PubMed

A purified preparation of endogenous RNA-dependent DNA-polymerase (reverse transcriptase) earlier identified in rat brain (Ivanov, V.A., Pakhotin, P.I., Bobkova, N.V., and Ilyin, Yu.V. parallel Dokl. RAN (1992). V. 323, P. 173-177) has been obtained. A comparative analysis of the enzyme and recombinant reverse transcriptase coded by the mobile genome element jockey earlier expressed in a heterological cell system (Ivanov V.V., Melnikov A.A., Siunov A.V., Fodor I.I., Ilyin, Yu.V. parallel EMBO J. (1991), V. 10, P. 2489-2495) has been carried out. Like retroviral RNA-dependent DNA-polymerases, these enzymes show preference for polyribonucleotides and can use poly(rCm) as template. Besides they are inhibited by SH-reagents and require bivalent cations (Mg2+ or Mn2+) and detergent and/or KCl as ionic strength carrier. The enzymes differ drastically from retrovirus reverse transcriptases by a number of catalytic properties (low optima of concentration of requisite cations and ionic strength, strong preference for Mn2+, highly efficiency in using poly(rCm), lack of associated RNase H activity) but exhibit a high degree of similarity among themselves with regard to the above properties. It is suggested that endogenous reverse transcriptase from rat brain is a product of expression of the mobile genome element of the LINE family. PMID:7578575

Ivanov, V A; Den'mukhametova, S V; Godukhin, O V; Il'in, Iu V

1995-08-01

300

Warfarin reversal.  

PubMed

Warfarin is the most commonly used oral anticoagulant in the UK. It is associated with few side effects apart from haemorrhage. The most appropriate way to reverse the anticoagulant effect of warfarin depends on the clinical circumstances. In serious bleeding, rapid reversal is required, whereas in minor bleeding or asymptomatic over anticoagulation, a more leisurely approach is usually appropriate. This review discusses the current approaches to warfarin reversal in clinical practice. The development of a uniform approach to warfarin reversal in the Northern Region is described. PMID:15509671

Hanley, J P

2004-11-01

301

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

Microsoft Academic Search

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

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

2009-01-01

302

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

Microsoft Academic Search

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

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

2006-01-01

303

Application of artificial neural network and genetic algorithm in flow and transport simulations  

NASA Astrophysics Data System (ADS)

Artificial neural network (ANN) is considered to be a powerful tool for solving groundwater problems which require a large number of flow and contaminant transport (GFCT) simulations. Often, GFCT models are nonlinear, and they are difficult to solve using traditional numerical methods to simulate specific input-output responses. In order to avoid these difficulties, ANN may be used to simulate the GFCT responses explicitly. In this manuscript, recent research related to the application of ANN in simulating GFCT responses is critically reviewed, and six research areas are identified. In order to study these areas, a one-dimensional unsaturated flow and transport scenario was developed, and ANN was used to simulate the effects of specific GFCT parameters on overall results. Using these results, ANN concepts related to architecture, sampling, training, and multiple function approximations are studied, and ANN training using back-propagation algorithm (BPA) and genetic algorithm (GA) are compared. These results are summarized, and appropriate conclusions are made.

Morshed, Jahangir; Kaluarachchi, Jagath J.

304

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

NASA Astrophysics Data System (ADS)

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

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

2001-12-01

305

Application of genetic algorithms to processing of reflectance spectra of semiconductor compounds  

NASA Astrophysics Data System (ADS)

The basic task of mathematical processing of reflectance spectra is the calculation of the dielectric function of the substance, which describe response of a crystal to an external electromagnetic field. The most modern and perspective way of the solution of this task is the dispersion analysis [Lorentz model (LM)]. However LM requires large volume of computing works at phonons optimum parameters selection. The rapid computer facilities development promotes overcoming of this difficulty. However without application of effective methods of optimization practically it is impossible to execute DA for composite reflectance spectra. The efficiency GA strongly depends on such details, as a solutions coding method, genetic operations embodying, selection mechanisms, other algorithm parameters adjustment, success criterion. In this paper we offer modification GA for the solution of the reflectance spectra processing problem and results of the obtained algorithm work.

Zaharov, Ivan S.; Kochura, Alexey V.; Kurkin, Alexandr Y.; Belogorohov, Alexandr I.

2004-11-01

306

A generalized Kruskal-Wallis test incorporating group uncertainty with application to genetic association studies.  

PubMed

Motivated by genetic association studies of SNPs with genotype uncertainty, we propose a generalization of the Kruskal-Wallis test that incorporates group uncertainty when comparing k samples. The extended test statistic is based on probability-weighted rank-sums and follows an asymptotic chi-square distribution with k - 1 degrees of freedom under the null hypothesis. Simulation studies confirm the validity and robustness of the proposed test in finite samples. Application to a genome-wide association study of type 1 diabetic complications further demonstrates the utilities of this generalized Kruskal-Wallis test for studies with group uncertainty. The method has been implemented as an open-resource R program, GKW. PMID:23441822

Acar, Elif F; Sun, Lei

2013-02-26

307

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

SciTech Connect

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

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

2012-01-01

308

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

NASA Astrophysics Data System (ADS)

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

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

2012-08-01

309

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

310

Analysis of tactile perceptions of textile materials using artificial intelligence techniques : Part 2: reverse engineering using genetic algorithm coupled neural network  

Microsoft Academic Search

Purpose – The second of a two-part series, this paper aims to explain the design and development of a hybrid system for reverse engineering. Design\\/methodology\\/approach – A prediction engine to map the perception of tactile sensations using a neural network engine was developed. Since seventeen mechanical properties form the input - and tactile compfort score is used as the output

B. Karthikeyan; Les M. Sztandera

2010-01-01

311

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

PubMed Central

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

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

2011-01-01

312

Examination of a genetic algorithm for the application in high-throughput downstream process development.  

PubMed

Compared to traditional strategies, application of high-throughput experiments combined with optimization methods can potentially speed up downstream process development and increase our understanding of processes. In contrast to the method of Design of Experiments in combination with response surface analysis (RSA), optimization approaches like genetic algorithms (GAs) can be applied to identify optimal parameter settings in multidimensional optimizations tasks. In this article the performance of a GA was investigated applying parameters applicable in high-throughput downstream process development. The influence of population size, the design of the initial generation and selection pressure on the optimization results was studied. To mimic typical experimental data, four mathematical functions were used for an in silico evaluation. The influence of GA parameters was minor on landscapes with only one optimum. On landscapes with several optima, parameters had a significant impact on GA performance and success in finding the global optimum. Premature convergence increased as the number of parameters and noise increased. RSA was shown to be comparable or superior for simple systems and low to moderate noise. For complex systems or high noise levels, RSA failed, while GA optimization represented a robust tool for process optimization. Finally, the effect of different objective functions is shown exemplarily for a refolding optimization of lysozyme. PMID:22700464

Treier, Katrin; Berg, Annette; Diederich, Patrick; Lang, Katharina; Osberghaus, Anna; Dismer, Florian; Hubbuch, Jürgen

2012-07-30

313

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

314

Mechanism studies on nanoPCR and applications of gold nanoparticles in genetic analysis.  

PubMed

Recently, the applications of nanomaterial-assisted polymerase chain reaction (nanoPCR) have received considerable attention. Several potential mechanisms have been proposed, but mainly according to the results of PCR assays under specific conditions and lacking direct and general evidence. The mechanism of nanoPCR has not been elucidated yet. Here, taking gold nanoparticles (AuNPs) as an example, we report the three general effects of AuNPs: (1) AuNPs adsorb polymerase and modulate the amount of active polymerase in PCR, which was directly demonstrated by a simple and straightforward colorimetric assay and the dynamic light scattering measurements. (2) AuNPs adsorb primers and decrease the melting temperatures (Tm) of the duplexes formed with perfectly matched and mismatched primers and increase the Tm difference between them. (3) AuNPs adsorb PCR products and facilitate the dissociation of them in the denaturing step. All these effects were confirmed by addition of a rationally selected surface adsorbent, bovine thrombin, to highly efficiently modulate the surface adsorption of PCR components. These findings suggested that AuNPs should have multiple effects on PCR: (1) to regulate PCR in a case-by-case way via modulating the amount of active polymerase in PCR; (2) to improve PCR specificity in the annealing step via increasing the Tm difference between the perfectly matched and mismatched primers; (3) to improve PCR efficiency via speeding up the dissociation of the PCR products in the denaturing step. Taken together, we proposed the mechanism of nanoPCR is that the surface interaction of PCR components (polymerase, primers, and products) with AuNPs regulates nanoPCR. We further demonstrated that the applications of these findings improve the PCR of the amelogenin genes and Hepatitis B virus gene for genetic analysis. These findings could also provide helpful insight for the applications of other nanomaterials in nanoPCR. PMID:23734951

Lou, Xinhui; Zhang, Ying

2013-06-28

315

Reversible cardiomyopathy.  

PubMed

We report a case of reversible dilated cardiomyopathy, in a middle-aged male. The patient presented with severe left ventricular dysfunction and atrial fibrillation. Inspite of vigorous medical therapy there was only mild clinical improvement. Subsequently laboratory test results diagnosed it as hyperthyroidism and then specific thyrostatic treatment was added. There was a prompt clinical and hemodynamic improvement in the form of reversal of left ventricular dysfunction and achievement of sinus rhythm at the end of two weeks. PMID:17212027

Dhadke, S V; Dhadke, V N

2006-09-01

316

Application of genetic algorithm in tracking convective cloud images from Chinese FY2C satellite  

Microsoft Academic Search

It is significance to identify and track convective clouds using satellite data in nowcasting and severe weather warning. This article uses genetic algorithm to match and track convection clouds identified from infrared channel images of FY - 2C satellite. The preliminary results suggest that the genetic algorithm need set up enough group size & genetic algebra, and can select appropriate

Xiaofang Pei; Nan Li; Yating Zhan

2010-01-01

317

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

PubMed

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

Schiefelbein, Julieanne H; Cheeseman, Susan E

2009-03-01

318

Repeatability in column preparation of a reversed-phase C18 monolith and its application to separation of tocopherol homologues.  

PubMed

This work investigated the repeatability of column preparation for a reversed-phase C18 monolith, namely stearyl methacrylate-co-ethylene glycol dimethacrylate (SMA-EDMA). The columns were thermally polymerised using three commonly available heating devices (GC oven, hot air oven and water bath) and their chromatographic performance evaluated using micro-liquid chromatography for separation of five test compounds. Precision in terms of %RSD of retention times were 9.0, 6.5, and 12.5 using GC oven, hot air oven and water bath, respectively. Between-batch precision for the hot air oven (n=3 days) was less than 10.4% for retention time. The SMA-EDMA monolith was applied to the separation of tocopherol homologues by capillary electrochromatography. Usually tocopherol homologues cannot be completely separated by conventional reversed-phase C8- or C18-packed bed or C18-silica based monolithic columns. Polymer monolith has been shown to give remarkable selectivity towards the tocopherols compared to the conventional microparticulate phase and silica based monolith. Successful separation of the tocopherol isomers was achieved on the SMA-EDMA monolith without any column modification. PMID:21641454

Kositarat, Sirichai; Smith, Norman William; Nacapricha, Duangjai; Wilairat, Prapin; Chaisuwan, Patcharin

2011-04-05

319

Applications  

NASA Astrophysics Data System (ADS)

Economic incentives have spurred numerous applications of genetically engineered organisms in manufacture of pharmaceuticals and industrial chemicals. These successes, involving a variety of methods of genetic manipulation, have dispelled early fears that genetic engineering could not be handled safely, even in the laboratory. Consequently, the potential for applications in the wider environment without physical containment is being considered for agriculture, mining, pollution control, and pest control. These proposed applications range from modest extensions of current plant breeding techniques for new disease-resistant species to radical combinations of organisms (for example, nitrogen-fixing corn plants). These applications raise concerns about potential ecological impacts (see chapter 5), largely because of adverse experiences with both deliberate and inadvertent introductions of nonindigenous species.

Stern, Arthur M.

1986-07-01

320

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

321

Thermo-reversible green tea catechin gel for local application in chronic periodontitis: a 4-week clinical trial.  

PubMed

Background: Green tea extract is a naturally occurring antimicrobial agent, consisting of polyphenols (catechin) with anticariogenic, anti-inflammatory, anticollagenolytic properties. Hence, in the present study, an attempt was made to develop a thermo-reversible sustained-release green tea gel and to study its clinical effects on patients with chronic periodontitis (CP). Methods: Thermo-reversible sustained-release green tea catechin gel was prepared and tested for its in vitro release characteristics. An in vivo controlled, randomized, split-mouth single-evaluator masked study was conducted. Thirty patients with two sites in the contralateral quadrants having probing depths (PDs) of ?4 mm were selected. Assessment of gingival index (GI), PD, and relative clinical attachment levels (rCALs) was done at baseline and at 4 weeks. Green tea and placebo gels were placed at test and control sites as an adjunct to Phase 1 periodontal therapy. Results: Comparison of the mean ± SD GI, PD, and rCAL values within the test group at baseline (1.92 ± 0.24, 4.93 ± 0.58, and 9.97 ± 0.72, respectively) and the end of 4 weeks (0.01 ± 0.04, 2.87 ± 0.51, and 7.87 ± 0.51, respectively) showed high statistical significance (P <0.001). Comparison of mean ± SD of GI, PD, and rCAL within the control group at baseline (1.95 ± 0.16, 4.77 ± 0.50, and 9.73 ± 0.45, respectively) and the end of 4 weeks (0.16 ± 0.11, 3.8 ± 0.48, and 8.76 ± 0.43, respectively) showed significance with P <0.001. High significance was observed between the delta of measurements (0 to 4 weeks) of GI, PD, and rCAL between test (1.91 ± 0.20, 2.06 ± 0.07, and 2.1 ± 0.21, respectively) and control (1.79 ± 0.05, 0.97 ± 0.02, and 0.97 ± 0.02, respectively) groups. Conclusion: Adjunctive local drug therapy with thermo-reversible green tea gel has shown to reduce pockets and inflammation during the 4 weeks of the clinical trial in patients with CP. PMID:23121459

Chava, Vijay Kumar; Vedula, Bhargavi Devi

2012-11-03

322

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

PubMed

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

2009-08-13

323

Application of genetic algorithms for the extraction of electrical parameters of multicrystalline silicon  

NASA Astrophysics Data System (ADS)

The application of the genetic algorithms (GAs) concept in measurements science deals with a fitting procedure used for the numerical prediction of physical parameters from an experimental data curve. In this work, GAs were applied for the extraction of electrical parameters of multicrystalline silicon solar cells. The experimental technique used is the light-beam-induced-current (LBIC). From LBIC measurements, we deduced the values of the diffusion length L and the grain boundary recombination velocity Vr of the minority carriers of the multicrystalline silicon wafers using the fitting procedure. The nonlinear fitting procedure is based on the minimization of the standard deviation of the theoretical LBIC profile from the experimental one. However, this criterion is not convex, and using traditional deterministic optimization algorithms leads to local minima solutions. To overcome this problem, the nonlinear least-square minimization technique was computed with the GAs strategy, increasing the probability of obtaining the best minimum value of the cost function in very reasonable time. The results of the proposed algorithm are presented and compared with the Levenberg-Marquardt algorithm and the Gauss-Newton method. The GAs-based numerical technique was found to be a promising and a powerful technique for numerical evaluation of the electrical parameters of silicon solar cells.

Sellami, A.; Zagrouba, M.; Bouaïcha, M.; Bessaïs, B.

2007-05-01

324

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

NASA Astrophysics Data System (ADS)

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

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

2008-04-01

325

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

PubMed Central

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

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

2010-01-01

326

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

327

[Application of case-based method in genetics and eugenics teaching].  

PubMed

Genetics and Eugenics is a cross-discipline between genetics and eugenics. It is a common curriculum in many Chinese universities. In order to increase the learning interest, we introduced case teaching method and got a better teaching effect. Based on our teaching practices, we summarized some experiences about this subject. In this article, the main problem of case-based method applied in Genetics and Eugenics teaching was discussed. PMID:22659437

Li, Ya-Xuan; Zhao, Xin; Zhang, Fei-Xiong; Hu, Ying-Kao; Yan, Yue-Ming; Cai, Min-Hua; Li, Xiao-Hui

2012-05-01

328

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

329

Advancing Genetic Theory and Application by Metabolic Quantitative Trait Loci Analysis  

PubMed Central

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

Kliebenstein, DanielJ.

2009-01-01

330

From reversible to irreversible computations  

Microsoft Academic Search

In this paper we study the relation between reversible and irreversible computation applicable to different models of computation — here we are considering classical and quantum computation. We develop an equational theory of reversible computations and an associated theory of irreversible computations which is obtained by marking some inputs as preinitialised heap and some outputs as garbage to be thrown

Alexander S. Green; Thorsten Altenkirch

2006-01-01

331

Reverse Logistics.  

National Technical Information Service (NTIS)

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

J. L. Walden

2001-01-01

332

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

333

Offering predictive testing for Huntington disease in a medical genetics clinic: Practical applications  

Microsoft Academic Search

Predictive testing for Huntington disease is presently offered in a select few medical genetics centers in the United States. This is in part due to the labor intensive counseling and psychological testing suggested by the research protocols. We discuss some specific suggestions for establishing programs for Huntington disease predictive testing within pre-existing medical genetics clinics to encourage more centers to

Robin L. Bennett; Thomas D. Bird; Linda Teri

1993-01-01

334

GENETIC NEURAL NETWORK BASED DATA MINING AND APPLICATION IN CASE ANALYSIS OF POLICE OFFICE  

Microsoft Academic Search

This paper puts forward a method that combines the learning algorithm of BP neural network with genetic algorithm to train BP network and optimize the weight values of the network in a global scale. This method is featured as global optimization, high accuracy and fast convergence. The data-mining model based on genetic neural network has been widely applied to the

LIU Han-li; LI Lin; ZHU Hai-hong

335

The Application of Bone Marrow Transplantation to the Treatment of Genetic Diseases  

Microsoft Academic Search

Genetic diseases can be treated by transplantation of either normal allogeneic bone marrow or, potentially, autologous bone marrow into which the normal gene has been inserted in vitro (gene therapy). Histocompatible allogeneic bone marrow transplantation is used for the treatment of genetic diseases whose clinical expression is restricted to lymphoid or hematopoietic cells. The therapeutic role of bone marrow transplantation

Robertson Parkman

1986-01-01

336

The application of combinatorial optimization by Genetic Algorithm and Neural Network  

Microsoft Academic Search

A optimization model of sizing the storage section in a renewable power generation system was set up, and two methods were used to solve the model: genetic algorithm or combinatorial optimization by genetic algorithm and neural network. The system includes the photovoltaic arrays, the lead-acid battery and a flywheel. The optimal sizing can be considered as a constrained optimization problem:

Shiqiong Zhou; Longyun Kang; Guifang Guo; Yanning Zhang; Jianbo Cao; Binggang Cao

2008-01-01

337

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

338

Genetic analysis without replications: Model evaluation and application in spring wheat  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genetic data collected from plant breeding and genetic studies may not be replicated in field designs even though field variation is present. In this study, we addressed this problem using spring wheat (Triticum eastivum L.) trial data collected from two locations. There were no intra-location repl...

339

First successful application of preimplantation genetic diagnosis and haplotyping for congenital hyperinsulinism  

Microsoft Academic Search

Congenital hyperinsulinism is the most common cause of persistent hypoglycaemia in infancy. Early surgical intervention is usually required to prevent brain damage. The prevention of the transmission to the offspring is important in families carrying the mutated gene. Preimplantation genetic diagnosis (PGD) is an early genetic testing procedure for couples at risk of transmitting inherited diseases. A 36-year-old Saudi woman

Wafa Qubbaj; Abdulrahman Al-Swaid; Saad Al-Hassan; Khalid Awartani; Hesham Deek; Serdar Coskun

2011-01-01

340

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

341

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

PubMed

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

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

2013-05-29

342

The Application of Bone Marrow Transplantation to the Treatment of Genetic Diseases  

NASA Astrophysics Data System (ADS)

Genetic diseases can be treated by transplantation of either normal allogeneic bone marrow or, potentially, autologous bone marrow into which the normal gene has been inserted in vitro (gene therapy). Histocompatible allogeneic bone marrow transplantation is used for the treatment of genetic diseases whose clinical expression is restricted to lymphoid or hematopoietic cells. The therapeutic role of bone marrow transplantation in the treatment of generalized genetic diseases, especially those affecting the central nervous system, is under investigation. The response of a generalized genetic disease to allogeneic bone marrow transplantation may be predicted by experiments in vitro. Gene therapy can be used only when the gene responsible for the disease has been characterized. Success of gene therapy for a specific genetic disease may be predicted by its clinical response to allogeneic bone marrow transplantation.

Parkman, Robertson

1986-06-01

343

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{sup -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

344

Critical overview of applications of genetic testing in sport talent identification.  

PubMed

Talent identification for future sport performance is of paramount interest for many groups given the challenges of finding and costs of training potential elite athletes. Because genetic factors have been implicated in many performance- related traits (strength, endurance, etc.), a natural inclination is to consider the addition of genetic testing to talent identification programs. While the importance of genetic factors to sport performance is generally not disputed, whether genetic testing can positively inform talent identification is less certain. The present paper addresses the science behind the genetic tests that are now commercially available (some under patent protection) and aimed at predicting future sport performance potential. Also discussed are the challenging ethical issues that emerge from the availability of these tests. The potential negative consequences associated with genetic testing of young athletes will very likely outweigh any positive benefit for sport performance prediction at least for the next several years. The paper ends by exploring the future possibilities for genetic testing as the science of genomics in sport matures over the coming decade(s). PMID:22789017

Roth, Stephen M

2012-12-01

345

Reverse Presentations  

Microsoft Academic Search

Reverse Presentations is a method for requirements validation in offshore software development. In this paper, the authors\\u000a present and conceptually refine this method and carry out an initial evaluation. The method provides cross-phase support and\\u000a is characterized by a structured and iterative validation process. In contrast to existing methods, it focuses on the client\\u000a perspective and takes into account social

Martin Wiener; Rolf Stephan

2010-01-01

346

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

347

Reverse convection  

SciTech Connect

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

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

1992-12-01

348

Calibration of Neural Networks Using Genetic Algorithms, with Application to Optimal Path Planning.  

National Technical Information Service (NTIS)

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 te...

T. R. Smith G. A. Pitney D. Greenwood

1987-01-01

349

Application of a multiple-trait, multiple-country genetic evaluation model for female fertility traits.  

PubMed

The need to implement a method that can handle multiple traits per country in international genetic evaluations is evident. Today, many countries have implemented multiple-trait national genetic evaluations and they may expect to have their traits simultaneously analyzed in international genetic evaluations. Traits from the same country are residually correlated and the method currently in use, single-trait multiple across-country evaluation (ST-MACE), cannot handle nonzero residual correlations. Therefore, multiple-trait, multiple across-country evaluation (MT-MACE) was proposed to handle several traits from the same country simultaneously. To test the robustness of MT-MACE on real data, female fertility was chosen as a complex trait with low heritability. Data from 7 Holstein populations, 3 with 2 traits and 4 with 1 trait, were used. The differences in the estimated genetic correlations by MT-MACE and the single ST-MACE analysis (average absolute deviation of 0.064) were due to the bias of considering several traits from the same country in the ST-MACE analysis. However, the differences between the estimated genetic correlations by MT-MACE and multiple ST-MACE analyses avoiding more than one trait per country in each analysis (average absolute deviation of 0.066) were due to the lack of analysis of the correlated traits from the same country together and using the reported within-country genetic correlations. Applying MT-MACE resulted in reliability gain in international genetic evaluations, which was different from trait to trait and from bull to bull. The average reliability gain by MT-MACE over ST-MACE was 3.0 points for domestic bulls and 6.3 points for foreign bulls. Even countries with 1 trait benefited from the joint analysis of traits from the 2-trait countries. Another superiority of MT-MACE over ST-MACE is that the bulls that do not have national genetic evaluation for some traits from multiple trait countries will receive international genetic evaluations for those traits. Rank correlations were high between ST-MACE and MT-MACE when considering all bulls. However, the situation was different for the top 100 bulls. Simultaneous analysis of traits from the same country affected bull ranks, especially for top 100 bulls. Multi-trait MACE is a recommendable and robust method for international genetic evaluations and is appropriate for handling multiple traits per country, which can increase the reliability of international genetic evaluations. PMID:21094772

Nilforooshan, M A; Jakobsen, J H; Fikse, W F; Berglund, B; Jorjani, H

2010-12-01

350

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

351

A Simple Real-Coded Compact Genetic Algorithm and its Application to Antenna Optimization  

Microsoft Academic Search

Based on Harik's compact genetic algorithm, in this paper a real-coded type of compact genetic algorithm, RCGA, based on probability distribution function of each gene is developed. The algorithm is applied to design a new small-size tapered monopole ultra-wideband antenna as a practical utilization. The antenna is a modified PTMA which is able to improve the bandwidth using eleven degrees

Soheil Radiom; H. Aliakbarian; G. Vandenbosch; G. Gielen

2007-01-01

352

Containment of a genetically engineered microorganism during a field bioremediation application  

Microsoft Academic Search

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

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

1999-01-01

353

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

PubMed

Recent developments in directed evolution technologies combined with innovations in robotics and screening methods have revolutionized protein engineering. These methods are being applied broadly to many fields of biotechnology, including chemical engineering, agriculture and human therapeutics. More specifically, DNA shuffling and other methods of genetic recombination and mutation have resulted in the improvement of proteins of therapeutic interest. Optimizing genetic diversity and fitness through iterative directed evolution will accelerate improvements in engineered protein therapeutics. PMID:11551464

Kurtzman, A L; Govindarajan, S; Vahle, K; Jones, J T; Heinrichs, V; Patten, P A

2001-08-01

354

Detection by hemi-nested reverse transcription polymerase chain reaction and genetic characterization of wild type strains of Canine distemper virus in suspected infected dogs.  

PubMed

A new highly sensitive and specific hemi-nested reverse transcription polymerase chain reaction (RT-PCR) assay was applied to detect nucleoprotein (NP) gene of Canine distemper virus (CDV) in samples collected from dogs showing respiratory, gastrointestinal, and neurological signs. Thirty-eight out of 86 samples were positive suggesting that despite the vaccination, canine distemper may still represent a high risk to the canine population. The 968 base pair (bp) fragments from the hemagglutinin (H) gene of 10 viral strains detected in positive samples were amplified and analyzed by restriction fragment length polymorphism (RFLP) using AluI and PsiI enzymes in order to differentiate among vaccine and wild-type CDV strains and to characterize the field viral strains. The products of the both enzymatic digestions allowed identification all viruses as wild strains of CDV. In addition, the RFLP analysis with AluI provided additional information about the identity level among the strains analyzed on the basis of the positions of the cleavage site in the nucleotide sequences of the H gene. The method could be a more useful and simpler method for molecular studies of CDV strains. PMID:22362940

Di Francesco, Cristina E; Di Francesco, Daniela; Di Martino, Barbara; Speranza, Roberto; Santori, Domenico; Boari, Andrea; Marsilio, Fulvio

2011-12-06

355

Combining genetic, historical and geographical data to reconstruct the dynamics of bioinvasions: application to the cane toad Bufo marinus.  

PubMed

We developed a spatially explicit model of a bioinvasion and used an approximate Bayesian computation (ABC) framework to make various inferences from a combination of genetic (microsatellite genotypes), historical (first observation dates) and geographical (spatial coordinates of introduction and sampled sites) information. Our method aims to discriminate between alternative introduction scenarios and to estimate posterior densities of demographically relevant parameters of the invasive process. The performance of our landscape-ABC method is assessed using simulated data sets differing in their information content (genetic and/or historical data). We apply our methodology to the recent introduction and spatial expansion of the cane toad, Bufo marinus, in northern Australia. We find that, at least in the context of cane toad invasion, historical data are more informative than genetic data for discriminating between introduction scenarios. However, the combination of historical and genetic data provides the most accurate estimates of demographic parameters. For the cane toad, we find some evidence for a strong bottleneck prior to introduction, a small initial number of founder individuals (about 15), a large population growth rate (about 400% per generation), a standard deviation of dispersal distance of 19?km per generation and a high invasion speed at equilibrium (50?km per year). Our approach strengthens the application of the ABC method to the field of bioinvasion by allowing statistical inferences to be made on the introduction and the spatial expansion dynamics of invasive species using a combination of various relevant sources of information. PMID:21565099

Estoup, Arnaud; Baird, Stuart J E; Ray, Nicolas; Currat, Mathias; Cornuet, Jean-Marie; Santos, Filipe; Beaumont, Mark A; Excoffier, Laurent

2010-06-02

356

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

PubMed Central

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

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

2011-01-01

357

Application of a spatially-weighted Relief algorithm for ranking genetic predictors of disease  

PubMed Central

Background Identification of genetic variants that are associated with disease is an important goal in elucidating the genetic causes of diseases. The genetic patterns that are associated with common diseases are complex and may involve multiple interacting genetic variants. The Relief family of algorithms is a powerful tool for efficiently identifying genetic variants that are associated with disease, even if the variants have nonlinear interactions without significant main effects. Many variations of Relief have been developed over the past two decades and several of them have been applied to single nucleotide polymorphism (SNP) data. Results We developed a new spatially weighted variation of Relief called Sigmoid Weighted ReliefF Star (SWRF*), and applied it to synthetic SNP data. When compared to ReliefF and SURF*, which are two algorithms that have been applied to SNP data for identifying interactions, SWRF* had significantly greater power. Furthermore, we developed a framework called the Modular Relief Framework (MoRF) that can be used to develop novel variations of the Relief algorithm, and we used MoRF to develop the SWRF* algorithm. Conclusions MoRF allows easy development of new Relief algorithms by specifying different interchangeable functions for the component terms. Using MORF, we developed a new Relief algorithm called SWRF* that had greater ability to identify interacting genetic variants in synthetic data compared to existing Relief algorithms.

2012-01-01

358

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

SciTech Connect

Acetoacetyl CoA thiolase (AACT, EC 2.3.1.9) catalyzes the condensation of two acetyl?CoA molecules to form acetoacetyl?CoA. Two AACT?encoding genes, At5g47720 (AACT1) and At5g48230 (AACT2), were functionally identified in the Arabidopsis genome by direct enzymological assays and functional expression in yeast. Promoter::GUS fusion experiments indicated that AACT1 is primarily expressed in the vascular system and AACT2 is highly expressed in root tips, young leaves, top stems and anthers. Characterization of T?DNA insertion mutant alleles at each AACT locus established that AACT2 function is required for embryogenesis and for normal male gamete transmission. In contrast, plants lacking AACT1 function are completely viable and show no apparent growth phenotypes, indicating that AACT1 is functionally redundant with respect to AACT2 function. RNAi lines that express reduced levels of AACT2 show pleiotropic phenotypes, including reduced apical dominance, elongated life span and flowering duration, sterility, dwarfing, reduced seed yield and shorter root length. Microscopic analysis reveals that the reduced stature is caused by a reduction in cell size and fewer cells, and male sterility is caused by loss of the pollen coat and premature degeneration of the tapetal cells. Biochemical analyses established that the roots of AACT2 RNAi plants show quantitative and qualitative alterations in phytosterol profiles. These phenotypes and biochemical alterations are reversed when AACT2 RNAi plants are grown in the presence of mevalonate, which is consistent with the role of AACT2 in generating the bulk of the acetoacetyl?CoA precursor required for the cytosol?localized, mevalonate?derived isoprenoid biosynthetic pathway.

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

2012-03-31

359

Judaism, Genetic Screening and Genetic Therapy  

Microsoft Academic Search

Genetic screening, gene therapy and other applications of genetic engineering are permissible in Judaism when used for the treatment, cure, or prevention of disease. Such genetic manipulation is not considered to be a violation of God's natural law, but a legitimate implementation of the biblical mandate to heal. If Tay-Sachs disease, diabetes, hemophilia, cystic fibrosis, Huntington's disease or other genetic

FRED ROSNER

360

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

2013-01-16

361

The application of new simulated annealing genetic algorithm in film characters measurement  

NASA Astrophysics Data System (ADS)

A new global optimization method for thin film thickness calculation is presented in this paper. A new adaptive simulated annealing (ASA) combining with genetic algorithm is brought out. Adding traditional genetic algorithm to simulated annealing process avoids the premature convergence problem and improves the ability of global searching effectively. Firstly it generates a new group of local optimums through genetic and mutation operation; then the solutions are accepted at a certain probability, and will be calculated respectively in ASA process as the initial solutions. At last conjugate gradient algorithm is utilized to search accurately and quickly. This new ASGA can effectively enhance the robustness of the algorithm and reduce the limitation of the searching area. The experimental results show that the proposed algorithm can calculate the thickness of single layer and 2-layer thin film within the range of 10nm to 1? m and less than 4% calculation error.

Chu, Dong; Gong, Xing-Zhi; Cheng, Liang; Yu, Fei-Hong

2009-11-01

362

Dilution of genetic traits  

US Patent & Trademark Office Database

Undesirable genetic traits, such as resistance to toxin, can be inhibited or reversed by introducing sexually compatible individuals substantially homozygous for the sensitive allele, such as the wild type, into the target population.

2011-08-16

363

Improvement of Influenza A/Fujian/411/02 (H3N2) Virus Growth in Embryonated Chicken Eggs by Balancing the Hemagglutinin and Neuraminidase Activities, Using Reverse Genetics  

PubMed Central

The H3N2 influenza A/Fujian/411/02-like virus strains that circulated during the 2003-2004 influenza season caused influenza epidemics. Most of the A/Fujian/411/02 virus lineages did not replicate well in embryonated chicken eggs and had to be isolated originally by cell culture. The molecular basis for the poor replication of A/Fujian/411/02 virus was examined in this study by the reverse genetics technology. Two antigenically related strains that replicated well in embryonated chicken eggs, A/Sendai-H/F4962/02 and A/Wyoming/03/03, were compared with the prototype A/Fujian/411/02 virus. A/Sendai differed from A/Fujian by three amino acids in the neuraminidase (NA), whereas A/Wyoming differed from A/Fujian by five amino acids in the hemagglutinin (HA). The HA and NA segments of these three viruses were reassorted with cold-adapted A/Ann Arbor/6/60, the master donor virus for the live attenuated type A influenza vaccines (FluMist). The HA and NA residues differed between these three H3N2 viruses evaluated for their impact on virus replication in MDCK cells and in embryonated chicken eggs. It was determined that replication of A/Fujian/411/02 in eggs could be improved by either changing minimum of two HA residues (G186V and V226I) to increase the HA receptor-binding ability or by changing a minimum of two NA residues (E119Q and Q136K) to lower the NA enzymatic activity. Alternatively, recombinant A/Fujian/411/02 virus could be adapted to grow in eggs by two amino acid substitutions in the HA molecule (H183L and V226A), which also resulted in the increased HA receptor-binding activity. Thus, the balance between the HA and NA activities is critical for influenza virus replication in a different host system. The HA or NA changes that increased A/Fujian/411/02 virus replication in embryonated chicken eggs were found to have no significant impact on antigenicity of these recombinant viruses. This study demonstrated that the reverse genetics technology could be used to improve the manufacture of the influenza vaccines.

Lu, Bin; Zhou, Helen; Ye, Dan; Kemble, George; Jin, Hong

2005-01-01

364

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

2012-07-06

365

The application of GM (1,1) — Connection improved genetic algorithm in power load forecasting  

Microsoft Academic Search

In this paper, a GM (1, 1)-connection improved genetic algorithm (GM (1, 1)-IGA) is put forward to solve the problem of short-term load forecasting (STLF) in power system. While Traditional GM (1, 1) forecasting model is not accurate and the value of parameter OC is constant, the proposed algorithm could overcome these disadvantages. In order to construct optimal grey model

Wei Li; Zhu-hua Han

2007-01-01

366

On the application of genetic algorithms for optimising composites against impact loading  

Microsoft Academic Search

A genetic algorithm (GA) was adopted to optimise the response of a composite laminate subject to impact. Two different impact scenarios are presented: low-velocity impact of a slender laminated strip and high-velocity impact of a rectangular plate by a spherical impactor. In these cases, the GA's objective was to, respectively, minimise the peak deflection and minimise penetration by varying the

M. Yong; B. G. Falzon; L. Iannucci

2008-01-01

367

A multi-objective genetic local search algorithm and its application to flowshop scheduling  

Microsoft Academic Search

We propose a hybrid algorithm for finding a set of nondominated solutions of a multi objective optimization problem. In the proposed algorithm, a local search procedure is applied to each solution (i.e., each individual) generated by genetic operations. Our algorithm uses a weighted sum of multiple objectives as a fitness function. The fitness function is utilized when a pair of

Hisao Ishibuchi; Tadahiko Murata

1998-01-01

368

Genetics of the Encephalitis Vector, 'Culex tarsalis' for Possible Application in Integrated Control.  

National Technical Information Service (NTIS)

The projects here reported part of an overall program designed to change Culex tarsalis genetically to inhibit its propagation in nature, and to render it less effective as a vector of disease. A resume of progress for the year 1978-79 is as follows: The ...

M. Asman

1979-01-01

369

Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle  

Technology Transfer Automated Retrieval System (TEKTRAN)

Selection on important genetic markers can improve estimates of additive and dominance association effects. A composite population of beef cattle was selected for intermediate frequencies of myostatin (GDF8) F94L and µ-calpain (CAPN1) polymorphisms. Important additive associations of the GDF8 locu...

370

Industrial applications of genetically modified microorganisms: gene technology at Chr. Hansen A\\/S  

Microsoft Academic Search

The use of recombinant DNA technology to produce genetically modified microorganisms is one of the most important scientific advances of the 20th century. It has great potential in research because it allows the development of highly sensitive analytical procedures. It also has potential in industry, leading to processes and products that would be difficult to develop using conventional techniques. These

Claus Maxel Henriksen; Dan Nilsson; Sven Hansen; Eric Johansen

1999-01-01

371

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

372

Polymorphic Simple Sequence Repeat Regions in Chloroplast Genomes: Applications to the Population Genetics of Pines  

Microsoft Academic Search

Simple sequence repeats (SSRs), consisting of tandemly repeated multiple copies of mono-, di-, tri-, or tetranucleotide motifs, are ubiquitous in eukaryotic genomes and are frequently used as genetic markers, taking advantage of their length polymorphism. We have examined the polymorphism of such sequences in the chloroplast genomes of plants, by using a PCR-based assay. GenBank searches identified the presence of

W. Powell; M. Morgante; R. McDevitt; G. G. Vendramin; J. A. Rafalski

1995-01-01

373

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

374

RESPONSE TO AN ASYMMETRIC DEMAND FOR ATTRIBUTES: AN APPLICATION TO THE MARKET FOR GENETICALLY MODIFIED CROPS  

Microsoft Academic Search

A framework is developed for examining the price and welfare effects of the introduction of genetically modified (GM) crops. In the short run, non-GM grain generally becomes another niche product. However, more profound market effects are observed under some reasonable parameterizations. In the long run, consumer and producer welfare are usually greater after the introduction of GM technology. Nevertheless, in

Sergio H. Lence; Dermot J. Hayes

2001-01-01

375

Application of Hardware Architecture of Genetic Algorithm for Optimal Packet Scheduling  

Microsoft Academic Search

In Dense Wavelength Division Multiplexing (DWDM) technologies, the optimal packet scheduling issue is commonly encountered in multiple channel networks. NP-hard problems deal with finding a way to rearrange packets from multiple channels into a finite and rare channel. Genetic Algorithm (GA) is one of the most efficient ways to solve these issues. We hope to find a better solution to

Rong-hou Wu; Yang-han Lee; Shiann-tsong Sheu; Hsien-wei Tseng; Ming-hsueh Chuang; Yung-kuang Wang

2006-01-01

376

Application of the Protection Motivation Theory to Genetic Testing for Breast Cancer Risk  

Microsoft Academic Search

Background. Many women, even women at low risk, are interested in genetic testing for breast cancer risk. However, the test has little to offer for women at low to moderate risk. We applied the Protection Motivation Theory (PMT) to investigate predictors of women's motivation to obtain such a test.Methods. Women at low to moderate risk (n = 330) were recruited

Almut W. Helmes

2002-01-01

377

Application of the Improved Genetic Algorithms With Real Code on GPS Data Processing  

Microsoft Academic Search

Because of some advantages, such as simpleness, parallel and robustness on resolving numerical value optimization problems, genetic algorithms (GA) were improved and applied on global positioning system (GPS) high precision positioning data processing. Aimed on the integer nature of double difference ambiguities and the real nature of baseline coordinates, the real-coded methods of GA were improved in order to satisfy

Zhimin Liu; Zhixing Du; Rong Zou

2007-01-01

378

Topology and parameter optimization of ANN using genetic algorithm for application of textiles  

Microsoft Academic Search

The BP feed-forward neural network is popular in solving many non-linear multivariate and complex problems. The most important problem with neural network is to decide optimal structure and parameter settings. Literature presents a multitude of methods but there is no rigorous and accurate analytical method. This paper presents the hybrid approach of genetic algorithm and neural network computing for establishment

Lalita Admuthe; Shaila Apte; Sunil Admuthe

2009-01-01

379

Single-cell DNA and FISH analysis for application to preimplantation genetic diagnosis.  

PubMed

Preimplantation genetic testing, which includes preimplantation genetic diagnosis (PGD) and preimplantation genetic screening (PGS), is a form of a very early prenatal testing. The goal of this method is to avoid transfer of embryos affected with a specific genetic disease or condition. This unit describes the steps involved in amplifying DNA from a single blastomere and specific assays for detecting a variety of DNA mutations. For some assays, whole-genome amplification by primer-extension preamplification (PEP) is performed prior to analysis. Support protocols describe the biopsy of one or two blastomeres from the developing preimplantation embryo, isolation for further investigation of all blastomeres from embryos shown to have the mutant allele, and isolation of single lymphocytes or lymphoblastoid cells as models for single-cell DNA analysis. A procedure for FISH analysis on single interphase blastomeres is provided along with support protocols for probe preparation and probe validation, which is recommended as a preliminary step before performing any PGD or PGS FISH analysis. PMID:20063266

Chong, Samuel S; Gore-Langton, Robert E; Hughes, Mark R; Weremowicz, Stanislawa

2010-01-01

380

Genetic Set Recombination and Its Application to Neural Network Topology Optimisation  

Microsoft Academic Search

Forma analysis is applied to the task of op- timising the connectivity of a feed-forward neural network with a single layer of hidden units. This problem is reformulated as a mul- tiset optimisation problem and techniques are developed to allow principled genetic search over fixed- and variable-size sets and multi- sets. These techniques require a further gen- eralisation of the

Nicholas J. Radcliffe

1993-01-01

381

Application of genetic algorithm for optimum design of bolted composite lap joints  

Microsoft Academic Search

The genetic algorithm (GA), a powerful optimization technique for multiple extrema functions in multidimensional search spaces, is applied in conjunction with stress analysis to achieve optimum designs of bolted composite lap joints. The objective of the optimization is to ensure the highest strength of the joint. In this study, the laminate thickness, laminate lay-up, bolt location, bolt flexibility, and bolt

V. Kradinov; E. Madenci; D. R. Ambur

2007-01-01

382

User-centered design by genetic algorithms: Application to brass musical instrument optimization  

Microsoft Academic Search

This work presents an implementation of genetic algorithms (GAs) for a user-centered design of products. It describes at first a methodology for a user-centered design, based on the coupling between a subjective study to define desirable features and on objective study to find out the influencing objective variables. It relies on two domains that remain generally distinct: the design with

Emilie Poirson; Philippe Dépincé; Jean-François Petiot

2007-01-01

383

Application of genetic algorithms to fault diagnosis in nuclear power plants  

Microsoft Academic Search

A nuclear power plant (NPP) is a complex and highly reliable special system. Without expert knowledge, fault confirmation in the NPP can be prevented by illusive and real-time signals. A new method of fault diagnosis, based on genetic algorithms (GAs) has been developed to resolve this problem. This NPP fault diagnosis method combines GAs and classical probability with an expert

Zhou Yangping; Zhao Bingquan; Wu DongXin

2000-01-01

384

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

Microsoft Academic Search

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

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

1994-01-01

385

An application of genetic algorithms to lot-streaming flow shop scheduling  

Microsoft Academic Search

A Hybrid Genetic Algorithm (HGA) approach is proposed for a lot-streaming flow shop scheduling problem, in which a job (lot) is split into a number of smaller sublots so that successive operations can be overlapped. The objective is the minimization of the mean weighted absolute deviation of job completion times from due dates. This performance criterion has been shown to

SUK-HUN YOON; JOSE A. VENTURA

2002-01-01

386

New tools for preimplantation genetic diagnosis of Huntington's disease and their clinical applications  

Microsoft Academic Search

Huntington's disease (HD) is a late-onset neurodegenerative disorder transmitted as an autosomal dominant trait. The causative mutation was characterised in 1993. For HD carriers willing to create a family, prenatal diagnosis (PND) or preimplantation genetic diagnosis (PGD) based on the mutation identification can be offered. For at-risk persons who do not want to undergo presymptomatic testing (PT), an exclusion test

Céline Moutou; Nathalie Gardes; Stéphane Viville

2004-01-01

387

The beneficial effects of preimplantation genetic diagnosis for aneuploidy support extensive clinical application  

Microsoft Academic Search

The aim of this study was to evaluate the clinical impact of preimplantation genetic diagnosis (PGD) for aneuploidy on 193 patients who subsequently achieved 208 clinical pregnancies, in relation to their reproductive history. The 208 clinical pregnancies included in the study resulted from 1029 assisted conception cycles in combination with PGD for aneuploidy in 740 couples with a history of

Luca Gianaroli; M Cristina Magli; Anna P Ferraretti; Carla Tabanelli; Vincenzo Trengia; Valeria Farfalli; Giorgio Cavallini

2005-01-01

388

Application of vector optimization employing modified genetic algorithm to permanent magnet motor design  

Microsoft Academic Search

This paper presents a method to solve the vector optimization problem that determines both the noninferior solution set and the best compromise solution employing a modified genetic algorithm. The algorithm differs from the conventional one in the definition of fitness value and convergence criterion. Some parameters of the algorithm are adjusted to the vector optimization. The algorithm also contains the

Dong-Joon Sim; Hyun-Kyo Jung; Song-Yop Hahn; Jong-Soo Won

1997-01-01

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

Research on Application of Genetic Algorithm for Intelligent Mobile Robot Navigation Based on Dynamic Approach  

Microsoft Academic Search

An intelligent mobile robot navigation model based on dynamic approach is constructed, which is integrated both head-for-target behavior and obstacle avoidance behavior. The model is described by nonlinear differential equations. It is based on the stability theory of dynamical system. The weight coefficient of each behavior which represents superiority in competition between behaviors is optimized by genetic algorithm. Navigation of

Shiqiang Yang; Weiping Fu; Dexin Li; Wen Wang

2007-01-01

391

On the Application of Multiple-Deme Parallel Genetic Algorithms in Astrophysics  

Microsoft Academic Search

We present a Parallel Genetic Algorithm (PGA) for the solution of a constrained global optimization problem arising in the detection of gravitational waves through the matched filter technique. This is a hard problem, since it has a black-box stochastic objective function, which is highly nonlinear, multiextremal and computationally expensive. Our PGA uses multiple subpopulations (demes) that evolve separately by the

Daniela di Serafino; Filippo Riccio

2010-01-01

392

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

393

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

394

A Genetic Programming System for Time Series Prediction and Its Application to El Niño Forecast  

Microsoft Academic Search

In this paper a system based on Genetic Programming for forecasting nonlinear time series is outlined. Our system is endowed\\u000a with two features. Firstly, at any given time t, it performs a ?-steps ahead prediction (i.e. it forecasts the value at time t + ?) based on the set of input values for the n time steps preceding t. Secondly,

I. De Falco; A. Della Cioppa; E. Tarantino

395

Fuzzy Logic Controller Based on Observed Signals and a Genetic Algorithm Application with STATCOM for Power System Stabilization  

NASA Astrophysics Data System (ADS)

Fuzzy logic control has been applied to various applications in power systems. Its control rules and membership functions are typically obtained by trial and error methods or experience knowledge. Proposed here is the application of a micro-genetic algorithm (micro-GA) to simultaneously design optimal membership functions and control rules for STATCOM. First, we propose a simple approach to extract membership functions and fuzzy logic control rules based on observed signals. Then a proposed GA will be applied to optimize membership functions and its control rules. To validate the effectiveness of the proposed approach, several simulation studies have been performed on a multimachine power system. Simulation results show that the proposed fuzzy logic controller with STATCOM can effectively and robustly enhance the damping of oscillations.

Hongesombut, Komsan; Mitani, Yasunori; Tsuji, Kiichiro

396

A fast fine-grained genetic algorithm for spectrum fitting: An application to X-ray spectra  

NASA Astrophysics Data System (ADS)

Often the result of the interaction of radiation with matter is represented by a spectrum. Regardless of the type of radiation used, a spectrum consists of peaks superimposed on a background. The important information is contained in the peak, so the derivation of the peaks parameters is fundamental. However, in most cases the fitting of the spectrum is an ill-posed problem, because of the presence of superimposed peaks. In this case the algorithms reported in the literature sometimes fail. For these reasons a genetic algorithm approach has been developed and is described here. Its novelty for this kind of application is represented by the use of a fine-grained strategy that makes it considerably faster than other implementations of this class of algorithms. Some results of its application to X-ray spectra are presented and discussed.

Brunetti, Antonio

2013-03-01

397

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

2013-09-23

398

Reversible simulation of irreversible computation  

NASA Astrophysics Data System (ADS)

Computer computations are generally irreversible while the laws of physics are reversible. This mismatch is penalized by among other things generating excess thermic entropy in the computation. Computing performance has improved to the extent that efficiency degrades unless all algorithms are executed reversibly, for example by a universal reversible simulation of irreversible computations. All known reversible simulations are either space hungry or time hungry. The leanest method was proposed by Bennett and can be analyzed using a simple `reversible' pebble game. The reachable reversible simulation instantaneous descriptions (pebble configurations) of such pebble games are characterized completely. As a corollary we obtain the reversible simulation by Bennett and, moreover, show that it is a space-optimal pebble game. We also introduce irreversible steps and give a theorem on the tradeoff between the number of allowed irreversible steps and the memory gain in the pebble game. In this resource-bounded setting the limited erasing needs to be performed at precise instants during the simulation. The reversible simulation can be modified so that it is applicable also when the simulated computation time is unknown.

Li, Ming; Tromp, John; Vitányi, Paul

1998-09-01

399

Cleft lip and palate genetics and application in early embryological development.  

PubMed

The development of the head involves the interaction of several cell populations and coordination of cell signalling pathways, which when disrupted can cause defects such as facial clefts. This review concentrates on genetic contributions to facial clefts with and without cleft palate (CP). An overview of early palatal development with emphasis on muscle and bone development is blended with the effects of environmental insults and known genetic mutations that impact human palatal development. An extensive table of known genes in syndromic and non-syndromic CP, with or without cleft lip (CL), is provided. We have also included some genes that have been identified in environmental risk factors for CP/L. We include primary and review references on this topic. PMID:19884679

Yu, Wenli; Serrano, Maria; Miguel, Symone San; Ruest, L Bruno; Svoboda, Kathy K H

2009-10-01

400

Containment of a genetically engineered microorganism during a field bioremediation application.  

PubMed

A field release of a genetically engineered microorganism was performed at the Field Lysimeter Site on the Oak Ridge Reservation. Six large lysimeters were filled with soil that had been contaminated with a mixture of naphthalene, phenanthrene, and anthracene. A genetically engineered bacterial strain, Pseudomonas fluorescens HK44, was sprayed onto the surface of the soil during soil loading. This strain contains a fusion between the lux genes of Vibrio fischeri and the promoter for the lower pathway of naphthalene degradation, enabling the strain to become bioluminescent when it is degrading naphthalene. Release of the bacteria outside the lysimeters was monitored, using selective agar plates and one-stage Anderson air samplers. Although approximately 10(14) bacteria were sprayed during the loading process, escape was only detected sporadically; the highest incidence of bacterial escape was found when the relative humidity and wind speed were low. PMID:10222588

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

1999-03-01

401

Paleothermometry via a Genetic Algorithm With an Application to GISP2 Borehole Data  

NASA Astrophysics Data System (ADS)

Borehole temperature-depth profiles of ice sheets contain information about local climate change stretching back more than a hundred thousand years to the Eemian. Surface temperature histories at the Greenland ice sheet drill sites, GRIP and GISP2, have been reconstructed in the literature using a Control Method (Cuffey et al., 1995) and an Inverse Monte Carlo method (Dahl-Jensen, et al., 1998). In contrast to previous inversion efforts, the flexibility of the proposed Genetic Algorithm based method makes it possible to easily incorporate other climate proxies obtained from the ice core itself as constraints into the inversion process either by augmenting the fitness function with appropriate penalty terms or by treating it as a multi-objective optimization problem. The Genetic Algorithm based surface temperature inversion is applied to synthetic borehole temperature profiles and the GISP2 borehole data. Comparisons between the reconstructed and prescribed temperature forcing in the synthetic cases demonstrate the robustness of the new inversion method. Inversion of GISP2 data shows that the retrodicted 40,000 year long surface temperature history obtained by the Genetic Algorithm agrees well with results of previous studies while using only minimal problem specific knowledge. The resulting surface temperature reconstruction is used as an independent calibration of the linear oxygen-isotope paleothermometer (? 18O = ? T + ? ) and yields a value for ? = 0.360 per mil ° C-1 and ? = -23.9 per mil. The Genetic Algorithm based inversion method enables a multi-proxy approach to ice sheet borehole temperature inversions which should improve the accuracy and resolution of surface temperature reconstructions and aid in the interpretation of very long ? 18O records from ice cores as a local temperature proxy.

Kim, Y.

2003-12-01

402

Application of EBV-based artificial chromosome to genetic engineering of mammalian cells and tissues  

Microsoft Academic Search

Although gene transduction offers a fundamental technology to analyze, manipulate, and regulate functions of mammalian cells, gene delivery systems so far established remains insufficient in terms of the efficiencies of delivery and expression as well as long-term stability. We have examined various non-viral gene transduction systems, including synthetic macromolecules and physical procedures, to genetically engineer a variety of cells\\/tissues\\/organs. Noteworthy,

Tsunao Kishida; Masaharu Shin-Ya; Jiro Imanishi; Osam Mazda

2005-01-01

403

Application of Multiple Fuzzy-Neuro Force Controllers in an Unknown Environment Using Genetic Algorithms  

Microsoft Academic Search

This paper presents an effective force control method in which multiple fuzzy-neuro force controllers are suitably and automatically combined with a proper rate in accordance with the unknown dynamics of an environment. The optimal combination rate of the fuzzy-neuro force controllers according to the environment dynamics is defined online by a neural network which is off-line trained with genetic algorithms.

Kazuo Kiguchi; Keigo Watanabe; Kiyotaka Izumi; Toshio Fukuda

2000-01-01

404

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

405

Genetic Algorithm Application to the Structural Properties of Si–Ge Mixed Clusters  

Microsoft Academic Search

Optimum geometries of silicon–germanium (Si–Ge) clusters are found using a single parent genetic algorithm. 100 atom and 150 atom clusters are studied with some variety of compositions and initial geometries. Total interaction energies, distances of Si and Ge atoms to the cluster centers, and average bond lengths are calculated. Si-core Ge-shell geometry is found to be favorable compared to other

Nazim Dugan; ?akir Erkoç

2009-01-01

406

Application of Genetic Algorithm and Finite Element Method for backcalculating layer moduli of flexible pavements  

Microsoft Academic Search

The backcalculation program, GAPAVE, which uses the Genetic Algorithm (GA) and Finite Element Method (FEM), is developed to\\u000a predict the layer moduli from Falling Weight Deflectometer (FWD) deflections. The use of the FEM in the forward calculation\\u000a that incorporates the GA improves the accuracy in backcalculating the pavement layer moduli. The optimum GA parameters are\\u000a selected from sensitivity analysis for

Seong-Wan Park; Hee Mun Park; Jung-Joon Hwang

2010-01-01

407

A review of the current applications of genetic algorithms in assembly line balancing  

Microsoft Academic Search

Most of the problems involving the design and plan of manufacturing systems are combinatorial and NP-hard. A well-known manufacturing\\u000a optimization problem is the assembly line balancing problem (ALBP). Due to the complexity of the problem, in recent years,\\u000a a growing number of researchers have employed genetic algorithms. In this article, a survey has been conducted from the recent\\u000a published literature

Seren Ozmehmet Tasan; Semra Tunali

2008-01-01

408

Application and adaptation of Genetic Algorithm in optimal Eco-friendly reservoir operation  

Microsoft Academic Search

Optimal reservoir operation is a complex problem that involves multiple objectives, multiple constraints as well as considerable risk and uncertainty. Eco-friendly reservoir operation makes it more complicated by taking into account a conflicting objective or highly nonlinear constraint related to ecosystem requirement. The study developed a model to optimize reservoir operation in an Eco-friendly manner by using Genetic Algorithm(GA) and

Duan Chen; Jibin Han; Jin Chen

2010-01-01

409

Development and Application of Microsatellites in Carcinus maenas: Genetic Differentiation between Northern and Central Portuguese Populations  

PubMed Central

Carcinus maenas, the common shore crab of European coastal waters, has recently gained notoriety due to its globally invasive nature associated with drastic ecological and economic effects. The native ubiquity and worldwide importance of C. maenas has resulted in it becoming one of the best-studied estuarine crustacean species globally. Accordingly, there is significant interest in investigating the population genetic structure of this broadly distributed crab along European and invaded coastlines. Here, we developed polymerase chain reaction (PCR) primers for one dinucleotide and two trinucleotide microsatellite loci, resulting from an enrichment process based on Portuguese populations. Combining these three new markers with six existing markers, we examined levels of genetic diversity and population structure of C. maenas in two coastal regions from Northern and Central Portugal. Genotypes showed that locus polymorphism ranged from 10 to 42 alleles (N?=?135) and observed heterozygosity per locus ranged from 0.745 to 0.987 with expected heterozygosity ranging from 0.711 to 0.960; values typical of marine decapods. The markers revealed weak, but significant structuring among populations (global FST?=?0.004) across a 450 km (over-water distance) spatial scale. Combinations of these and existing markers will be useful for studying population genetic parameters at a range of spatial scales of C. maenas throughout its expanding species range.

Pascoal, Sonia; Creer, Simon; Taylor, Martin I.; Queiroga, Henrique; Carvalho, Gary; Mendo, Sonia

2009-01-01

410

Preimplantation genetic haplotyping a new application for diagnosis of translocation carrier’s embryos preliminary observations of two robertsonian translocation carrier families  

Microsoft Academic Search

Purpose  Preimplantation genetic diagnosis using fluorescence in-situ hybridization (PGD-FISH) is currently the most common reproductive\\u000a solution for translocation carriers. However, this technique usually does not differentiate between embryos carrying the balanced\\u000a form of the translocation and those carrying the homologous normal chromosomes. We developed a new application of preimplantation\\u000a genetic haplotyping (PGH) that can identify and distinguish between all forms of

Jana Shamash; Shlomit Rienstein; Haike Wolf-Reznik; Elon Pras; Michal Dekel; Talia Litmanovitch; Masha Brengauz; Boleslav Goldman; Hagith Yonath; Jehoshua Dor; Jacob Levron; Ayala Aviram-Goldring

2011-01-01

411

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.

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

2012-01-01

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.

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

Artificial neural network, genetic algorithm, and logistic regression applications for predicting renal colic in emergency settings  

Microsoft Academic Search

Background  Logistic regression is the most common statistical model for processing multivariate data in the medical literature. Artificial\\u000a intelligence models like an artificial neural network (ANN) and genetic algorithm (GA) may also be useful to interpret medical\\u000a data.\\u000a \\u000a \\u000a \\u000a Aims  The purpose of this study was to perform artificial intelligence models on a medical data sheet and compare to logistic regression.\\u000a \\u000a \\u000a \\u000a Methods  ANN, GA,

Cenker Eken; Ugur Bilge; Mutlu Kartal; Oktay Eray

2009-01-01

414

[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

415

[Application of DNA extraction kit, 'GM quicker' for detection of genetically modified soybeans].  

PubMed

Several DNA extraction methods have been officially introduced to detect genetically modified soybeans, but the choice of DNA extraction kits depend on the nature of the samples, such as grains or processed foods. To overcome this disadvantage, we examined whether the GM quicker kit is available for both grains and processed foods. We compared GM quicker with four approved DNA extraction kits in respect of DNA purity, copy numbers of lectin gene, and working time. We found that the DNA quality of GM quicker was superior to that of the other kits for grains, and the procedure was faster. However, in the case of processed foods, GM quicker was not superior to the other kits. We therefore investigated an unapproved GM quicker 3 kit, which is available for DNA extraction from processed foods, such as tofu and boiled soybeans. The GM quicker 3 kit provided good DNA quality from both grains and processed foods, so we made a minor modification of the GM quicker-based protocol that was suitable for processed foods, using GM quicker and its reagents. The modified method enhanced the performance of GM quicker with processed foods. We believe that GM quicker with the modified protocol is an excellent tool to obtain high-quality DNA from grains and processed foods for detection of genetically modified soybeans. PMID:22450668

Sato, Noriko; Sugiura, Yoshitsugu; Tanaka, Toshitsugu

2012-01-01

416

Establishment of a genetic transformation system and its application in Thermoanaerobacter tengcongensis.  

PubMed

The whole-genome sequence of Thermoanaerobacter tengcongensis, an anaerobic thermophilic bacterium isolated from the Tengchong hot spring in China, was completed in 2002. However, in vivo studies on the genes of this strain have been hindered in the absence of genetic manipulation system. In order to establish such a system, the plasmid pBOL01 containing the replication origin of the T. tengcongensis chromosome and a kanamycin resistance cassette, in which kanamycin resistance gene expression was controlled by the tte1482 promoter from T. tengcongensis, was constructed and introduced into T. tengcongensis via electroporation. Subsequently, the high transformation efficiency occurred when using freshly cultured T. tengcongensis cells without electroporation treatment, suggesting that T. tengcongensis is naturally competent under appropriate growth stage. A genetic transformation system for this strain was then established based on these important components, and this system was proved to be available for studying physiological characters of T. tengcongensis in vivo by means of hisG gene disruption and complementation. PMID:23089366

Liu, Bo; Wang, Chuan; Yang, Haihua; Tan, Huarong

2012-07-24

417

Flow of genetic information through agricultural ecosystems: a generic modelling framework with application to pesticide-resistance weeds and genetically modified crops  

Microsoft Academic Search

Unintended spatial spread of genetic information is one of the major problems in modern agriculture. The vertical distribution of transgenic properties and the spatial spread of resistant weeds and pests are likely to develop under long-term pesticide use. These are complex systems that require an integrated view of population dynamics, genetics, and physical transport processes. Mathematical models may be utilised

O. Richter; R. Seppelt

2004-01-01

418

Utility of a multiplex reverse transcriptase-polymerase chain reaction assay (HemaVision) in the evaluation of genetic abnormalities in Korean children with acute leukemia: a single institution study  

PubMed Central

Purpose In children with acute leukemia, bone marrow genetic abnormalities (GA) have prognostic significance, and may be the basis for minimal residual disease monitoring. Since April 2007, we have used a multiplex reverse transcriptase-polymerase chain reaction tool (HemaVision) to detect of GA. Methods In this study, we reviewed the results of HemaVision screening in 270 children with acute leukemia, newly diagnosed at The Catholic University of Korea from April 2007 to December 2011, and compared the results with those of fluorescence in situ hybridization (FISH), and G-band karyotyping. Results Among the 270 children (153 males, 117 females), 187 acute lymphoblastic leukemia and 74 acute myeloid leukemia patients were identified. Overall, GA was detected in 230 patients (85.2%). HemaVision, FISH, and G-band karyotyping identified GA in 125 (46.3%), 126 (46.7%), and 215 patients (79.6%), respectively. TEL-AML1 (20.9%, 39/187) and AML1-ETO (27%, 20/74) were the most common GA in ALL and AML, respectively. Overall sensitivity of HemaVision was 98.4%, with false-negative results in 2 instances: 1 each for TEL-AML1 and MLL-AF4. An aggregate of diseasesspecific FISH showed 100% sensitivity in detection of GA covered by HemaVision for actual probes utilized. G-band karyotype revealed GA other than those covered by HemaVison screening in 133 patients (49.3%). Except for hyperdiplody and hypodiploidy, recurrent GA as defined by the World Health Organizationthat were not screened by HemaVision, were absent in the karyotype. Conclusion HemaVision, supported by an aggregate of FISH tests for important translocations, may allow for accurate diagnosis of GA in Korean children with acute leukemia.

Kim, Hye-Jin; Oh, Hyun Jin; Jang, Pil-Sang; Chung, Nack-Gyun; Kim, Myungshin; Lim, Jihyang; Cho, Bin; Kim, Hack-Ki

2013-01-01

419

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.

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

2011-01-01

420

Detection of Intergenerational Genetic Effects with Application to HLA-B Matching as a Risk Factor for Schizophrenia  

PubMed Central

Background and Methods Association studies using unrelated individuals cannot detect intergenerational genetic effects contributing to disease. To detect these effects, we improve the extended maternal-fetal genotype (EMFG) incompatibility test to estimate any combination of maternal effects, offspring effects, and their interactions at polymorphic loci or multiple SNPs, using any size pedigrees. We explore the advantages of using extended pedigrees rather than nuclear families. We apply our methods to schizophrenia pedigrees to investigate whether the previously associated mother-daughter HLA-B matching is a genuine risk or the result of bias. Results Simulations demonstrate that using the EMFG test with extended pedigrees increases power and precision, while partitioning extended pedigrees into nuclear families can underestimate intergenerational effects. Application to actual data demonstrates that mother-daughter HLA-B matching remains a schizophrenia risk factor. Furthermore, ascertainment and mate selection biases cannot by themselves explain the observed HLA-B matching and schizophrenia association. Conclusions Our results demonstrate the power of the EMFG test to examine intergenerational genetic effects, highlight the importance of pedigree rather than case/control or case-mother/control-mother designs, illustrate that pedigrees provide a means to examine alternative, non-causal mechanisms, and they strongly support the hypothesis that HLA-B matching is causally involved in the etiology of schizophrenia in females.

Childs, Erica J.; Sobel, Eric M.; Palmer, Christina G.S.; Sinsheimer, Janet S.

2011-01-01

421

Reverse Genetic Approaches to Cloning Deafness Genes  

Microsoft Academic Search

Not Available Bibtex entry for this abstract Preferred format for this abstract (see Preferences) Find Similar Abstracts: Use: Authors Title Return: Query Results Return items starting with number Query Form Database: Astronomy Physics arXiv e-prints

S. D. M. Brown; K. A. Brown; M. J. Sutcliffe; J. S. Cavanna; A. J. Greenfield; K. P. Steel

1991-01-01

422

Binary Classification using Decision Tree based Genetic Programming and Its Application to Analysis of Bio-mass Data  

NASA Astrophysics Data System (ADS)

In machine learning, pattern recognition may be the most popular task. ``Similar'' patterns identification is also very important in biology because first, it is useful for prediction of patterns associated with disease, for example cancer tissue (normal or tumor) second, similarity or dissimilarity of the kinetic patterns is used to identify coordinately controlled genes or proteins involved in the same regulatory process. Third, similar genes (proteins) share similar functions. In this paper, we present an algorithm which uses genetic programming to create decision tree for binary classification problem. The application of the algorithm was implemented on five real biological databases. Base on the results of comparisons with well-known methods, we see that the algorithm is outstanding in most of cases.

To, Cuong; Pham, Tuan D.

2010-01-01

423

Intertransaction Class Association Rule Mining Based on Genetic Network Programming and Its Application to Stock Market Prediction  

NASA Astrophysics Data System (ADS)

Intertransaction association rules have been reported to be useful in many fields such as stock market prediction, but still there are not so many efficient methods to dig them out from large data sets. Furthermore, how to use and measure these more complex rules should be considered carefully. In this paper, we propose a new intertransaction class association rule mining method based on Genetic Network Programming (GNP), which has the ability to overcome some shortages of Apriori-like based intertransaction association methods. Moreover, a general classifier model for intertransaction rules is also introduced. In experiments on the real world application of stock market prediction, the method shows its efficiency and ability to obtain good results and can bring more benefits with a suitable classifier considering larger interval span.

Yang, Yuchen; Mabu, Shingo; Shimada, Kaoru; Hirasawa, Kotaro

424

Theory of nematic order with aggregate dehydration for reversibly assembling proteins in concentrated solutions: Application to sickle-cell hemoglobin polymers  

Microsoft Academic Search

The reversible association of globular protein molecules in concentrated solution leads to highly polydisperse fibers, e.g., actin filaments, microtubules, and sickle-cell hemoglobin fibers. At high concentrations, excluded-volume interactions between the fibers lead to spontaneous alignment analogous to that in simple lyotropic liquid crystals. However, the phase behavior of reversibly associating proteins is complicated by the threefold coupling between the growth,

Reinhard Hentschke; Judith Herzfeld

1991-01-01

425

Multi-Resonator Generation by Genetic Optimization for Application to Planar-Circuit Bandpass Filters  

NASA Astrophysics Data System (ADS)

This paper proposes a design method of arbitrarily-shaped bandpass filters with multiple resonators in the limited space. Although the proposed method is based on the genetic-algorithm (GA) optimization, we newly introduce the fitness function which estimates not only the magnitude of S-parameters but also the phase characteristics in a passband. Conventional GAs without phase evaluation are difficult to design a filter having the specified number of resonators efficiently, whereas the present method can easily construct such a filter. As an example, arbitrarily-shaped planar-circuit filters with 3 and 4 resonators are optimized in the limited space and fabricated. The effectiveness of the present technique is verified by comparison of frequency responses between the calculated and the measured results.

Tsuji, Mikio; Deguchi, Hiroyuki; Kido, Akinori; Ohira, Masataka

426

Application of genetic algorithm in the evaluation of the profile error of archimedes helicoid surface  

NASA Astrophysics Data System (ADS)

According to minimum zone condition, a method for evaluating the profile error of Archimedes helicoid surface based on Genetic Algorithm (GA) is proposed. The mathematic model of the surface is provided and the unknown parameters in the equation of surface are acquired through least square method. Principle of GA is explained. Then, the profile error of Archimedes Helicoid surface is obtained through GA optimization method. To validate the proposed method, the profile error of an Archimedes helicoid surface, Archimedes Cylindrical worm (ZA worm) surface, is evaluated. The results show that the proposed method is capable of correctly evaluating the profile error of Archimedes helicoid surface and satisfy the evaluation standard of the Minimum Zone Method. It can be applied to deal with the measured data of profile error of complex surface obtained by three coordinate measurement machines (CMM).

Zhu, Lianqing; Chen, Yunfang; Chen, Qingshan; Meng, Hao

2010-12-01

427

Genetic Network Programming with Reinforcement Learning and Its Application to Making Mobile Robot Behavior  

NASA Astrophysics Data System (ADS)

A new graph-based evolutionary algorithm called “Genetic Network Programming, GNP" has been proposed. The solutions of GNP are represented as graph structures, which can improve the expression ability and performance. In addition, GNP with Reinforcement Learning (GNP-RL) has been proposed to search for solutions efficiently. GNP-RL can use current information (state and reward) and change its programs during task execution. Thus, it has an advantage over evolution-based algorithms in case much information can be obtained during task execution. The GNP we proposed in the previous research deals with discrete information, but in this paper, we extend the conventional GNP-RL which can deal with numerical information. The proposed method is applied to the controller of Khepera simulator and its performance is evaluated.

Mabu, Shingo; Hatakeyama, Hiroyuki; Thu, Moe Thu; Hirasawa, Kotaro; Hu, Jinglu

428

Tree genetic engineering and applications to sustainable forestry and biomass production.  

PubMed

Forest trees provide raw materials, help to maintain biodiversity and mitigate the effects of climate change. Certain tree species can also be used as feedstocks for bioenergy production. Achieving these goals may require the introduction or modified expression of genes to enhance biomass production in a sustainable and environmentally responsible manner. Tree genetic engineering has advanced to the point at which genes for desirable traits can now be introduced and expressed efficiently; examples include biotic and abiotic stress tolerance, improved wood properties, root formation and phytoremediation. Transgene confinement, including flowering control, may be needed to avoid ecological risks and satisfy regulatory requirements. This and stable expression are key issues that need to be resolved before transgenic trees can be used commercially. PMID:20970211

Harfouche, Antoine; Meilan, Richard; Altman, Arie

2010-10-21

429

Genetic regulation and potentially therapeutic application of cancer-associated fibroblasts in oral cancer.  

PubMed

Carcinoma-associated fibroblast (CAF) is the most important host cell type in tumor microenvironment, which greatly contributes to tumor initiation, progression, and metastasis. Therefore, a large amount of data has emerged, showing the cancer-promoting function of these cells via paracrine effects that escort tumor cells through all the steps of cancer development. CAF is a heterogeneous cell population that can arise from the differentiation of resting fibroblasts, epithelial cells, endothelial cells, and mesenchymal stem cells. This review summarizes the current knowledge of the role of CAFs in tumor progression, with a particular focus on the cellular and molecular features and recent advances in researches on the genetic status and microRNA regulation, and addresses the potential prognostic and therapeutic values for patients with oral cancer by targeting CAFs. PMID:23782231

Wang, Jingyi; Min, Anjie; Gao, Shan; Tang, Zhangui

2013-06-19

430

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

431

Mining Genetic Epidemiology Data with Bayesian Networks Application to APOE Gene Variation and Plasma Lipid Levels  

PubMed Central

There is a critical need for data-mining methods that can identify SNPs that predict among-individual variation in a phenotype of interest and reverse-engineer the biological network of relationships between SNPs, phenotypes, and other factors. This problem is both challenging and important in light of the large number of SNPs in many genes of interest and across the human genome. A potentially fruitful form of exploratory data analysis is the Bayesian or Belief network. A Bayesian or Belief network provides an analytic approach for identifying robust predictors of among-individual variation in a disease endpoints or risk factor levels. We have applied Belief networks to SNP variation in the human APOE gene and plasma apolipoprotein E levels from two samples: 702 African-Americans from Jackson, MS, and 854 non-Hispanic whites from Rochester, MN. Twenty variable sites in the APOE gene were genotyped in both samples. In Jackson, MS, SNPs 4036 and 4075 were identified to influence plasma apoE levels. In Rochester, MN, SNPs 3937 and 4075 were identified to influence plasma apoE levels. All three SNPs had been previously implicated in affecting measures of lipid and lipoprotein metabolism. Like all data-mining methods, Belief networks are meant to complement traditional hypothesis-driven methods of data analysis. These results document the utility of a Belief network approach for mining large scale genotype–phenotype association data.

RODIN, ANDREI; MOSLEY, THOMAS H.; CLARK, ANDREW G.; SING, CHARLES F.; BOERWINKLE, ERIC

2005-01-01

432

Determination and evaluation of genetic coefficients of peanut lines for breeding applications  

Microsoft Academic Search

Application of a crop simulation model as a plant breeding tool requires cultivar-specific coefficients for a large number of breeding lines which are commonly not available. These cultivar coefficients are normally estimated from field experiments conducted under optimum conditions over several environments, that include a combination of multiple planting dates or locations. However, it is difficult to adhere to this

P. Banterng; A. Patanothai; K. Pannangpetch; S. Jogloy; G. Hoogenboom

2004-01-01

433

Applications of High-Performance Computing (HPC) in Plant Breeding, Conservation, and Genetics  

Technology Transfer Automated Retrieval System (TEKTRAN)

Increasingly powerful and informative DNA sequencing and genotyping techniques, instruments, and software are being developed and used for a wide variety of applications in agriculture. However, the increasing flux and accumulation of data will also require more HPC facilities and expertise. In co...

434

The use of yeast genetic diversity for agricultural and biotechnological applications  

Technology Transfer Automated Retrieval System (TEKTRAN)

Many types of yeast have been shown to be effective for biocontrol of field, greenhouse, and storage diseases of agricultural crops. Yeasts are generally regarded as safe for a wide variety of applications and some species establish large populations on leaf and fruit surfaces, resulting in disease ...

435

Genetically modified lactic acid bacteria: applications to food or health and risk assessment  

Microsoft Academic Search

Lactic acid bacteria have a long history of use in fermented food products. Progress in gene technology allows their modification by introducing new genes or by modifying their metabolic functions. These modifications may lead to improvements in food technology (bacteria better fitted to technological processes, leading to improved organoleptic properties…), or to new applications including bacteria producing therapeutic molecules that

Pierre Renault

2002-01-01

436

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

437

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

438

Application of the PHO5-gene-fusion technology to molecular genetics and biotechnology in yeast  

Microsoft Academic Search

Modern biological scientists employ numerous approaches for solving their problems. Among these approaches, the gene fusion is surely one of the well-established valuable tools in various fields of biological sciences. A wide range of applications have been developed to analyze a variety of biological phenomena such as transriptional regulation, pre-mRNA processing, mRNA decay, translation, protein localization and even protein transport

Satoshi Harashima; Yoshinobu Kaneko

2001-01-01

439

Application of siRNA Library in High-Throughput Genetic Screens of Mammalian Cells  

Microsoft Academic Search

Small interfering (si)RNA directs gene-specific silencing in both model organisms and mammalian cells through RNA interference. The discovery of this phenomenon has provided a valuable tool to study loss-of-function phenotype of gene. The most recent breakthrough in the generation of large-scale mammalian siRNA libraries fur- ther moves forward the application of RNA interference, providing a powerful plat- form to carry

Li-Na Zhao; Ting-Ting Li; Yang-Lin Pan; Han-Bing Ning; Zhi-Guo Liu; Dai-Ming Fan

2005-01-01

440