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Sample records for selective recombinant genotyping

  1. Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination.

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    Joseph A Ross

    2011-07-01

    Full Text Available The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by the central, low-recombination domain is highly correlated between species. However, the C. briggsae intra-species comparison reveals striking variation in the distribution of recombination between domains. Hybrid lines made with the more divergent pair of strains also exhibit pervasive marker transmission ratio distortion, evidence of selection acting on hybrid genotypes. The strongest effect, on chromosome III, is explained by a developmental delay phenotype exhibited by some hybrid F2 animals. In addition, on chromosomes IV and V, cross direction-specific biases towards one parental genotype suggest the existence of cytonuclear epistatic interactions. These interactions are discussed in relation to surprising mitochondrial genome polymorphism in C. briggsae, evidence that the two strains diverged in allopatry, the potential for local adaptation, and the evolution of Dobzhansky-Muller incompatibilities. The genetic and genomic resources resulting from this work will support future efforts to understand inter-strain divergence as well as facilitate studies of gene function, natural variation, and the evolution of recombination in Caenorhabditis nematodes.

  2. Fruit characteristics of the selected fig genotypes

    African Journals Online (AJOL)

    GREGORY

    2010-09-13

    Sep 13, 2010 ... The aim of this research was determine of fruit characteristics and select of some significant fig genotypes grown in Kiziltepe district of Mardin province. No studies have been made on the fig genotypes in Kiziltepe district by researchers up to now. Therefore, this study was very important. In this research, six ...

  3. Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping.

    Science.gov (United States)

    Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung

    2018-01-11

    The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018. Published by Elsevier Inc.

  4. Participatory selection of mungbean genotypes in Uganda ...

    African Journals Online (AJOL)

    We captured twenty five traits during farmer interviews out of which six traits were identified (through group discussions) as the most often used by farmers when selecting the best mungbean genotypes. The traits were; yield, overall performance, seed size, seed colour, marketability and early maturity. Nine out of eleven ...

  5. Carbon isotope fractionation for cotton genotype selection

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    Giovani Greigh de Brito

    2014-09-01

    Full Text Available The objective of this work was to evaluate the carbon isotope fractionation as a phenomic facility for cotton selection in contrasting environments and to assess its relationship with yield components. The experiments were carried out in a randomized block design, with four replicates, in the municipalities of Santa Helena de Goiás (SHGO and Montividiu (MONT, in the state of Goiás, Brazil. The analysis of carbon isotope discrimination (Δ was performed in 15 breeding lines and three cultivars. Subsequently, the root growth kinetic and root system architecture from the selected genotypes were determined. In both locations, Δ analyses were suitable to discriminate cotton genotypes. There was a positive correlation between Δ and seed-cotton yield in SHGO, where water deficit was more severe. In this site, the negative correlations found between Δ and fiber percentage indicate an integrative effect of gas exchange on Δ and its association with yield components. As for root robustness and growth kinetic, the GO 05 809 genotype performance contributes to sustain the highest values of Δ found in MONT, where edaphoclimatic conditions were more suitable for cotton. The use of Δ analysis as a phenomic facility can help to select cotton genotypes, in order to obtain plants with higher efficiency for gas exchange and water use.

  6. Cotton genotypes selection through artificial neural networks.

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    Júnior, E G Silva; Cardoso, D B O; Reis, M C; Nascimento, A F O; Bortolin, D I; Martins, M R; Sousa, L B

    2017-09-27

    Breeding programs currently use statistical analysis to assist in the identification of superior genotypes at various stages of a cultivar's development. Differently from these analyses, the computational intelligence approach has been little explored in genetic improvement of cotton. Thus, this study was carried out with the objective of presenting the use of artificial neural networks as auxiliary tools in the improvement of the cotton to improve fiber quality. To demonstrate the applicability of this approach, this research was carried out using the evaluation data of 40 genotypes. In order to classify the genotypes for fiber quality, the artificial neural networks were trained with replicate data of 20 genotypes of cotton evaluated in the harvests of 2013/14 and 2014/15, regarding fiber length, uniformity of length, fiber strength, micronaire index, elongation, short fiber index, maturity index, reflectance degree, and fiber quality index. This quality index was estimated by means of a weighted average on the determined score (1 to 5) of each characteristic of the HVI evaluated, according to its industry standards. The artificial neural networks presented a high capacity of correct classification of the 20 selected genotypes based on the fiber quality index, so that when using fiber length associated with the short fiber index, fiber maturation, and micronaire index, the artificial neural networks presented better results than using only fiber length and previous associations. It was also observed that to submit data of means of new genotypes to the neural networks trained with data of repetition, provides better results of classification of the genotypes. When observing the results obtained in the present study, it was verified that the artificial neural networks present great potential to be used in the different stages of a genetic improvement program of the cotton, aiming at the improvement of the fiber quality of the future cultivars.

  7. Combination treatment with hepatitis C virus protease and NS5A inhibitors is effective against recombinant genotype 1a, 2a, and 3a viruses

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Jensen, Sanne B; Li, Yi-Ping

    2013-01-01

    -FL) recombinants relying only on the JFH1 NS3 helicase, NS5B, and the 3' untranslated region. With identified adaptive mutations, semi-FL recombinants of genotypes(isolates) 1a(TN) and 3a(S52) produced supernatant infectivity titers of ~4 log(10) focus-forming units/ml in Huh7.5 cells. Genotype 1a(TN) adaptive......With the development of directly acting antivirals, hepatitis C virus (HCV) therapy entered a new era. However, rapid selection of resistance mutations necessitates combination therapy. To study combination therapy in infectious culture systems, we aimed at developing HCV semi-full-length (semi....... Inhibitors showed synergism at drug concentrations reported in vivo. In summary, semi-FL HCV recombinants, including the most advanced reported genotype 3a infectious culture system, permitted genotype-specific analysis of combination treatment in the context of the complete viral life cycle. Despite...

  8. Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections.

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    Mark D Stenglein

    2015-05-01

    Full Text Available Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L and small (S genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on

  9. Fruit characteristics of the selected fig genotypes | Simsek | African ...

    African Journals Online (AJOL)

    The aim of this research was determine of fruit characteristics and select of some significant fig genotypes grown in Kiziltepe district of Mardin province. No studies have been made on the fig genotypes in Kiziltepe district by researchers up to now. Therefore, this study was very important. In this research, six fig genotypes ...

  10. Ascaris: development of selected genotypes in mice.

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    Peng, Weidong; Yuan, Keng; Peng, Guohua; Qiu, Lin; Dai, Zhifang; Yuan, Fang; Hu, Yinying; Hu, Ningyan

    2012-05-01

    Using nucleotide variation in the first internal transcribed spacer of nuclear ribosomal DNA, five different genotypes (designated G1-G5) have been identified and the preponderance of genotype G1 in humans and of genotype G3 in pigs led to the proposal that parasites bearing the two genotypes have an affinity for a particular host species. A subsequent study using eggs of genotype G1 from humans and G3 from pigs to infect pigs and mice indicated that there is a significant difference in the ability to infect and establish as larvae in mice and as adults in pigs between the two genotypes. Extending previous investigations, the present study investigated whether there are differences in development as designated by egg hatching, larvae migration and distribution in the mice between the Ascaris strains with known genotypes. Ascaris eggs of genotypes G1 (predominating in human-derived worms) and G3 (predominating in pig-derived worms) were used to infect C57BL/6 mice orally. Eggs/larvae were examined from the small and large intestines, thoracic and abdominal cavities, peripheral blood, livers and lungs at intervals of 2h until 12h post-infection, then periodically until 34 days of infection. Results showed distinct differences in egg hatching (the timing and location of hatching, and the numbers hatched), and in larvae migration and distribution (the means and constituent ratios, the time of peak recovery, and larvae reappearing in intestines) between the two strains. The results can explain the findings of significantly higher larval recovery of genotype G1 than G3 in the mice, and may shed some enlightenment to understand the difference in host affiliation of Ascaris of different genotypes. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Responses of some selected Malaysian rice genotypes to callus ...

    African Journals Online (AJOL)

    The aim of this study is to identify the most suitable medium and to assess the genotype performance for in vitro salt stress responses in some selected Malaysian rice genotypes. Differences in culture conditions, growth rate, plant hormone responses and accumulation of proline content were monitored. All the selected ...

  12. Identification of Some Walnut Genotypes in Lorestan Province of Iran and Selection of 54 Superior Genotypes

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    A. Mohammadi

    2015-06-01

    Full Text Available Identification and selection of superior genotypes is the first step in walnut breeding programs. For identifying superior genotypes in Lorestan province, Iran, 35000 seedling genotypes were evaluated during 2008-2009. 29 Phenological traits were evaluated using IPGIRI descriptors in 288 selected seedling genotypes. Finally 54 promising genotypes with 10 major phenological traits were evaluated and classified to five groups. Based on the results, The first group included B17 alone as a late leafing genotype. The second group included A11, J14, K20, H19, M13, J1, B14, E14, E6, G17, M7, O9, B7, L6, L10, F12, D6, J15, J16, N5 and N15 genotypes with high kernel percentage, very bright kernel colors, less shell thickness and medium basal fruit pore. M9 with the highest kernel percent among all of the genotypes and 80% of lateral bearing, closed basal fruit pore, less shell thickness and high fruit and kernel weight was classified in another groupe. A7, C5, N3, N18, A17, D1, N14, D4, I4, J6, K17, N4, N19, C10, E13, N13 and N16 genotypes with medium to high fruit diameter, less shell thickness, medium fruit and kernel weight and kernel percentage were classified in the next group. The fifth group included 10 promising genotypes consisting A1, A2, C12, D10, D11, D13, F3, D17, A3, N7, I13, J7, K9 and N11 with quite late leafing and lateral fruit bearing of more than 90% .

  13. Reduced effectiveness of selection caused by a lack of recombination.

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    Betancourt, Andrea J; Welch, John J; Charlesworth, Brian

    2009-04-28

    Genetic recombination associated with sexual reproduction is expected to have important consequences for the effectiveness of natural selection. These effects may be evident within genomes, in the form of contrasting patterns of molecular variation and evolution in regions with different levels of recombination. Previous work reveals patterns that are consistent with a benefit of recombination for adaptation at the level of protein sequence: both positive selection for adaptive variants and purifying selection against deleterious ones appear to be compromised in regions of low recombination [1-11]. Here, we re-examine these patterns by using polymorphism and divergence data from the Drosophila dot chromosome, which has a long history of reduced recombination. To avoid confounding selection and demographic effects, we collected these data from a species with an apparently stable demographic history, Drosophila americana. We find that D. americana dot loci show several signatures of ineffective purifying and positive selection, including an increase in the rate of protein evolution, an increase in protein polymorphism, and a reduction in the proportion of amino acid substitutions attributable to positive selection.

  14. Mercury resistance as a selective marker for recombinant mycobacteria.

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    Baulard, A; Escuyer, V; Haddad, N; Kremer, L; Locht, C; Berche, P

    1995-04-01

    The use of antibiotic-resistance markers for the selection of recombinant mycobacteria is widespread but questionable considering the development of live recombinant BCG vaccines. In contrast, vector-encoded resistance to heavy metals such as mercury may represent an interesting alternative for the development of live vaccines compatible with use in humans and in animals. The mercury resistance genes (mer) from Pseudomonas aeruginosa and from Serratia marcescens were cloned into the Escherichia coli-Mycobacterium shuttle vector pRR3. The resulting vectors, designated pMR001 and pVN2, were introduced by electroporation into Mycobacterium smegmatis, Mycobacterium bovis BCG and Mycobacterium tuberculosis. The recombinant mycobacteria were stable in vitro and in vivo, and had high-level mercury resistance, thus indicating that the mer genes can be useful as selective markers in mycobacteria.

  15. Generation and Selection of Orf Virus (ORFV) Recombinants.

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    Rziha, Hanns-Joachim; Rohde, Jörg; Amann, Ralf

    2016-01-01

    Orf virus (ORFV) is an epitheliotropic poxvirus, which belongs to the genus Parapoxvirus. Among them the highly attenuated, apathogenic strain D1701-V is regarded as a promising candidate for novel virus vector vaccines. Our recent work demonstrated that those ORFV-based recombinants were able to induce protective, long-lasting immunity in various hosts that are non-permissive for ORFV. In this chapter we describe procedures for the generation, selection, propagation, and titration of ORFV recombinants as well as transgene detection by PCR or immunohistochemical staining.

  16. Genetic diversity among selected genotypes of almond Prunus ...

    African Journals Online (AJOL)

    Average polymorphic information content (PIC) value of 16 selected primers was 0.684 and maximum and minimum PIC value was 0.8687 and 0.2551 for primers S073 and S081, respectively. Cophenetic correlation was found to be 0.89. RAPD data on genetic diversity matched classification of studied genotypes based on ...

  17. Evaluation of selected fig genotypes from South east Turkey ...

    African Journals Online (AJOL)

    Turkey has great variations and distributions in wild fig forms as well as fig cultivars. This study was carried out in Mardin and anlýurfa provinces during 2004 - 2005. Nine fig genotypes were evaluated in this selection study for two years. In this study, some morphological characteristics investigated were tree growth habit, ...

  18. Comparison of some local melon genotypes selected from Lake Van ...

    African Journals Online (AJOL)

    This study aimed to compare some local melon (Cucumis melo L.) genotypes selected from the Lake Van Basin (65 ER 02, 65 ER 04, and 13 TAT 05) with some commercial melon cultivars (Ananas, Makdimon F1, and Rambo F1) for some yield and quality related traits observed in field and high tunnel conditions for two ...

  19. Highly productive mutant genotypes in barley - direct use in practice and in successive recombination

    International Nuclear Information System (INIS)

    Gustafsson, Aa.; Lundqvist, U.

    1984-01-01

    Three special cases of induced mutations in barley are discussed in this paper. They are denoted here as the Gunilla, the Pallas and the Mari cases, after the three named varieties to which the original mutants gave rise. The original mutants described represent just a small sample of the induced mutants, many of which have been tested in practice and have been further studied in basic genetics and evolutionary research. The three approved varieties have given rise to further recombination families, which also to some extent have been fused. Two of the mutant cases - Pallas and Mari - were directly useful in practice and officially approved. The third case involved a mutant of special appearance - a ''bushy type'' with an intense blue wax coating and with a supreme lodging resistance. The mutant was used in developing the Gunilla variety, which arose by recombination breeding. This variety has been highly satisfactory in further gene recombination work. A similar situation has prevailed with regard to the Pallas and Mari families arising after gene recombination, too. Up to now, the Gunilla, Pallas and Mari families include a long series of released and officially approved varieties. Several of them represent valuable agricultural contributions with wide areas of cultivation. These three mutants - with their recombination families - led to greatly increased straw stiffness and high grain production. Their phenotypic expression often corresponds to a dwarf or semidwarf description. One of the mutants - the Mari genotype - represents a group of genes and alleles which give rise to profound changes in the photoperiod (and partially also in the thermoperiod) behaviour. In fact, often even such small changes have a fundamental influence on adaptation and distribution. Data are presented analysing the property of lodging resistance with the background of plant, tiller and internode structure. A method of partial back-mutation was worked out in separating traits generally

  20. Novel hepatitis B virus strain developing due to recombination between genotypes H and B strains isolated from a Japanese patient.

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    Uchida, Yoshihito; Kouyama, Jun-Ichi; Naiki, Kayoko; Sugawara, Kayoko; Inao, Mie; Nakayama, Nobuaki; Mochida, Satoshi

    2014-10-01

    In Japan, genotypes B and C are the predominant genotypes isolated from patients with chronic hepatitis B, while genotype A predominates in patients with acute hepatitis B. Globalization, however, appears to have changed the distribution of the hepatitis B virus (HBV) genotypes. Thus, the viral characteristics of HBV genotypes other than genotypes A, B and C were examined. Screening of genotypes was performed by enzyme immunoassay and/or polymerase chain reaction INVADER method in 222 patients with HBV. The full-length nucleotide sequences of unusual strains were compared to those in the database, followed by construction of a phylogenetic tree. Unusual HBV strains were isolated from two patients: a 27-year-old Japanese bisexual man with acute hepatitis B with HIV co-infection and a 52-year-old Japanese man with chronic hepatitis B. The former strain was classified as genotype H, showing an overall identity of 99.8% to the Thailand strain (EU498228), while the nucleotide sequence of the latter strain showed similarity to the genotype B strains isolated in Malaysia (JQ027316) and Indonesia (JQ429079) between DR2 and DR1 in the X region, with identities of 96.9%. However, this strain was classified as genotype H by full-length sequence analysis, and the sequence between nt2023 and nt2262 showed no similarity to that in any previously reported strains. HBV strains showing recombination between genotype B and H strains were found even in chronic hepatitis patients in Japan. Globalization may yield HBV strains of possible novel genotypes containing novel nucleotide sequences in the precore/core region. © 2013 The Japan Society of Hepatology.

  1. On the causes of selection for recombination underlying the red queen hypothesis.

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    Salathé, Marcel; Kouyos, Roger D; Bonhoeffer, Sebastian

    2009-07-01

    The vast majority of plant and animal species reproduce sexually despite the costs associated with sexual reproduction. Genetic recombination might outweigh these costs if it helps the species escape parasite pressure by creating rare or novel genotypes, an idea known as the Red Queen hypothesis. Selection for recombination can be driven by short- and long-term effects, but the relative importance of these effects and their dependency on the parameters of an antagonistic species interaction remain unclear. We use computer simulations of a mathematical model of host-parasite coevolution to measure those effects under a wide range of parameters. We find that the real driving force underlying the Red Queen hypothesis is neither the immediate, next-generation, short-term effect nor the long-term effect but in fact a delayed short-term effect. Our results highlight the importance of differentiating clearly between immediate and delayed short-term effects when attempting to elucidate the mechanism underlying selection for recombination in the Red Queen hypothesis.

  2. Differential efficacy of protease inhibitors against HCV genotypes 2a, 3a, 5a, and 6a NS3/4A protease recombinant viruses

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Scheel, Troels K H; Jensen, Tanja B

    2011-01-01

    The hepatitis C virus (HCV) genotype influences efficacy of interferon (IFN)-based therapy. HCV protease inhibitors are being licensed for treatment of genotype 1 infection. Because there are limited or no data on efficacy against HCV genotypes 2-7, we aimed at developing recombinant infectious c...

  3. Evidence of recombination and positive selection in cetacean papillomaviruses

    International Nuclear Information System (INIS)

    Robles-Sikisaka, Refugio; Rivera, Rebecca; Nollens, Hendrik H.; St Leger, Judy; Durden, Wendy N.; Stolen, Megan; Burchell, Jennifer; Wellehan, James F.X.

    2012-01-01

    Papillomaviruses (PVs) are small DNA viruses that have been associated with increased epithelial proliferation. Over one hundred PV types have been identified in humans; however, only three have been identified in bottlenose dolphins (Tursiops truncatus) to date. Using rolling circle amplification and degenerate PCR, we identified four novel PV genomes of bottlenose dolphins. TtPV4, TtPV5 and TtPV6 were identified in genital lesions while TtPV7 was identified in normal genital mucosa. Bayesian analysis of the full-length L1 genes found that TtPV4 and TtPV7 group within the Upsilonpapillomavirus genus while TtPV5 and TtPV6 group with Omikronpapillomavirus. However, analysis of the E1 gene did not distinguish these genera, implying that these genes may not share a common history, consistent with recombination. Recombination analyses identified several probable events. Signals of positive selection were found mostly in the E1 and E2 genes. Recombination and diversifying selection pressures constitute important driving forces of cetacean PV evolution.

  4. Evidence of recombination and positive selection in cetacean papillomaviruses

    Energy Technology Data Exchange (ETDEWEB)

    Robles-Sikisaka, Refugio, E-mail: refugio.robles1@gmail.com [Hubbs-SeaWorld Research Institute, Center for Marine Veterinary Virology, 2595 Ingraham Street, San Diego, CA 92109 (United States); Rivera, Rebecca, E-mail: RRivera@hswri.org [Hubbs-SeaWorld Research Institute, Center for Marine Veterinary Virology, 2595 Ingraham Street, San Diego, CA 92109 (United States); Nollens, Hendrik H., E-mail: Hendrik.Nollens@SeaWorld.com [Hubbs-SeaWorld Research Institute, Center for Marine Veterinary Virology, 2595 Ingraham Street, San Diego, CA 92109 (United States); College of Veterinary Medicine, University of Florida, PO Box 110885, Gainesville, FL 32611 (United States); SeaWorld San Diego, 500 SeaWorld Drive, San Diego, CA 92109 (United States); St Leger, Judy, E-mail: Judy.St.Leger@SeaWorld.com [SeaWorld San Diego, 500 SeaWorld Drive, San Diego, CA 92109 (United States); Durden, Wendy N., E-mail: WNoke@hswri.org [Hubbs-SeaWorld Research Institute, 3830 South Highway A1A 4-181, Melbourne Beach, FL 32951 (United States); Stolen, Megan, E-mail: MStolen@hswri.org [Hubbs-SeaWorld Research Institute, 3830 South Highway A1A 4-181, Melbourne Beach, FL 32951 (United States); Burchell, Jennifer, E-mail: JBurchell@hswri.org [Hubbs-SeaWorld Research Institute, Center for Marine Veterinary Virology, 2595 Ingraham Street, San Diego, CA 92109 (United States); Wellehan, James F.X., E-mail: WellehanJ@ufl.edu [College of Veterinary Medicine, University of Florida, PO Box 110885, Gainesville, FL 32611 (United States)

    2012-06-05

    Papillomaviruses (PVs) are small DNA viruses that have been associated with increased epithelial proliferation. Over one hundred PV types have been identified in humans; however, only three have been identified in bottlenose dolphins (Tursiops truncatus) to date. Using rolling circle amplification and degenerate PCR, we identified four novel PV genomes of bottlenose dolphins. TtPV4, TtPV5 and TtPV6 were identified in genital lesions while TtPV7 was identified in normal genital mucosa. Bayesian analysis of the full-length L1 genes found that TtPV4 and TtPV7 group within the Upsilonpapillomavirus genus while TtPV5 and TtPV6 group with Omikronpapillomavirus. However, analysis of the E1 gene did not distinguish these genera, implying that these genes may not share a common history, consistent with recombination. Recombination analyses identified several probable events. Signals of positive selection were found mostly in the E1 and E2 genes. Recombination and diversifying selection pressures constitute important driving forces of cetacean PV evolution.

  5. A simple negative selection method to identify adenovirus recombinants using colony PCR

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    Yongliang Zhao

    2014-01-01

    Conclusions: The negative selection method to identify AdEasy adenovirus recombinants by colony PCR can identify the recombined colony within a short time-period, and maximally avoid damage to the recombinant plasmid by limiting recombination time, resulting in improved adenovirus packaging.

  6. Comparison of selective genotyping strategies for prediction of breeding values in a population undergoing selection.

    Science.gov (United States)

    Boligon, A A; Long, N; Albuquerque, L G; Weigel, K A; Gianola, D; Rosa, G J M

    2012-12-01

    Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values, and 5) Less Related: less genetically related animals. The number of individuals in G(0) and G(1) was fixed at 2,500 each, and different levels of heritability were considered (0.10, 0.25, and 0.50). Additionally, all 5 selective genotyping strategies (Random, Top, Bottom, Extreme, and Less Related) were applied to an indicator trait in generation G(0,) and the results were evaluated for the target trait in generation G(1), with the genetic correlation between the 2 traits set to 0.50. The 5 genotyping strategies applied to individuals in G(0) (reference population) were compared in terms of their ability to predict the genetic values of the animals in G(1) (selection

  7. Dynamic HIV-1 genetic recombination and genotypic drug resistance among treatment-experienced adults in northern Ghana.

    Science.gov (United States)

    Nii-Trebi, Nicholas Israel; Brandful, James Ashun Mensah; Ibe, Shiro; Sugiura, Wataru; Barnor, Jacob Samson; Bampoh, Patrick Owiredu; Yamaoka, Shoji; Matano, Tetsuro; Yoshimura, Kazuhisa; Ishikawa, Koichi; Ampofo, William Kwabena

    2017-11-01

    There have been hardly any reports on the human immunodeficiency virus type 1 (HIV-1) drug-resistance profile from northern Ghana since antiretroviral therapy (ART) was introduced over a decade ago. This study investigated prevailing HIV-1 subtypes and examined the occurrence of drug resistance in ART-experienced patients in Tamale, the capital of the Northern Region of Ghana. A cross-sectional study was carried out on HIV-infected adult patients receiving first-line ART. HIV viral load (VL) and CD4 + T-cell counts were measured. The pol gene sequences were analysed for genotypic resistance by an in-house HIV-1 drug-resistance test; the prevailing HIV-1 subtypes were analysed in detail.Results/Key findings. A total of 33 subjects were studied. Participants comprised 11 males (33.3 %) and 22 (66.7 %) females, with a median age of 34.5 years [interquartile range (IQR) 30.0-40.3]. The median duration on ART was 12 months (IQR 8.0-24). Of the 24 subjects successfully genotyped, 10 (41.7 %) viruses possessed at least one mutation conferring resistance to nucleoside or non-nucleoside reverse-transcriptase inhibitors (NRTIs/NNRTIs). Two-class drug resistance to NRTI and NNRTI was mostly detected (25 %, 6/24). The most frequent mutations were lamivudine-resistance M184V and efavirenz/nevirapine-resistance K103N. HIV-1 subtype CRF02_AG was predominant (79.2 %). Other HIV-1 subtypes detected were G (8.3 %), A3 (4.2 %) and importantly two (8.3 %) unique HIV-1 recombinant forms with CRF02_AG/A3 mosaic. HIV-1 shows high genetic diversity and on-going viral genetic recombination in the study region. Nearly 42 % of the patients studied harboured a drug-resistant virus. The study underscores the need for continued surveillance of HIV-1 subtype diversity; and of drug-resistance patterns to guide selection of second-line regimens in northern Ghana.

  8. Index selection of tropical maize genotypes for nitrogen use efficiency

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    Ítalo Stefanine Correia Granato

    2014-06-01

    Full Text Available Nitrogen (N limitation in maize crops is related to the fact that the efficiency of nitrogen fertilization in maize does not exceed 50%, primarily due to volatilization, denitrification and soil leaching. Therefore, the development of new nitrogen use efficient (NUE cultivars is necessary. The aim of the present study was to develop indices for the accurate selection of NUE maize genotypes for use in conditions of both high and low N availability. The experiment was conducted in a greenhouse (20º45'14"S; 42º52'53"W at the Federal University of Viçosa during October 2010. A total of 39 experimental hybrid combinations and 14 maize lines differing in NUE were evaluated under two N availability conditions. We determined the relative importance of the studied characters using principal component analysis, factor analysis and by developing efficient selection indices. We conclude that indirect and early selection of tropical maize genotypes can be performed using the indices I HN = 0.022 SDM + 0.35 RSDM + 0.35 RL A + 0.35 NUE for high N availability environments and I LN = -0.06 RSDM + 0.35 RSA A + 0.35 RL A + 0.39 SDM for low N availability environments.

  9. A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency.

    Science.gov (United States)

    Lee, Yu Nee; Frugoni, Francesco; Dobbs, Kerry; Walter, Jolan E; Giliani, Silvia; Gennery, Andrew R; Al-Herz, Waleed; Haddad, Elie; LeDeist, Francoise; Bleesing, Jack H; Henderson, Lauren A; Pai, Sung-Yun; Nelson, Robert P; El-Ghoneimy, Dalia H; El-Feky, Reem A; Reda, Shereen M; Hossny, Elham; Soler-Palacin, Pere; Fuleihan, Ramsay L; Patel, Niraj C; Massaad, Michel J; Geha, Raif S; Puck, Jennifer M; Palma, Paolo; Cancrini, Caterina; Chen, Karin; Vihinen, Mauno; Alt, Frederick W; Notarangelo, Luigi D

    2014-04-01

    The recombination-activating gene (RAG) 1/2 proteins play a critical role in the development of T and B cells by initiating the VDJ recombination process that leads to generation of a broad T-cell receptor (TCR) and B-cell receptor repertoire. Pathogenic mutations in the RAG1/2 genes result in various forms of primary immunodeficiency, ranging from T(-)B(-) severe combined immune deficiency to delayed-onset disease with granuloma formation, autoimmunity, or both. It is not clear what contributes to such heterogeneity of phenotypes. We sought to investigate the molecular basis for phenotypic diversity presented in patients with various RAG1 mutations. We have developed a flow cytometry-based assay that allows analysis of RAG recombination activity based on green fluorescent protein expression and have assessed the induction of the Ighc locus rearrangements in mouse Rag1(-/-) pro-B cells reconstituted with wild-type or mutant human RAG1 (hRAG1) using deep sequencing technology. Here we demonstrate correlation between defective recombination activity of hRAG1 mutant proteins and severity of the clinical and immunologic phenotype and provide insights on the molecular mechanisms accounting for such phenotypic diversity. Using a sensitive assay to measure the RAG1 activity level of 79 mutations in a physiologic setting, we demonstrate correlation between recombination activity of RAG1 mutants and the severity of clinical presentation and show that RAG1 mutants can induce specific abnormalities of the VDJ recombination process. Copyright © 2013 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

  10. Differences between selection on sex versus recombination in red queen models with diploid hosts.

    Science.gov (United States)

    Agrawal, Aneil F

    2009-08-01

    The Red Queen hypothesis argues that parasites generate selection for genetic mixing (sex and recombination) in their hosts. A number of recent papers have examined this hypothesis using models with haploid hosts. In these haploid models, sex and recombination are selectively equivalent. However, sex and recombination are not equivalent in diploids because selection on sex depends on the consequences of segregation as well as recombination. Here I compare how parasites select on modifiers of sexual reproduction and modifiers of recombination rate. Across a wide set of parameters, parasites tend to select against both sex and recombination, though recombination is favored more often than is sex. There is little correspondence between the conditions favoring sex and those favoring recombination, indicating that the direction of selection on sex is often determined by the effects of segregation, not recombination. Moreover, when sex was favored it is usually due to a long-term advantage whereas short-term effects are often responsible for selection favoring recombination. These results strongly indicate that Red Queen models focusing exclusively on the effects of recombination cannot be used to infer the type of selection on sex that is generated by parasites on diploid hosts.

  11. Effect of manipulating recombination rates on response to selection in livestock breeding programs.

    Science.gov (United States)

    Battagin, Mara; Gorjanc, Gregor; Faux, Anne-Michelle; Johnston, Susan E; Hickey, John M

    2016-06-22

    In this work, we performed simulations to explore the potential of manipulating recombination rates to increase response to selection in livestock breeding programs. We carried out ten replicates of several scenarios that followed a common overall structure but differed in the average rate of recombination along the genome (expressed as the length of a chromosome in Morgan), the genetic architecture of the trait under selection, and the selection intensity under truncation selection (expressed as the proportion of males selected). Recombination rates were defined by simulating nine different chromosome lengths: 0.10, 0.25, 0.50, 1, 2, 5, 10, 15 and 20 Morgan, respectively. One Morgan was considered to be the typical chromosome length for current livestock species. The genetic architecture was defined by the number of quantitative trait variants (QTV) that affected the trait under selection. Either a large (10,000) or a small (1000 or 500) number of QTV was simulated. Finally, the proportions of males selected under truncation selection as sires for the next generation were equal to 1.2, 2.4, 5, or 10 %. Increasing recombination rate increased the overall response to selection and decreased the loss of genetic variance. The difference in cumulative response between low and high recombination rates increased over generations. At low recombination rates, cumulative response to selection tended to asymptote sooner and the genetic variance was completely eroded. If the trait under selection was affected by few QTV, differences between low and high recombination rates still existed, but the selection limit was reached at all rates of recombination. Higher recombination rates can enhance the efficiency of breeding programs to turn genetic variation into response to selection. However, to increase response to selection significantly, the recombination rate would need to be increased 10- or 20-fold. The biological feasibility and consequences of such large increases in

  12. Evaluation of some Phenological and Pomological Characteristics of Selected Walnut Genotypes from Shahroud-Iran

    Directory of Open Access Journals (Sweden)

    Sara Akhiani

    2017-05-01

    Full Text Available The first step in walnut breeding programs is to identify and evaluate superior genotypes of fruit trees. Hence, there are various walnut breeding programs in various areas of Iran. A study aimed to evaluate the morphological and chemical characteristics of selected superior genotypes of walnut was conducted in the Shahroud region in 2011-2012.  The following genotypes were selected in this study as the best walnut genotypes:  X-18 homogamous genotypes due to desirable late leafing;   genotype X-11 for its high percentage of kernel production, easily removal of shell, thin shell; genotype X-52 due to its kernel plumpness compared to other genotypes, thin shell and high percentage of kernel and genotype X-70 for its kernel brightness, easily kernel extracting and high percentage of kernels. The X-49 and X-5 genotypes had the highest amount of linoleic and linolenic fatty acids and higher nutritional quality compared to other genotypes. Three genotypes, X-3, X-11 and X-22, had the highest amount of oil. Genotypes X-9 and X-45 had the highest amount of protein. The difference between oil content and fatty acid compositions was presumably due to genetic diversity and ecological conditions of the studied genotypes cultivation.

  13. Resistance of Selected Sorghum Genotypes to Maize Weevil (Coleoptera: Curculionidae).

    Science.gov (United States)

    Vyavhare, Suhas S; Pendleton, Bonnie B; Peterson, Gary C

    2018-04-09

    The maize weevil, Sitophilus zeamais (Motschulsky) (Coleoptera: Curculionidae), is a major insect pest of stored grain. This study evaluated resistance of grain of 26 sorghum genotypes, Sorghum bicolor (L.) Moench, to maize weevil under laboratory conditions. Three female and two male newly emerged maize weevils were reared with 5 g of grain in each of 10 vials for each of the 26 sorghum genotypes in a laboratory experiment. The weevils and grain of each genotype were scored once every 3 wk for a total of five times during 105 d. The numbers of live and newly emerged maize weevils, dead weevils from the initial population, damage score (scale of 1-5), and grain weight loss were used to indicate resistance. The least percentage weight loss of 23.9 and 24.1% was recorded for sorghum genotypes Sureño and (5BRON151*Tegemeo)-HG7, respectively. Genotypes B.HF8 and (A964*P850029)-HW6 had the most weight loss, 70.6 and 67.7%, at 105 d after infestation. Genotypes B.HF8 and (A964*P850029)-HW6 consistently exhibited the highest numbers of maize weevil, 63 and 84, per vial at 105 d after infestation. Sorghum genotypes Sureño, (SV1*Sima/IS23250)-LG15, (5BRON151*Tegemeo)-HG7, and (B35*B9501)-HD9 ranked among the top four genotypes with least damage rating more often than any other genotype across the five sampling dates. On the other hand, genotypes B.HF8, (A964*P850029)-HW6, (Segaolane*WM#322)LG2, and (Tx2880*(Tx2880*(Tx2864*(Tx436*(Tx2864*PI550607)))))-PR3-CM1 were more often ranked among the top four genotypes with the highest damage rating. Our results indicate that grain of genotype Sureno is most resistant to the maize weevil among screened genotypes.

  14. participatory selection of mungbean genotypes in uganda abstract ...

    African Journals Online (AJOL)

    ACSS

    2017-05-29

    May 29, 2017 ... best mungbean genotypes. The traits were; yield, overall performance, seed size, seed colour, marketability and ... that there were no significant differences in genotype choices based on gender (χ2 = 2.5419, P-value = 0.97). However, there were ... Key Words: Gender, preferences, Vigna radiata. RÉSUMÉ.

  15. Genetic divergence in selected durum wheat genotypes of Ethiopian ...

    African Journals Online (AJOL)

    genotypes of diverse origin, and clustering them into homogenous groups for the hybridisation programme. Genetic divergence analysis was done based on multivariate analysis using Mahalanobis's D2 statistic, which grouped the durum wheat genotypes into ten clusters. The highest inter-cluster distance was between ...

  16. Toward fully automated genotyping: Allele assignment, pedigree construction, phase determination, and recombination detection in Duchenne muscular dystrophy

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Burks, M.B. [Carnegie Mellon Univ., Pittsburgh, PA (United States); Hoop, R.C.; Hoffman, E.P. [Univ. of Pittsburgh School of Medicine, PA (United States)

    1994-10-01

    Human genetic maps have made quantum leaps in the past few years, because of the characterization of >2,000 CA dinucleotide repeat loci: these PCR-based markers offer extraordinarily high PIC, and within the next year their density is expected to reach intervals of a few centimorgans per marker. These new genetic maps open new avenues for disease gene research, including large-scale genotyping for both simple and complex disease loci. However, the allele patterns of many dinucleotide repeat loci can be complex and difficult to interpret, with genotyping errors a recognized problem. Furthermore, the possibility of genotyping individuals at hundreds or thousands of polymorphic loci requires improvements in data handling and analysis. The automation of genotyping and analysis of computer-derived haplotypes would remove many of the barriers preventing optimal use of dense and informative dinucleotide genetic maps. Toward this end, we have automated the allele identification, genotyping, phase determinations, and inheritance consistency checks generated by four CA repeats within the 2.5-Mbp, 10-cM X-linked dystrophin gene, using fluorescein-labeled multiplexed PCR products analyzed on automated sequencers. The described algorithms can deconvolute and resolve closely spaced alleles, despite interfering stutter noise; set phase in females; propagate the phase through the family; and identify recombination events. We show the implementation of these algorithms for the completely automated interpretation of allele data and risk assessment for five Duchenne/Becker muscular dystrophy families. The described approach can be scaled up to perform genome-based analyses with hundreds or thousands of CA-repeat loci, using multiple fluorophors on automated sequencers. 16 refs., 5 figs., 1 tab.

  17. Engineering recombinant EF-hand peptides for selective uranium uptake

    Energy Technology Data Exchange (ETDEWEB)

    Berthomieu, C.; Pardoux, R.; Beccia, M.R.; Lemaire, D.; Sauge-Merle, S. [CEA, DSV, IBEB, UMR7265 CNRS CEA Aix-Marseille Univ. (France); Guilbaud, P. [CEA, DRCPC, SMCS, LILA (France); Delangle, P. [CEA, INAC, Service de Chimie Inorganique et Biologique (France)

    2014-07-01

    In spite of an increasing number of publications in recent years, information regarding the mechanism of uranium interaction with proteins at the molecular level is limited and few quantitative studies have investigated the binding properties of uranyl with proteins or peptides. It is thus of great interest to better characterize these interactions, and to analyze structural factors governing uranyl binding and thermodynamic stabilization in proteins. Research in this direction will benefit our understanding of the molecular factors governing uranyl toxicity and speciation in cells and will also aid in developing new molecules for selectively binding uranium that could be used for uranium bioremediation purposes. Uranyl coordination properties have similarities with those of calcium, i.e electrostatic interactions preferentially with hard donor oxygen ligands and pentagonal bipyramidal structures. The EF-hand structural motif is the most prevalent Ca2{sup +-}binding site in proteins and is very appealing to analyse uranyl binding properties and develop affine and specific uranyl binding sites for biotechnology approaches. We selected the recombinant N-terminal domain of calmodulin from A. thaliana as a structured template that contains two EF-hand motifs (site I and site II) to analyze its uranyl binding properties and to engineer peptide variants with increased uranyl affinity and specificity. We showed that both site I and site II bind uranyl, with a dissociation constant in the nano-molar range for site I (K{sub d} ≅ 25 nM at pH 6). Using in vitro phosphorylation of a threonine located in the uranyl binding loop, we measured how adding a phosphoryl group affects the calcium and uranium binding affinities. The phosphorylated peptide exhibited a very large affinity for uranyl at pH 7, with a dissociation constant in the sub-nano-molar range K{sub d} = 0.25 ±0.06 nM, and FTIR analysis demonstrated that the phosphoryl group plays a determining role in uranyl

  18. Recombinant protein expression by targeting pre-selected chromosomal loci

    Directory of Open Access Journals (Sweden)

    Krömer Wolfgang

    2009-12-01

    Full Text Available Abstract Background Recombinant protein expression in mammalian cells is mostly achieved by stable integration of transgenes into the chromosomal DNA of established cell lines. The chromosomal surroundings have strong influences on the expression of transgenes. The exploitation of defined loci by targeting expression constructs with different regulatory elements is an approach to design high level expression systems. Further, this allows to evaluate the impact of chromosomal surroundings on distinct vector constructs. Results We explored antibody expression upon targeting diverse expression constructs into previously tagged loci in CHO-K1 and HEK293 cells that exhibit high reporter gene expression. These loci were selected by random transfer of reporter cassettes and subsequent screening. Both, retroviral infection and plasmid transfection with eGFP or antibody expression cassettes were employed for tagging. The tagged cell clones were screened for expression and single copy integration. Cell clones producing > 20 pg/cell in 24 hours could be identified. Selected integration sites that had been flanked with heterologous recombinase target sites (FRTs were targeted by Flp recombinase mediated cassette exchange (RMCE. The results give proof of principle for consistent protein expression upon RMCE. Upon targeting antibody expression cassettes 90-100% of all resulting cell clones showed correct integration. Antibody production was found to be highly consistent within the individual cell clones as expected from their isogenic nature. However, the nature and orientation of expression control elements revealed to be critical. The impact of different promoters was examined with the tag-and-targeting approach. For each of the chosen promoters high expression sites were identified. However, each site supported the chosen promoters to a different extent, indicating that the strength of a particular promoter is dominantly defined by its chromosomal context

  19. High recombination frequency creates genotypic diversity in colonies of the leaf-cutting ant Acromyrmex echinatior

    DEFF Research Database (Denmark)

    Sirviö, A.; Gadau, J.; Rueppell, O.

    2006-01-01

    Honeybees are known to have genetically diverse colonies because queens mate with many males and the recombination rate is extremely high. Genetic diversity among social insect workers has been hypothesized to improve general performance of large and complex colonies, but this idea has not been...... tested in other social insects. Here, we present a linkage map and an estimate of the recombination rate for Acromyrmex echinatior, a leaf-cutting ant that resembles the honeybee in having multiple mating of queens and colonies of approximately the same size. A map of 145 AFLP markers in 22 linkage...... groups yielded a total recombinational size of 2076 cM and an inferred recombination rate of 161 kb cM-1 (or 6.2 cM Mb-1). This estimate is lower than in the honeybee but, as far as the mapping criteria can be compared, higher than in any other insect mapped so far. Earlier studies on A. echinatior have...

  20. Whole-gene analysis of two groups of hepatitis B virus C/D inter-genotype recombinant strains isolated in Tibet, China.

    Directory of Open Access Journals (Sweden)

    Tiezhu Liu

    Full Text Available Tibet is a highly hepatitis B virus (HBV endemic area. Two types of C/D recombinant HBV are commonly isolated in Tibet and have been previously described. In an effort to better understand the molecular characteristic of these C/D recombinant strains from Tibet, we undertook a multistage random sampling project to collect HBsAg positive samples. Molecular epidemiological and bio-informational technologies were used to analyze the characteristics of the sequences found in this study. There were 60 samples enrolled in the survey, and we obtained 19 whole-genome sequences. 19 samples were all C/D recombinant, and could be divided into two sub-types named C/D1 and C/D2 according to the differences in the location of the recombinant breakpoint. The recombination breakpoint of the 10 strains belonging to the C/D1 sub-type was located at nt750, while the 9 stains belonging to C/D2 had their recombination break point at nt1530. According to whole-genome sequence analysis, the 19 identified strains belong to genotype C, but the nucleotide distance was more than 5% between the 19 strains and sub-genotypes C1 to C15. The distance between C/D1with C2 was 5.8±2.1%, while the distance between C/D2 with C2 was 6.4±2.1%. The parental strain was most likely sub-genotype C2. C/D1 strains were all collected in the middle and northern areas of Tibet including Lhasa, Linzhi and Ali, while C/D2 was predominant in Shannan in southern Tibet. This indicates that the two recombinant genotypes are regionally distributed in Tibet. These results provide important information for the study of special HBV recombination events, gene features, virus evolution, and the control and prevention policy of HBV in Tibet.

  1. Whole-gene analysis of two groups of hepatitis B virus C/D inter-genotype recombinant strains isolated in Tibet, China.

    Science.gov (United States)

    Liu, Tiezhu; Wang, Fuzhen; Zhang, Shuang; Wang, Feng; Meng, Qingling; Zhang, Guomin; Cui, Fuqiang; Dunzhu, Dorji; Yin, Wenjiao; Bi, Shengli; Shen, Liping

    2017-01-01

    Tibet is a highly hepatitis B virus (HBV) endemic area. Two types of C/D recombinant HBV are commonly isolated in Tibet and have been previously described. In an effort to better understand the molecular characteristic of these C/D recombinant strains from Tibet, we undertook a multistage random sampling project to collect HBsAg positive samples. Molecular epidemiological and bio-informational technologies were used to analyze the characteristics of the sequences found in this study. There were 60 samples enrolled in the survey, and we obtained 19 whole-genome sequences. 19 samples were all C/D recombinant, and could be divided into two sub-types named C/D1 and C/D2 according to the differences in the location of the recombinant breakpoint. The recombination breakpoint of the 10 strains belonging to the C/D1 sub-type was located at nt750, while the 9 stains belonging to C/D2 had their recombination break point at nt1530. According to whole-genome sequence analysis, the 19 identified strains belong to genotype C, but the nucleotide distance was more than 5% between the 19 strains and sub-genotypes C1 to C15. The distance between C/D1with C2 was 5.8±2.1%, while the distance between C/D2 with C2 was 6.4±2.1%. The parental strain was most likely sub-genotype C2. C/D1 strains were all collected in the middle and northern areas of Tibet including Lhasa, Linzhi and Ali, while C/D2 was predominant in Shannan in southern Tibet. This indicates that the two recombinant genotypes are regionally distributed in Tibet. These results provide important information for the study of special HBV recombination events, gene features, virus evolution, and the control and prevention policy of HBV in Tibet.

  2. Impact of selective genotyping in the training population on accuracy and bias of genomic selection.

    Science.gov (United States)

    Zhao, Yusheng; Gowda, Manje; Longin, Friedrich H; Würschum, Tobias; Ranc, Nicolas; Reif, Jochen C

    2012-08-01

    Estimating marker effects based on routinely generated phenotypic data of breeding programs is a cost-effective strategy to implement genomic selection. Truncation selection in breeding populations, however, could have a strong impact on the accuracy to predict genomic breeding values. The main objective of our study was to investigate the influence of phenotypic selection on the accuracy and bias of genomic selection. We used experimental data of 788 testcross progenies from an elite maize breeding program. The testcross progenies were evaluated in unreplicated field trials in ten environments and fingerprinted with 857 SNP markers. Random regression best linear unbiased prediction method was used in combination with fivefold cross-validation based on genotypic sampling. We observed a substantial loss in the accuracy to predict genomic breeding values in unidirectional selected populations. In contrast, estimating marker effects based on bidirectional selected populations led to only a marginal decrease in the prediction accuracy of genomic breeding values. We concluded that bidirectional selection is a valuable approach to efficiently implement genomic selection in applied plant breeding programs.

  3. Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon

    Directory of Open Access Journals (Sweden)

    Hsin-Yuan Tsai

    2017-04-01

    Full Text Available Genomic selection uses genome-wide marker information to predict breeding values for traits of economic interest, and is more accurate than pedigree-based methods. The development of high density SNP arrays for Atlantic salmon has enabled genomic selection in selective breeding programs, alongside high-resolution association mapping of the genetic basis of complex traits. However, in sibling testing schemes typical of salmon breeding programs, trait records are available on many thousands of fish with close relationships to the selection candidates. Therefore, routine high density SNP genotyping may be prohibitively expensive. One means to reducing genotyping cost is the use of genotype imputation, where selected key animals (e.g., breeding program parents are genotyped at high density, and the majority of individuals (e.g., performance tested fish and selection candidates are genotyped at much lower density, followed by imputation to high density. The main objectives of the current study were to assess the feasibility and accuracy of genotype imputation in the context of a salmon breeding program. The specific aims were: (i to measure the accuracy of genotype imputation using medium (25 K and high (78 K density mapped SNP panels, by masking varying proportions of the genotypes and assessing the correlation between the imputed genotypes and the true genotypes; and (ii to assess the efficacy of imputed genotype data in genomic prediction of key performance traits (sea lice resistance and body weight. Imputation accuracies of up to 0.90 were observed using the simple two-generation pedigree dataset, and moderately high accuracy (0.83 was possible even with very low density SNP data (∼250 SNPs. The performance of genomic prediction using imputed genotype data was comparable to using true genotype data, and both were superior to pedigree-based prediction. These results demonstrate that the genotype imputation approach used in this study can

  4. Antioxidant activity in selected tomato genotypes cultivated in ...

    African Journals Online (AJOL)

    The present study is a compilation of results obtained at the Vegetable Research and Development Station Bacau regarding the influence of the culture system on the quantitative and qualitative yield of tomatoes. The present study provides comparative information regarding yield achievements of tomato genotypes ...

  5. Selection of superior wheat genotypes against end- season drought ...

    African Journals Online (AJOL)

    teryson

    2012-08-28

    Aug 28, 2012 ... genotypes against stress from mean productivity (MP), geometric mean productivity (GMP) and stress susceptibility index ... analysis showed that yield component was justified 64% of the changes; tolerance indices component .... ANOVA for yield in two different environments (stressed and non stressed).

  6. Responses of some selected Malaysian rice genotypes to callus ...

    African Journals Online (AJOL)

    user

    2011-01-17

    Jan 17, 2011 ... embryogenic callus culture (Yin et al., 1993). In this study, overall, the callus from the MS medium had a good texture. Furthermore, some genotypes also produced better callus in other concentrations of 2,4-D treatment, however, the quality of callus was not as good as those in. 10 µM 2,4-D. Notably, the ...

  7. Microsatellite analysis of selected Lablab purpureus genotypes in ...

    African Journals Online (AJOL)

    cntaganda

    Abstract. Lablab (Lablab Purpureus) is a legume of high nutritional value and broad social acceptance ranging from human food to soil fertility improvement to foarge. Information on genetic worth and diversity of lablab genotypes in Kenya is scanty and this is a great impediment to the improvement of the crop hence its ...

  8. β-Carotene content of selected banana genotypes from Uganda

    African Journals Online (AJOL)

    carotene with values as high as 2594.0 μg/100 g edible pulp. A positive correlation existed between pulp color intensity and β-carotene concentration. Accessions with relatively high levels of β-carotene,especially the PNG genotypes, could be ...

  9. Identification of Novel Recombinant Forms of Hepatitis B Virus Generated from Genotypes Ae and G in HIV-1-Positive Japanese Men Who Have Sex with Men.

    Science.gov (United States)

    Kojima, Yoko; Kawahata, Takuya; Mori, Haruyo; Furubayashi, Keiichi; Taniguchi, Yasushi; Itoda, Ichiro; Komano, Jun

    2015-07-01

    The rare hepatitis B virus (HBV) genotype G (HBV/G) coinfects HIV-1-positive individuals along with HBV/A and generates recombinants. However, the circulation of HBV A/G recombinants remains poorly understood. This molecular epidemiologic study examined HBV A/G recombinants in Japanese HIV-1-positive men who have sex with men (MSM). Initially, blood specimens submitted for confirmatory tests of HIV infection in Osaka and Tokyo, Japan, from 2006 to 2013 were examined for HIV-1, and HIV-1-positive specimens were screened for HBV. Among 817 specimens from HIV-1-positive individuals, HBsAg was detected in 59 specimens; of these, HBV/Ae (alternatively A2), a subgenotype of HBV/A prevalent in Europe and North America, was identified in 70.2%, HBV/C in 17.5%, and HBV/G in 10.5%, and HBV/E in 1.8% according to the core gene sequence. The full-length genome analysis of HBV was performed on HBV/G-positive specimens because some HBV A/G recombinants were historically overlooked by genotyping based on a partial genome analysis. It revealed that five of the specimens contained novel Ae/G recombinants, the core gene of which had a high sequence similarity to HBV/G. Detailed analyses showed that novel recombinants were coinfected with HBV/Ae in a recombinant-dominant fashion. No major drug-resistant mutations were found in the newly identified HBV Ae/G recombinants. Some of the individuals asymptomatically coinfected with HIV/HBV suffered mild liver injury. This study demonstrated that novel Ae/G HBV recombinants were identified in Japanese HIV-1-positive MSM. The pathogenicity of novel HBV Ae/G recombinants should be examined in a future longitudinal study. Surveillance of such viruses in HIV-1-positive individuals should be emphasized.

  10. Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes

    Directory of Open Access Journals (Sweden)

    Jon Mark Scriber

    2013-12-01

    Full Text Available Comprising 50%–75% of the world’s fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including “invasive species” in various ecosystems as they may become disrupted in different ways by rapid climate change. “Invasive genes” (into new species and populations need to be recognized for their positive creative potential and addressed in conservation programs. “Genetic rescue” via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae with their long-term historical data base (phylogeographical diversity changes and recent (3-decade climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced “reshuffling” (recombinations of species composition, genotypes

  11. Exploration and Selection of the Wild Olive Genotypes

    OpenAIRE

    , H. Ismaili; , C. Cantini; , G. Ianni; , I. Lloshi

    2016-01-01

    Exploration on wild olive diversity carried out during the period 20002011, recorded a number of 27 wild forms. Morphological marker based analysis were performed for olive identity characterization, to determine their localization, usage limits as well as to build in-situ & ex-situ collection of 27 wild olive forms. Morphological description (Rezgen) was done for each olive genotype, in total of 49 characters; of tree, leaf, inflorescence, fruit and endocarp were measured during the ...

  12. A selectable and excisable marker system for the rapid creation of recombinant poxviruses.

    Directory of Open Access Journals (Sweden)

    Julia L Rintoul

    Full Text Available Genetic manipulation of poxvirus genomes through attenuation, or insertion of therapeutic genes has led to a number of vector candidates for the treatment of a variety of human diseases. The development of recombinant poxviruses often involves the genomic insertion of a selectable marker for purification and selection purposes. The use of marker genes however inevitably results in a vector that contains unwanted genetic information of no therapeutic value.Here we describe an improved strategy that allows for the creation of marker-free recombinant poxviruses of any species. The Selectable and Excisable Marker (SEM system incorporates a unique fusion marker gene for the efficient selection of poxvirus recombinants and the Cre/loxP system to facilitate the subsequent removal of the marker. We have defined and characterized this new methodological tool by insertion of a foreign gene into vaccinia virus, with the subsequent removal of the selectable marker. We then analyzed the importance of loxP orientation during Cre recombination, and show that the SEM system can be used to introduce site-specific deletions or inversions into the viral genome. Finally, we demonstrate that the SEM strategy is amenable to other poxviruses, as demonstrated here with the creation of an ectromelia virus recombinant lacking the EVM002 gene.The system described here thus provides a faster, simpler and more efficient means to create clinic-ready recombinant poxviruses for therapeutic gene therapy applications.

  13. Simultaneous selection for cowpea (Vigna unguiculata L.) genotypes with adaptability and yield stability using mixed models.

    Science.gov (United States)

    Torres, F E; Teodoro, P E; Rodrigues, E V; Santos, A; Corrêa, A M; Ceccon, G

    2016-04-29

    The aim of this study was to select erect cowpea (Vigna unguiculata L.) genotypes simultaneously for high adaptability, stability, and yield grain in Mato Grosso do Sul, Brazil using mixed models. We conducted six trials of different cowpea genotypes in 2005 and 2006 in Aquidauana, Chapadão do Sul, Dourados, and Primavera do Leste. The experimental design was randomized complete blocks with four replications and 20 genotypes. Genetic parameters were estimated by restricted maximum likelihood/best linear unbiased prediction, and selection was based on the harmonic mean of the relative performance of genetic values method using three strategies: selection based on the predicted breeding value, having considered the performance mean of the genotypes in all environments (no interaction effect); the performance in each environment (with an interaction effect); and the simultaneous selection for grain yield, stability, and adaptability. The MNC99542F-5 and MNC99-537F-4 genotypes could be grown in various environments, as they exhibited high grain yield, adaptability, and stability. The average heritability of the genotypes was moderate to high and the selective accuracy was 82%, indicating an excellent potential for selection.

  14. Genetic parameters and simultaneous selection for root yield, adaptability and stability of cassava genotypes

    Directory of Open Access Journals (Sweden)

    João Tomé de Farias Neto

    2013-12-01

    Full Text Available The objective of this work was to estimate genetic parameters and to evaluate simultaneous selection for root yield and for adaptability and stability of cassava genotypes. The effects of genotypes were assumed as fixed and random, and the mixed model methodology (REML/Blup was used to estimate genetic parameters and the harmonic mean of the relative performance of genotypic values (HMRPGV, for simultaneous selection purposes. Ten genotypes were analyzed in a complete randomized block design, with four replicates. The experiment was carried out in the municipalities of Altamira, Santarém, and Santa Luzia do Pará in the state of Pará, Brazil, in the growing seasons of 2009/2010, 2010/2011, and 2011/2012. Roots were harvested 12 months after planting, in all tested locations. Root yield had low coefficients of genotypic variation (4.25% and broad-sense heritability of individual plots (0.0424, which resulted in low genetic gain. Due to the low genotypic correlation (0.15, genotype classification as to root yield varied according to the environment. Genotypes CPATU 060, CPATU 229, and CPATU 404 stood out as to their yield, adaptability, and stability.

  15. A Gateway recombination herpesvirus cloning system with negative selection that produces vectorless progeny.

    Science.gov (United States)

    Kunec, Dusan; van Haren, Sandra; Burgess, Shane C; Hanson, Larry A

    2009-01-01

    Crossover recombination based on the lambda phage integration/excision functions enables insertion of a gene of interest into a specific locus by a simple one-step in vitro recombination reaction. Recently, a highly efficient recombination system for targeted mutagenesis, which utilizes lambda phage crossover recombination cloning, has been described for a human herpesvirus 2 bacterial artificial chromosome (BAC). The disadvantages of the system are that it allows only neutral selection (loss of green fluorescent protein) of desired recombinants and that it regenerates herpesvirus progeny containing the BAC sequence inserted in the herpesvirus genome. In this study, the existing channel catfish herpesvirus (CCV) infectious clone (in the form of overlapping fragments) was modified to allow introduction of foreign genes by modified lambda phage crossover recombination cloning. This novel system enables negative and neutral selection and regenerates vectorless herpesvirus progeny. Construction of two CCV mutants expressing lacZ, one from the native CCV ORF5 promoter and the other from the immediate-early cytomegalovirus promoter, demonstrated the efficiency and reliability of this system. This novel cloning system enables rapid incorporation, direct delivery and high-level expression of foreign genes by a herpesvirus. This system has broad utility and could be used to facilitate development of recombinant viruses, viral vectors and better vaccines.

  16. Development and validation of a genotype 3 recombinant protein-based immunoassay for hepatitis E virus serology in swine

    Directory of Open Access Journals (Sweden)

    W.H.M. van der Poel

    2014-04-01

    Full Text Available Hepatitis E virus (HEV is classified within the family Hepeviridae, genus Hepevirus. HEV genotype 3 (Gt3 infections are endemic in pigs in Western Europe and in North and South America and cause zoonotic infections in humans. Several serological assays to detect HEV antibodies in pigs have been developed, at first mainly based on HEV genotype 1 (Gt1 antigens. To develop a sensitive HEV Gt3 ELISA, a recombinant baculovirus expression product of HEV Gt3 open reading frame-2 was produced and coated onto polystyrene ELISA plates. After incubation of porcine sera, bound HEV antibodies were detected with anti-porcine anti-IgG and anti-IgM conjugates. For primary estimation of sensitivity and specificity of the assay, sets of sera were used from pigs experimentally infected with HEV Gt3. For further validation of the assay and to set the cutoff value, a batch of 1100 pig sera was used. All pig sera were tested using the developed HEV Gt3 assay and two other serologic assays based on HEV Gt1 antigens. Since there is no gold standard available for HEV antibody testing, further validation and a definite setting of the cutoff of the developed HEV Gt3 assay were performed using a statistical approach based on Bayes' theorem. The developed and validated HEV antibody assay showed effective detection of HEV-specific antibodies. This assay can contribute to an improved detection of HEV antibodies and enable more reliable estimates of the prevalence of HEV Gt3 in swine in different regions.

  17. Gene flow, recombination, and positive selection in Stenotrophomonas maltophilia: mechanisms underlying the diversity of the widespread opportunistic pathogen.

    Science.gov (United States)

    Yu, Dong; Yin, Zhiqiu; Li, Beiping; Jin, Yuan; Ren, Hongguang; Zhou, Jing; Zhou, Wei; Liang, Long; Yue, Junjie

    2016-12-01

    Stenotrophomonas maltophilia is a global multidrug-resistant human opportunistic pathogen in clinical environments. Stenotrophomonas maltophilia is also ubiquitous in aqueous environments, soil, and plants. Various molecular typing methods have revealed that S. maltophilia exhibits high levels of phenotypic and genotypic diversity. However, information regarding the genomic diversity within S. maltophilia and the corresponding genetic mechanisms resulting in said diversity remain scarce. The genome sequences of 17 S. maltophilia strains were selected to investigate the mechanisms contributing to genetic diversity at the genome level. The core and large pan-genomes of the species were first estimated, resulting in a large, open pan-genome. A species phylogeny was also reconstructed based on 344 orthologous genes with one copy per genome, and the contribution of four evolutionary mechanisms to the species genome diversity was quantified: 15%-35% of the genes showed evidence for recombination, 0%-25% of the genes in one genome were likely gained, 0%-44% of the genes in some genomes were likely lost, and less than 0.3% of the genes in a genome were under positive selection pressures. We observed that, among the four main mechanisms, homologous recombination plays a key role in maintaining diversity in S. maltophilia. In this study, we provide an overview of evolution in S. maltophilia to provide a better understanding of its evolutionary dynamics and its relationship with genome diversity.

  18. Interlocus sexually antagonistic coevolution can create indirect selection for increased recombination.

    Science.gov (United States)

    Dapper, Amy L; Lively, Curtis M

    2014-04-01

    The ubiquity of recombination in nature is a paradox because it breaks up combinations of alleles favored by natural selection. Theoretical work has shown that antagonistic coevolution between hosts and parasites can result in rapid fluctuations in epistasis that can create a short-term advantage to recombination. Here, we show that another kind of antagonistic coevolution, interlocus sexually antagonistic coevolution (SAC), can also create indirect selection for modifiers that increase the rate of recombination, and that it can lead to very high levels of recombination at equilibrium. Recombination is favored because interlocus SAC creates heterogeneity in the strength and direction of selection, both within and between generations, which maintains an excess of disadvantageous haplotypes in the population. This result is similar to and consistent with dynamics of fluctuating epistasis produced in models of host-parasite coevolution. However, the conditions under which interlocus SAC provides an advantage to recombination are more permissive. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  19. KIR genotyping in the selected population in Andhra Pradesh (India).

    Science.gov (United States)

    Vaishnav, G; Krupanidhi, S; Sanjeevi, C B

    2014-01-01

    The population is not always homogeneous in relation to the representation and functioning of genes. Therefore, the presence of allogenicity is a universal phenomenon. The profound variability is noticed among the members of the human population with reference to the resistance against infections and late onset of diseases. In this line, a few sets of alleles which come under the domain of immune function namely KIRs (Killer immunoglobulin-like receptor genes) and HLA-I have been chosen to report in the population of Puttaparthi (India). The genotyping of the population is the current ongoing focus of our team wherein the distribution of the following alleles has been taken up in the mixed ethnic groups of Puttaparthi as a prelude to earmark them as genotypic markers in future studies relating to susceptible diseases. The PCR protocols for the identified immune related genes viz., KIR- 2DL1, 2DL2, 2DL3, 2DL4, 2DL5, 3DL1, 3DL2, 3DL3, 3DS1, 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 2DP1, 3DP1; HLA- C1 and HLA-C2 have been standardized. In the present study, except KIR 2DL2, the other non-framework inhibitory KIR genes were represented at higher percentage and ranged from 57% to 80% in the chosen population which would suggest its higher survival adaptation. Interestingly, the majority of activating KIR genes were least represented and varied between 5% to 32.5% which is also in compliance with the survival adaptation of the chosen population. The carrier gene frequencies of KIRs were compared with the other populations' viz., Chinese Mongolian, Chinese Han, Greek and Brazilian data. The expected heterozygosity of KIR alleles and their rank in gene diversity among the population of Puttaparthi were also discussed.

  20. Highly variable recombinational landscape modulates efficacy of natural selection in birds.

    Science.gov (United States)

    Gossmann, Toni I; Santure, Anna W; Sheldon, Ben C; Slate, Jon; Zeng, Kai

    2014-08-01

    Determining the rate of protein evolution and identifying the causes of its variation across the genome are powerful ways to understand forces that are important for genome evolution. By using a multitissue transcriptome data set from great tit (Parus major), we analyzed patterns of molecular evolution between two passerine birds, great tit and zebra finch (Taeniopygia guttata), using the chicken genome (Gallus gallus) as an outgroup. We investigated whether a special feature of avian genomes, the highly variable recombinational landscape, modulates the efficacy of natural selection through the effects of Hill-Robertson interference, which predicts that selection should be more effective in removing deleterious mutations and incorporating beneficial mutations in high-recombination regions than in low-recombination regions. In agreement with these predictions, genes located in low-recombination regions tend to have a high proportion of neutrally evolving sites and relaxed selective constraint on sites subject to purifying selection, whereas genes that show strong support for past episodes of positive selection appear disproportionally in high-recombination regions. There is also evidence that genes located in high-recombination regions tend to have higher gene expression specificity than those located in low-recombination regions. Furthermore, more compact genes (i.e., those with fewer/shorter introns or shorter proteins) evolve faster than less compact ones. In sum, our results demonstrate that transcriptome sequencing is a powerful method to answer fundamental questions about genome evolution in nonmodel organisms. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  1. Genomic selection improves response to selection in resilience by exploiting genotype by environment interactions

    Directory of Open Access Journals (Sweden)

    Han Mulder

    2016-10-01

    Full Text Available Genotype by environment interactions (GxE are very common in livestock and hamper genetic improvement. On the other hand, GxE is a source of genetic variation: genetic variation in response to environment, e.g. environmental perturbations such as heat stress or disease. In livestock breeding, there is tendency to ignore GxE because of increased complexity of models for genetic evaluations and lack of accuracy in extreme environments. GxE, however, creates opportunities to increase resilience of animals towards environmental perturbations. The main aim of the paper is to investigate to which extent GxE can be exploited with traditional and genomic selection methods. Furthermore, we investigated the benefit of reaction norm models compared to conventional methods ignoring GxE. The questions were addressed with selection index theory. GxE was modelled according to a linear reaction norm model in which the environmental gradient is the contemporary group mean. Economic values were based on linear and non-linear profit equations.Accuracies of environment-specific (GEBV were highest in intermediate environments and lowest in extreme environments. Reaction norm models had higher accuracies of (GEBV in extreme environments than conventional models ignoring GxE. Genomic selection always resulted in higher response to selection in all environments than sib or progeny testing schemes. The increase in response was with genomic selection between 9% and 140% compared to sib testing and between 11% and 114% compared to progeny testing when the reference population consisted of 1 million animals across all environments. When the aim was to decrease environmental sensitivity, the response in slope of the reaction norm model with genomic selection was between 1.09 and 319 times larger than with sib or progeny testing and in the right direction in contrast to sib and progeny testing that still increased environmental sensitivity. This shows that genomic selection

  2. Exploiting translational coupling for the selection of cells producing toxic recombinant proteins from expression vectors.

    Science.gov (United States)

    Tagliavia, Marcello; Cuttitta, Angela

    2016-01-01

    High rates of plasmid instability are associated with the use of some expression vectors in Escherichia coli, resulting in the loss of recombinant protein expression. This is due to sequence alterations in vector promoter elements caused by the background expression of the cloned gene, which leads to the selection of fast-growing, plasmid-containing cells that do not express the target protein. This phenomenon, which is worsened when expressing toxic proteins, results in preparations containing very little or no recombinant protein, or even in clone loss; however, no methods to prevent loss of recombinant protein expression are currently available. We have exploited the phenomenon of translational coupling, a mechanism of prokaryotic gene expression regulation, in order to select cells containing plasmids still able to express recombinant proteins. Here we designed an expression vector in which the cloned gene and selection marker are co-expressed. Our approach allowed for the selection of the recombinant protein-expressing cells and proved effective even for clones encoding toxic proteins.

  3. A Novel Hybrid Clonal Selection Algorithm with Combinatorial Recombination and Modified Hypermutation Operators for Global Optimization

    Science.gov (United States)

    Lin, Jingjing; Jing, Honglei

    2016-01-01

    Artificial immune system is one of the most recently introduced intelligence methods which was inspired by biological immune system. Most immune system inspired algorithms are based on the clonal selection principle, known as clonal selection algorithms (CSAs). When coping with complex optimization problems with the characteristics of multimodality, high dimension, rotation, and composition, the traditional CSAs often suffer from the premature convergence and unsatisfied accuracy. To address these concerning issues, a recombination operator inspired by the biological combinatorial recombination is proposed at first. The recombination operator could generate the promising candidate solution to enhance search ability of the CSA by fusing the information from random chosen parents. Furthermore, a modified hypermutation operator is introduced to construct more promising and efficient candidate solutions. A set of 16 common used benchmark functions are adopted to test the effectiveness and efficiency of the recombination and hypermutation operators. The comparisons with classic CSA, CSA with recombination operator (RCSA), and CSA with recombination and modified hypermutation operator (RHCSA) demonstrate that the proposed algorithm significantly improves the performance of classic CSA. Moreover, comparison with the state-of-the-art algorithms shows that the proposed algorithm is quite competitive. PMID:27698662

  4. A genome-wide identification of genes undergoing recombination and positive selection in Neisseria.

    Science.gov (United States)

    Yu, Dong; Jin, Yuan; Yin, Zhiqiu; Ren, Hongguang; Zhou, Wei; Liang, Long; Yue, Junjie

    2014-01-01

    Currently, there is particular interest in the molecular mechanisms of adaptive evolution in bacteria. Neisseria is a genus of gram negative bacteria, and there has recently been considerable focus on its two human pathogenic species N. meningitidis and N. gonorrhoeae. Until now, no genome-wide studies have attempted to scan for the genes related to adaptive evolution. For this reason, we selected 18 Neisseria genomes (14 N. meningitidis, 3 N. gonorrhoeae and 1 commensal N. lactamics) to conduct a comparative genome analysis to obtain a comprehensive understanding of the roles of natural selection and homologous recombination throughout the history of adaptive evolution. Among the 1012 core orthologous genes, we identified 635 genes with recombination signals and 10 genes that showed significant evidence of positive selection. Further functional analyses revealed that no functional bias was found in the recombined genes. Positively selected genes are prone to DNA processing and iron uptake, which are essential for the fundamental life cycle. Overall, the results indicate that both recombination and positive selection play crucial roles in the adaptive evolution of Neisseria genomes. The positively selected genes and the corresponding amino acid sites provide us with valuable targets for further research into the detailed mechanisms of adaptive evolution in Neisseria.

  5. Recombinant HCV variants with NS5A from genotypes 1-7 have different sensitivities to an NS5A inhibitor but not interferon-a

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Gottwein, Judith M; Mikkelsen, Lotte S

    2011-01-01

    Heterogeneity in the hepatitis C virus (HCV) protein NS5A influences its sensitivity to interferon-based therapy. Furthermore, NS5A is an important target for development of HCV-specific inhibitors. We aimed to develop recombinant infectious cell culture systems that express NS5A from isolates...... of the 7 major HCV genotypes, and determining their sensitivity to a specific NS5A inhibitor and to interferon-a....

  6. [Rapid selection of recombinant orf virus expression vectors using green fluorescent protein].

    Science.gov (United States)

    Zhang, Jiachun; Guo, Xianfeng; Zhang, Min; Wu, Feifan; Peng, Yongzheng

    2016-01-01

    To construct a universal, highly attenuated orf virus expression vector for exogenous genes using green fluorescent protein (GFP) as the reporter gene. The flanking regions of the ORFV132 of orf virus DNA were amplified by PCR to construct the shuttle plasmid pSPV-132LF-EGFP-132RF. The shuttle plasmid was transfected into OFTu cells and GFP was incorporated into orf virus IA82Delta 121 by homologous recombination. The recombinant IA82Delta121-V was selected by green fluorescent signal. The deletion gene was identified by PCR and sequencing. The effects of ORFV132 knockout were evaluated by virus titration and by observing the proliferation of the infected vascular endothelial cells in vitro. The recombinant orf virus IA82Delta121-V was obtained successfully and quickly, and the deletion of ORFV132 did not affect the replication of the virus in vitro but reduced its virulence. Green fluorescent protein is a selectable marker for rapid, convenient and stable selection of the recombinant viruses. Highly attenuated recombinant orf virus IA82Delta121-V can serve as a new expression vector for exogenous genes.

  7. Genetic diversity among selected genotypes of almond Prunus ...

    African Journals Online (AJOL)

    rohit

    2012-10-16

    Oct 16, 2012 ... introductions, as well as indigenous selections (Table 1). Genomic. DNA was isolated from freshly collected leaves following modified. CTAB method (Doyle and Doyle, 1987, 1990). Phenolics and tannins were removed by repeated purification of DNA following phenol and chloroform treatment. Also during ...

  8. Comparative analysis of juice volatiles in selected mandarins, mandarin relatives and other citrus genotypes.

    Science.gov (United States)

    Yu, Yuan; Bai, Jinhe; Chen, Chunxian; Plotto, Anne; Baldwin, Elizabeth A; Gmitter, Frederick G

    2018-02-01

    Citrus fruit flavor is an important attribute prioritized in variety improvement. The present study compared juice volatiles compositions from 13 selected citrus genotypes, including six mandarins (Citrus reticulata), three sour oranges (Citrus aurantium), one blood orange (Citrus sinensis), one lime (Citrus limonia), one Clementine (Citrus clementina) and one satsuma (Citrus unshiu). Large differences were observed with respect to volatile compositions among the citrus genotypes. 'Goutou' sour orange contained the greatest number of volatile compounds and the largest volatile production level. 'Ponkan' mandarin had the smallest number of volatiles and 'Owari' satsuma yielded the lowest volatile production level. 'Goutou' sour orange and 'Moro' blood orange were clearly distinguished from other citrus genotypes based on the analysis of volatile compositions, even though they were assigned into one single group with two other sour oranges by the molecular marker profiles. The clustering analysis based on the aroma volatile compositions was able to differentiate mandarin varieties and natural sub-groups, and was also supported by the molecular marker study. The gas chromatography-mass spectrometry analysis of citrus juice aroma volatiles can be used as a tool to distinguish citrus genotypes and assist in the assessment of future citrus breeding programs. The aroma volatile profiles of the different citrus genotypes and inter-relationships detected among volatile compounds and among citrus genotypes will provide fundamental information on the development of marker-assisted selection in citrus breeding. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  9. In vitro application of integrated selection index for screening drought tolerant genotypes in common wheat

    Directory of Open Access Journals (Sweden)

    Ezatollah FARSHADFAR

    2016-10-01

    Full Text Available This experiment was conducted on 20 wheat genotypes during 2010-2011 growing season at the Razi University, Kermanshah, Iran. A completely randomized design with six replications was used for callus induction and a 20 × 2 factorial experiment with three replications was used for response of genotypes to in vitro drought stress. ANOVA exhibited highly significant differences among the genotypes for callus growth rate, relative fresh mass growth, relative growth rate, callus water content, percent of callus chlorosis and proline content under stress condition (15 % PEG. PCA showed that the integrated selection index was correlated with callus growth index, relative fresh mass growth, relative growth rate and proline content indicating that these screening techniques can be useful for selecting drought tolerant genotypes. Screening drought tolerant genotypes and in vitro indicators of drought tolerance using mean rank, standard deviation of ranks and biplot analysis, discriminated genotypes 2, 18 and 10 as the most drought tolerant. Therefore they are recommended to be used as parents for genetic analysis, gene mapping and improvement of drought tolerance.

  10. Efficient Culture Adaptation of Hepatitis C Virus Recombinants with Genotype-Specific Core-NS2 by Using Previously Identified Mutations

    DEFF Research Database (Denmark)

    Scheel, Troels Kasper Høyer; Gottwein, Judith M; Carlsen, Thomas H R

    2011-01-01

    Hepatitis C virus (HCV) is an important cause of chronic liver disease, and interferon-based therapy cures only 40 to 80% of patients, depending on HCV genotype. Research was accelerated by genotype 2a (strain JFH1) infectious cell culture systems. We previously developed viable JFH1-based...... mutations did not adapt to culture. Universal adaptive effects of mutations in NS3 (Q1247L, I1312V, K1398Q, R1408W, and Q1496L) and NS5A (V2418L) were investigated for JFH1-based genotype 1 to 5 core-NS2 recombinants; several mutations conferred adaptation to H77C (1a), J4 (1b), S52 (3a), and SA13 (5a......-specific patterns in HCV disease and control....

  11. Genotypic gain with simultaneous selection of production, nutrition, and culinary traits in cowpea crosses and backcrosses using mixed models.

    Science.gov (United States)

    Oliveira, D G; Rocha, M M; Damasceno-Silva, K J; Sá, F V; Lima, L R L; Resende, M D V

    2017-08-17

    The aim of this study was to estimate the genotypic gain with simultaneous selection of production, nutrition, and culinary traits in cowpea crosses and backcrosses and to compare different selection indexes. Eleven cowpea populations were evaluated in a randomized complete block design with four replications. Fourteen traits were evaluated, and the following parameters were estimated: genotypic variation coefficient, genotypic determination coefficient, experimental quality indicator and selection reliability, estimated genotypic values ​​- BLUE, genotypic correlation coefficient among traits, and genotypic gain with simultaneous selection of all traits. The genotypic gain was estimated based on tree selection indexes: classical, multiplicative, and the sum of ranks. The genotypic variation coefficient was higher than the environmental variation coefficient for the number of days to start flowering, plant type, the weight of one hundred grains, grain index, and protein concentration. The majority of the traits presented genotypic determination coefficient from medium to high magnitude. The identification of increases in the production components is associated with decreases in protein concentration, and the increase in precocity leads to decreases in protein concentration and cooking time. The index based on the sum of ranks was the best alternative for simultaneous selection of traits in the cowpea segregating populations resulting from the crosses and backcrosses evaluated, with emphasis on the F 4 BC 12 , F 4 C 21 , and F 4 C 12 populations, which had the highest genotypic gains.

  12. Class switch recombination in selective IgA-deficient subjects

    DEFF Research Database (Denmark)

    Jensen, Lone Hummelshøj; Ryder, L P; Nielsen, L K

    2006-01-01

    Selective IgA deficiency is a common immunodeficiency in Caucasians, but the molecular basis of the disorder remains elusive. To address this issue we examined the molecular events leading to IgA production. Naive IgD positive B cells were purified from four donors with IgA deficiency and four......-beta in combination, induced IgA production, albeit lower than found in B cells from controls. The B cells from the IgA-deficient subjects were less effective in differentiating into CD138(+) X-box binding protein 1 (XBP-1)(+) plasma cells when stimulated with TGF-beta, IFN-gamma or IL-10. Interestingly, when adding...... IL-4 to TGF-beta alone or in combination with IL-10, the immunoglobulin production in B cells from IgA-deficient donors was comparable with those of normal controls. These data show that in healthy subjects in vitro IgA production can be up-regulated by addition of IL-10 to CD40-stimulated B cells...

  13. Cow genotyping strategies for genomic selection in a small dairy cattle population.

    Science.gov (United States)

    Jenko, J; Wiggans, G R; Cooper, T A; Eaglen, S A E; Luff, W G de L; Bichard, M; Pong-Wong, R; Woolliams, J A

    2017-01-01

    This study compares how different cow genotyping strategies increase the accuracy of genomic estimated breeding values (EBV) in dairy cattle breeds with low numbers. In these breeds, few sires have progeny records, and genotyping cows can improve the accuracy of genomic EBV. The Guernsey breed is a small dairy cattle breed with approximately 14,000 recorded individuals worldwide. Predictions of phenotypes of milk yield, fat yield, protein yield, and calving interval were made for Guernsey cows from England and Guernsey Island using genomic EBV, with training sets including 197 de-regressed proofs of genotyped bulls, with cows selected from among 1,440 genotyped cows using different genotyping strategies. Accuracies of predictions were tested using 10-fold cross-validation among the cows. Genomic EBV were predicted using 4 different methods: (1) pedigree BLUP, (2) genomic BLUP using only bulls, (3) univariate genomic BLUP using bulls and cows, and (4) bivariate genomic BLUP. Genotyping cows with phenotypes and using their data for the prediction of single nucleotide polymorphism effects increased the correlation between genomic EBV and phenotypes compared with using only bulls by 0.163±0.022 for milk yield, 0.111±0.021 for fat yield, and 0.113±0.018 for protein yield; a decrease of 0.014±0.010 for calving interval from a low base was the only exception. Genetic correlation between phenotypes from bulls and cows were approximately 0.6 for all yield traits and significantly different from 1. Only a very small change occurred in correlation between genomic EBV and phenotypes when using the bivariate model. It was always better to genotype all the cows, but when only half of the cows were genotyped, a divergent selection strategy was better compared with the random or directional selection approach. Divergent selection of 30% of the cows remained superior for the yield traits in 8 of 10 folds. Copyright © 2017 American Dairy Science Association. Published by

  14. Analysis of ORF5 and Full-Length Genome Sequences of Porcine Reproductive and Respiratory Syndrome Virus Isolates of Genotypes 1 and 2 Retrieved Worldwide Provides Evidence that Recombination Is a Common Phenomenon and May Produce Mosaic Isolates

    DEFF Research Database (Denmark)

    Martín-Valls, G. E.; Kvisgaard, Lise Kirstine; Tello, M.

    2014-01-01

    different geographical areas, including 2 Asian, 1 American, and 7 European regions, and three sets of genotype 2, including sets from China, Mexico, and the United States, were analyzed separately. Potential recombination breakpoints were detected in 10/11 genotype 1 sets, including 9 cases in which...

  15. Genotyping by sequencing (GBS, an ultimate marker-assisted selection (MAS tool to accelerate plant breeding

    Directory of Open Access Journals (Sweden)

    Jiangfeng eHe

    2014-09-01

    Full Text Available Marker-assisted selection (MAS refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP, have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping by sequencing (GBS has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS, genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection (GS under a large scale of plant breeding programs.

  16. Multi-generational imputation of single nucleotide polymorphism marker genotypes and accuracy of genomic selection.

    Science.gov (United States)

    Toghiani, S; Aggrey, S E; Rekaya, R

    2016-07-01

    Availability of high-density single nucleotide polymorphism (SNP) genotyping platforms provided unprecedented opportunities to enhance breeding programmes in livestock, poultry and plant species, and to better understand the genetic basis of complex traits. Using this genomic information, genomic breeding values (GEBVs), which are more accurate than conventional breeding values. The superiority of genomic selection is possible only when high-density SNP panels are used to track genes and QTLs affecting the trait. Unfortunately, even with the continuous decrease in genotyping costs, only a small fraction of the population has been genotyped with these high-density panels. It is often the case that a larger portion of the population is genotyped with low-density and low-cost SNP panels and then imputed to a higher density. Accuracy of SNP genotype imputation tends to be high when minimum requirements are met. Nevertheless, a certain rate of genotype imputation errors is unavoidable. Thus, it is reasonable to assume that the accuracy of GEBVs will be affected by imputation errors; especially, their cumulative effects over time. To evaluate the impact of multi-generational selection on the accuracy of SNP genotypes imputation and the reliability of resulting GEBVs, a simulation was carried out under varying updating of the reference population, distance between the reference and testing sets, and the approach used for the estimation of GEBVs. Using fixed reference populations, imputation accuracy decayed by about 0.5% per generation. In fact, after 25 generations, the accuracy was only 7% lower than the first generation. When the reference population was updated by either 1% or 5% of the top animals in the previous generations, decay of imputation accuracy was substantially reduced. These results indicate that low-density panels are useful, especially when the generational interval between reference and testing population is small. As the generational interval

  17. Characterization and Selection of Phosphorus Deficiency Tolerant Rice Genotypes in Sri Lanka

    Directory of Open Access Journals (Sweden)

    Y.C. Aluwihare

    2016-07-01

    Full Text Available Phosphorus (P deficiency in soil is a major constrain for rice production. An important set of rice genotypes (landraces, old improved and new improved varieties were screened for P deficiency tolerance in two major cropping seasons of Sri Lanka, in 2012. The Ultisol soil, which was collected from a plot cultivated with rice without fertilizer application for past 40 years (P0 at the Rice Research and Development Institute (RRDI, Bathalagoda, Sri Lanka, was used as the potting medium for greenhouse trials. Two field trials were conducted in the same plots at RRDI. Both P0 and P30 (30 mg/kg P2O5 conditions were used in the two greenhouse trials. At the early vegetative (three weeks after transplanting, late vegetative (six weeks after transplanting and flowering stages, plant height and number of tillers per plant were recorded. At the flowering stage, shoots were harvested and shoot dry weight, shoot P concentration, shoot P uptake and P utilization efficiency were measured. All data were statistically analyzed using analysis of variance, regression and cluster procedures. The measured parameters were significantly different between P0 and P30 conditions (P < 0.05. Higher shoot dry weight was reported by the rice genotypes H4 and Marss under P0 conditions. The regression analysis between shoot dry weight and P utilization efficiency revealed that the studied rice genotypes could be categorized to three P deficiency tolerance classes. A total of 13 genotypes could be considered as highly tolerant and 4 genotypes as sensitive for P deficiency. These results could be used to select parental genotypes for breeding and genetic studies and also to select interesting varieties or landraces for organic rice production.

  18. Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach.

    Science.gov (United States)

    Fariello, María Inés; Boitard, Simon; Mercier, Sabine; Robelin, David; Faraut, Thomas; Arnould, Cécile; Recoquillay, Julien; Bouchez, Olivier; Salin, Gérald; Dehais, Patrice; Gourichon, David; Leroux, Sophie; Pitel, Frédérique; Leterrier, Christine; SanCristobal, Magali

    2017-07-01

    Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans increases detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score approach to account for linkage disequilibrium in genome scans for selection, cumulating (possibly small) signals from single markers over a genomic segment, to clearly pinpoint a selection signal. Using computer simulations, we demonstrate that this approach detects selection with higher power than several state-of-the-art single-marker, windowing or haplotype-based approaches. We illustrate this on two benchmark data sets including individual genotypes, for which we obtain similar results with the local score and one haplotype-based approach. Finally, we apply the local score approach to Pool-Seq data obtained from a divergent selection experiment on behaviour in quail and obtain precise and biologically coherent selection signals: while competing methods fail to highlight any clear selection signature, our method detects several regions involving genes known to act on social responsiveness or autistic traits. Although we focus here on the detection of positive selection from multiple population data, the local score approach is general and can be applied to other genome scans for selection or other genomewide analyses such as GWAS. © 2017 John Wiley & Sons Ltd.

  19. The joint effects of background selection and genetic recombination on local gene genealogies.

    Science.gov (United States)

    Zeng, Kai; Charlesworth, Brian

    2011-09-01

    Background selection, the effects of the continual removal of deleterious mutations by natural selection on variability at linked sites, is potentially a major determinant of DNA sequence variability. However, the joint effects of background selection and genetic recombination on the shape of the neutral gene genealogy have proved hard to study analytically. The only existing formula concerns the mean coalescent time for a pair of alleles, making it difficult to assess the importance of background selection from genome-wide data on sequence polymorphism. Here we develop a structured coalescent model of background selection with recombination and implement it in a computer program that efficiently generates neutral gene genealogies for an arbitrary sample size. We check the validity of the structured coalescent model against forward-in-time simulations and show that it accurately captures the effects of background selection. The model produces more accurate predictions of the mean coalescent time than the existing formula and supports the conclusion that the effect of background selection is greater in the interior of a deleterious region than at its boundaries. The level of linkage disequilibrium between sites is elevated by background selection, to an extent that is well summarized by a change in effective population size. The structured coalescent model is readily extendable to more realistic situations and should prove useful for analyzing genome-wide polymorphism data.

  20. Genomic selection improves response to selection in resilience by exploiting genotype by environment interactions

    NARCIS (Netherlands)

    Mulder, Herman

    2016-01-01

    Genotype by environment interactions (GxE) are very common in livestock and hamper genetic improvement. On the other hand, GxE is a source of genetic variation: genetic variation in response to environment, e.g., environmental perturbations such as heat stress or disease. In livestock breeding,

  1. Differential sensitivity of 5'UTR-NS5A recombinants of hepatitis C virus genotypes 1-6 to protease and NS5A inhibitors

    DEFF Research Database (Denmark)

    Li, Yi-Ping; Ramirez, Santseharay; Humes, Daryl

    2014-01-01

    BACKGROUND & AIMS: Hepatitis C virus (HCV) therapy will benefit from the preclinical evaluation of direct-acting antiviral (DAA) agents in infectious culture systems that test the effects on different virus genotypes. We developed HCV recombinants comprising the 5' untranslated region-NS5A (5-5A......, by incorporating additional recovered mutations that increased their propagation in Huh7.5 cells. Concentration-response profiles were determined for each DAA agent in replicate infected Huh7.5 cells. RESULTS: Developed efficient 1a(H77), 1a(TN), 3a(S52), 4a(ED43), 5a(SA13), and 6a(HK6a) 5-5A recombinants did...... daclatasvir. The 1a(TN) 5-5A and JFH1-independent full-length viruses had similar levels of sensitivity to the DAA agents, validating the 5-5A recombinants as surrogates for full-length viruses in DAA testing. Compared with the 1a(TN) full-length virus, the 3a(S52) 5-5A recombinant was highly resistant to all...

  2. Different sexual traits show covariation among genotypes: implications for sexual selection

    OpenAIRE

    Alison F. Cooperman; Michal Polak; Christopher S. Evans; Phillip W. Taylor

    2007-01-01

    An unresolved question in sexual selection research is whether different secondary sexual traits are developmentally independent or instead whether their degree of expression is a manifestation of a general resource pool (i.e., condition) within the organism. If degree of expression of different sexual traits reflects ability to accumulate condition, then covariation should exist across genotypes in the expression of these traits, even if they are very different in kind. Here we present evide...

  3. CGTS: a site-clustering graph based tagSNP selection algorithm in genotype data.

    Science.gov (United States)

    Wang, Jun; Guo, Mao-zu; Wang, Chun-yu

    2009-01-30

    Recent studies have shown genetic variation is the basis of the genome-wide disease association research. However, due to the high cost on genotyping large number of single nucleotide polymorphisms (SNPs), it is essential to choose a small subset of informative SNPs (tagSNPs), which are able to capture most variation in a population, to represent the rest SNPs. Several methods have been proposed to find the minimum set of tagSNPs, but most of them still have some disadvantages such as information loss and block-partition limit. This paper proposes a new hybrid method named CGTS which combines the ideas of the clustering and the graph algorithms to select tagSNPs on genotype data. This method aims to maximize the number of the discarding nontagSNPs in the given set. CGTS integrates the information of the LD association and the genotype diversity using the site graphs, discards redundant SNPs using the algorithm based on these graph structures. The clustering algorithm is used to reduce the running time of CGTS. The efficiency of the algorithm and quality of solutions are evaluated on biological data and the comparisons with three popular selecting methods are shown in the paper. Our theoretical analysis and experimental results show that our algorithm CGTS is not only more efficient than other methods but also can be get higher accuracy in tagSNP selection.

  4. Selection of Superior Genotypes of Coffea Canephora Pierre on ControlledHybrid Population Using Cluster Analysis Method

    Directory of Open Access Journals (Sweden)

    Ucu Sumirat

    2007-05-01

    Full Text Available Selection of superior genotypes of robusta coffee (Coffea canephora to improve its important agronomic characters should be conducted continuously to get better planting productivity. The aim of this research was to select superior genotypes of Robusta coffee for high yield and high proportion of large bean. Selection was conducted on controlled hybrid populations, developed from three crossing parental clones, i.e. BP 961 x Q 121 (A, BP 409 x Q 121 (B and BP 961 x BP 409 (C. Selection was done by applying cluster analysis with complete linkage and Euclidean distance as the clustering method. The result of the research showed that the selection was successful to identify superior genotypes of Robusta coffee for high yield and high proportion of large bean. The parameters used (cherries weight/tree, bean weight/tree, bean size percentage > 6.5 mm and 100 cherries weight were effective in clustering the superior genotypes, indicated by increased minimum and average value of population. Yield potential and percentage of bean size > 6.5 mm of those genotypes were having better performance than the control genotype and its parent. The selection code A 95, B 28, B 62, B 66, B 74 and C 38 were considered  as promising superior genotypes of Robusta coffee, respectively. Key words: Coffea canephora, selection, bean size, yield, cluster analysis

  5. The typical RB76 recombination breakpoint of the invasive recombinant tomato yellow leaf curl virus of Morocco can be generated experimentally but is not positively selected in tomato.

    Science.gov (United States)

    Belabess, Z; Urbino, C; Granier, M; Tahiri, A; Blenzar, A; Peterschmitt, M

    2018-01-02

    TYLCV-IS76 is an unusual recombinant between the highly recombinogenic tomato yellow leaf curl virus (TYLCV) and tomato yellow leaf curl Sardinia virus (TYLCSV), two Mediterranean begomoviruses (Geminiviridae). In contrast with the previously reported TYLCV/TYLCSV recombinants, it has a TYLCSV derived fragment of only 76 nucleotides, and has replaced its parental viruses in natural conditions (Morocco, Souss region). The viral population shift coincided with the deployment of the popular Ty-1 resistant tomato cultivars, and according to experimental studies, has been driven by a strong positive selection in such resistant plants. However, although Ty-1 cultivars were extensively used in Mediterranean countries, TYLCV-IS76 was not reported outside Morocco. This, in combination with its unusual recombination pattern suggests that it was generated through a rare and possibly multistep process. The potential generation of a recombination breakpoint (RB) at locus 76 (RB76) was investigated over time in 10 Ty-1 resistant and 10 nearly isogenic susceptible tomato plants co-inoculated with TYLCV and TYLCSV clones. RB76 could not be detected in the recombinant progeny using the standard PCR/sequencing approach that was previously designed to monitor the emergence of TYLCV-IS76 in Morocco. Using a more sensitive PCR test, RB76 was detected in one resistant and five susceptible plants. The results are consistent with a very low intra-plant frequency of RB76 bearing recombinants throughout the test and support the hypothesis of a rare emergence of TYLCV-IS76. More generally, RBs were more scattered in resistant than in susceptible plants and an unusual RB at position 141 (RB141) was positively selected in the resistant cultivar; interestingly, RB141 bearing recombinants were detected in resistant tomato plants from the field. Scenarios of TYLCV-IS76 pre-emergence are proposed. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Songbirds as general transmitters but selective amplifiers of Borrelia burgdorferi sensu lato genotypes in Ixodes rinicus ticks.

    Science.gov (United States)

    Heylen, Dieter; Matthysen, Erik; Fonville, Manoj; Sprong, Hein

    2014-09-01

    We investigated to what extent a European songbird (Parus major) selectively transmits and amplifies Borrelia burgdorferi s.l. bacteria. Borrelia-naïve birds were recurrently exposed to Ixodes ricinus nymphs carrying a community of more than 34 5S-23S genotypes belonging to five genospecies (Borrelia garinii, Borrelia valaisiana, Borrelia afzelii, B. burgdorferi s.s. and Borrelia spielmanii). Fed ticks were screened for Borrelia after moulting. We found evidence for co-feeding transmission of avian and possibly also mammalian genotypes. Throughout the course of infestations, the infection rate of B. garinii and B. valaisiana increased, indicating successful amplification and transmission, while the infection rate for B. afzelii, B. burgdorferi s.s and B. spielmanii tended to decrease. Within the B. garinii and B. valaisiana genotype communities, certain genotypes were transmitted more than others. Moreover, birds were able to host mixed infections of B. garinii and B. valaisiana, as well as mixed infections of genotypes of the same genospecies. We experimentally show that resident songbirds transmit a broad range of Borrelia genotypes, but selectively amplify certain genotypes, and that one bird can transmit simultaneously several genotypes. Our results highlight the need to explicitly consider the association between genotypes and hosts, which may offer opportunities to point out which hosts are most responsible for the Borrelia presence in questing ticks. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. Selection of common bean genotypes for the Cerrado/Pantanal ecotone via mixed models and multivariate analysis.

    Science.gov (United States)

    Corrêa, A M; Pereira, M I S; de Abreu, H K A; Sharon, T; de Melo, C L P; Ito, M A; Teodoro, P E; Bhering, L L

    2016-10-17

    The common bean, Phaseolus vulgaris, is predominantly grown on small farms and lacks accurate genotype recommendations for specific micro-regions in Brazil. This contributes to a low national average yield. The aim of this study was to use the methods of the harmonic mean of the relative performance of genetic values (HMRPGV) and the centroid, for selecting common bean genotypes with high yield, adaptability, and stability for the Cerrado/Pantanal ecotone region in Brazil. We evaluated 11 common bean genotypes in three trials carried out in the dry season in Aquidauana in 2013, 2014, and 2015. A likelihood ratio test detected a significant interaction between genotype x year, contributing 54% to the total phenotypic variation in grain yield. The three genotypes selected by the joint analysis of genotypic values in all years (Carioca Precoce, BRS Notável, and CNFC 15875) were the same as those recommended by the HMRPGV method. Using the centroid method, genotypes BRS Notável and CNFC 15875 were considered ideal genotypes based on their high stability to unfavorable environments and high responsiveness to environmental improvement. We identified a high association between the methods of adaptability and stability used in this study. However, the use of centroid method provided a more accurate and precise recommendation of the behavior of the evaluated genotypes.

  8. Evaluation of Hepatitis C Virus Core Antigen Assays in Detecting Recombinant Viral Antigens of Various Genotypes

    Science.gov (United States)

    Saeed, Mohsan; Suzuki, Ryosuke; Kondo, Madoka; Aizaki, Hideki; Kato, Takanobu; Mizuochi, Toshiaki; Wakita, Takaji; Watanabe, Haruo; Suzuki, Tetsuro

    2009-01-01

    A single substitution within the hepatitis C virus core antigen sequence, A48T, which is observed in ∼30% of individuals infected with genotype 2a virus, reduces the sensitivity of a commonly used chemiluminescence enzyme immunoassay. Quantitation of the antigen is improved by using a distinct anticore antibody with a different epitope. PMID:19812276

  9. Physiological characterisation of recombinant Aspergillus nidulans strains with different creA genotypes expressing A-oryzae alpha-amylase

    DEFF Research Database (Denmark)

    Agger, Teit; Petersen, J.B.; O'Connor, S.M.

    2002-01-01

    The physiology of three strains of Aspergillus nidulans was examined-a creA deletion strain, a wild type creA genotype and a strain containing extra copies of the creA gene, all producing Aspergillus oryzae alpha-amylase. The strains were cultured in batch and continuous cultivations and the biom...

  10. Selection of Rice Genotypes for Salinity Tolerance Through Morpho-Biochemical Assessment

    Directory of Open Access Journals (Sweden)

    Md. Nasim ALI

    2014-09-01

    Full Text Available The present study reported the morpho-biochemical evaluation of 15 selected rice genotypes for salt tolerance at the seedling stage. Growth parameters including shoot length, root length, plant biomass, plant turgid weight, plant dry weight along with relative water content were measured after exposure to saline solution (with electrical conductivity value of 12 dS/m. Genotypes, showing significant differential responses towards salinity in the fields, were assessed through 14 salinity-linked morpho-biochemical attributes, measured at 14 d after exposure of seedling in saline nutrient solution. Relative water content, chlorophyll a/b, peroxidase activity and plant biomass were identified as potential indicators of salt tolerance. Principal component analysis and successive Hierarchical clustering using Euclidean distance revealed that Talmugur, Gheus, Ghunsi, Langalmura, Sabitapalui, and Sholerpona were promising genotypes for further breeding programmes in rice. The maximum Euclidean distance was plotted between Thavallakanan and Talmugur (7.49, followed by Thavallakanan and Langalmura (6.82, indicating these combinations may be exploited as parental lines in hybridization programmes to develop salinity tolerant variety.

  11. Selection for wide adaptability and high phenotypic stability of Brazilian soybean genotypes.

    Science.gov (United States)

    Oliveira, V M; Hamawaki, O T; Nogueira, A O; Sousa, L B; Santos, F M; Hamawaki, R L

    2016-03-31

    Advances in genetic enhancement techniques have led to an increase in soybean production. Thus, soybean is currently one the most economically important cultured species worldwide. The objectives of the present study were to study the interaction of soybean genotypes per environment in terms of grain productivity and to evaluate their phenotypic adaptability and stability, with the final aim of selecting lineages with high productivity, wide adaptability, and high stability. Seven soybean genotypes, consisting of five lineages developed by the soybean genetic enhancement program of the Universidade Federal de Uberlândia (Brazil) and two controls, were evaluated during several annual cycles in seven different environments. A randomized complete block design (RCBD) with three replicates was adopted in each site. This study followed the methodology proposed by Eberhart and Russel and Lin and Binns, with modifications by Carneiro, and the AMMI (additive main effects and multiplicative interaction model) analysis. The average productivity of soybean cultivars in the trials was 2739.26 kg/ha. The L01V13 genotype and the UFUS Guarani cultivar had wide adaptation according to the methodology proposed by Eberhart and Russel and Lin and Binns, with modifications by Carneiro. When analyzed with the AMMI model, the UFUS Guarani cultivar showed high stability. In general, the methodologies studied are complementary and, when used together, increase the reliability of the classification, providing support for the use of specific soybean cultivars in different environments.

  12. Determination of yield related traits of sesame genotypes selected from world collection and mutant material

    International Nuclear Information System (INIS)

    Silme, R. S.; Cagirgan, M. I.

    2009-01-01

    Sesame (Sesamum indicum L.) is an important plant of Turkey that secondary gen center and very used of food industry's a lot of area. Mutation breeding of sesame research continued coordinately with IAEA since 1993. it is aimed in these breeding programmes to improve lines that have dehiscent capsule, determinate growth and resistance to wilting traits. This study was conducted in Antalya City, at Akdeniz University Agricultural Faculty experiment fields under second crop conditions in 2007. At this study, 19 genotypes selected from world sesame collection, 4 mutant genotypes and 2 local cultivars were sown. The experiments were conducted according to Complete Randomized Block Design with three replications. It was found that first flowering date varied between 35 to 45 days, 50% flowering date from 39 to 54 days, last flowering date from 63 to 88 days, first capsule date from 42 to 51 days, first capsule height from 44 to 116 cm, plant height from 102 to 177 cm, number of branch per plant from 0.1 to 2.7, number of pod per plant from 28 to 63, number of seeds in capsule 2.3-4.3 g, 1000 seed weight ranged from 2.3 to 4.3 g, seed yield per da from 18 to 77 kg. The highest yield per da (77 kg/da) was obtained from mutant genotype, wt-5.

  13. Mutans streptococci enumeration and genotype selection using different bacitracin-containing media.

    Science.gov (United States)

    Momeni, Stephanie S; Patrick, Paul; Wiener, Howard W; Cutter, Gary R; Ruby, John D; Cheon, Kyounga; Whiddon, Jennifer; Moser, Stephen A; Childers, Noel K

    2014-08-01

    The primary etiological agents associated with dental caries include the mutans streptococci (MS) comprised of Streptococcus mutans and Streptococcus sobrinus. The effective cultivation and isolation of MS are necessary for the study of MS, including their proper clinical assessment in the epidemiological study of dental caries. Several selective media have been developed for the isolation, enumeration, and characterization of MS. However, inhibition of MS may occur, reducing counts and perhaps limiting selection of some strains. The purpose of this study was to compare five culture media containing bacitracin recommended for the isolation of MS. Five commonly used bacitracin-containing media (MSB, MSKB, GTSB, TYS20B, and TYCSB) used for MS isolation were quantitatively evaluated. Standard plate counts were performed in duplicate for 2 prototype MS strains (S. mutans UA159 and S. sobrinus 6715) and for MS isolates from clinical saliva samples obtained from 16 children (approximate age 5years) to determine total plate counts, and total S. mutans counts. Selected isolates (n=249) from all five media for 5 saliva samples were further confirmed as S. mutans with real-time PCR then subsequently evaluated qualitatively with rep-PCR for genotype determination. All media resulted in variable enumeration with no significant difference in MS counts. MS prototype strains grew well on all five media; clinical isolates demonstrated more variability in counts but no overall significant differences were found. MSB demonstrated comparable ability to grow S. mutans but allowed for more non-S. mutans growth. All 5 media identified a consistent predominant genotype by rep-PCR. Recovery of minor genotypes was not inhibited by media type. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Adapted J6/JFH1-based Hepatitis C virus recombinants with genotype-specific NS4A show similar efficacies against lead protease inhibitors, alpha interferon, and a putative NS4A inhibitor

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Jensen, Sanne B; Serre, Stéphanie B N

    2013-01-01

    (HK6a), and 7a (QC69), with peak infectivity titers of ∼3.5 to 4.5 log10 focus-forming units per ml. Except for genotype 2a (J6), growth depended on adaptive mutations identified in long-term culture. Genotype 1a, 1b, and 4a recombinants were adapted by amino acid substitutions F772S (p7) and V1663A...

  15. Effective selection criteria for screening drought tolerant recombinant inbred lines of sunflower

    Directory of Open Access Journals (Sweden)

    Abdi Nishtman

    2013-01-01

    Full Text Available In this study, seventy two sunflower recombinant inbred lines were tested for their yielding ability under both water-stressed and well-watered states. The inbred lines were evaluated in a rectangular 8´9 lattice design with two replications in both well-watered and water-stressed conditions, separately. Eight drought tolerance indices including stability tolerance index (STI, mean productivity (MP, geometric mean productivity (GMP, harmonic mean (HM, stress susceptibility index (SSI, tolerance index (TOL, yield index (YI and yield stability index (YSI were calculated based on grain yield for every genotype. Results showed the highest values of mean productivity (MP index, geometric mean productivity (GMP, yield index (YI, harmonic mean (HM and stress tolerance index (STI indices for ‘C134a’ inbred line and least values of stress susceptibility index (SSI and tolerance (TOL for C61 inbred line. According to correlation of indices with yield performance under both drought stress and non-stress states and principle component analysis, indices including HM, MP, GMP and STI could properly distinguish drought tolerant sunflower inbred lines with high yield performance under both states. Cluster analysis of inbred lines using Ys, Yp and eight indices, categorized them into four groups including 19, 6, 26 and 19 inbred lines.

  16. The evolution of obligate sex: the roles of sexual selection and recombination

    Science.gov (United States)

    Kleiman, Maya; Hadany, Lilach

    2015-01-01

    The evolution of sex is one of the greatest mysteries in evolutionary biology. An even greater mystery is the evolution of obligate sex, particularly when competing with facultative sex and not with complete asexuality. Here, we develop a stochastic simulation of an obligate allele invading a facultative population, where males are subject to sexual selection. We identify a range of parameters where sexual selection can contribute to the evolution of obligate sex: Especially when the cost of sex is low, mutation rate is high, and the facultative individuals do not reproduce sexually very often. The advantage of obligate sex becomes larger in the absence of recombination. Surprisingly, obligate sex can take over even when the population has a lower mean fitness as a result. We show that this is due to the high success of obligate males that can compensate the cost of sex. PMID:26257871

  17. Selection, Recombination and History in a Parasitic Flatworm (Echinococcus Inferred from Nucleotide Sequences

    Directory of Open Access Journals (Sweden)

    KL Haag

    1998-09-01

    Full Text Available Three species of flatworms from the genus Echinococcus (E. granulosus, E. multilocularis and E. vogeli and four strains of E. granulosus (cattle, horse, pig and sheep strains were analysed by the PCR-SSCP method followed by sequencing, using as targets two non-coding and two coding (one nuclear and one mitochondrial genomic regions. The sequencing data was used to evaluate hypothesis about the parasite breeding system and the causes of genetic diversification. The calculated recombination parameters suggested that cross-fertilisation was rare in the history of the group. However, the relative rates of substitution in the coding sequences showed that positive selection (instead of purifying selection drove the evolution of an elastase and neutrophil chemotaxis inhibitor gene (AgB/1. The phylogenetic analyses revealed several ambiguities, indicating that the taxonomic status of the E. granulosus horse strain should be revised

  18. Strategy for selection of soybean genotypes tolerant to drought during germination.

    Science.gov (United States)

    Dantas, S A G; Silva, F C S; Silva, L J; Silva, F L

    2017-05-10

    Water deficit is the main reason for instability in the context of soybean culture. The development of strategies for the selection of more tolerant genotypes is necessary. These strategies include the use of polyethylene glycol 6000 solutions (PEG-6000) for conducting the germination test under conditions of water restriction. Thus, the objective of this study was to determine the osmotic potential and the main characteristics that promote the discrimination of soybean genotypes with regard to water stress tolerance during germination and the vigor test. Thirteen soybean cultivars were used. The seeds were allowed to germinate on sheets of germitest paper moistened in solution with PEG-6000, simulating different levels of water availability, which is expressed as osmotic potential (0.0, -0.2, -0.4, and -0.6 MPa). We assessed germination, length, and dry mass for seedlings and seeds, as well as reserve dynamics. Germination and variables related to the dynamics of reservation have great influence on the expression of variability in environments under stress. Among the different osmotic potentials, the -0.2 MPa was the most efficient for the expression of genetic variability among the cultivars. Conducting the germination test with PEG-6000 solution to -0.2 MPa was efficient for selecting soybean cultivars tolerant to water stress. This was accomplished by evaluating the percentage of germination, along with variables related to the dynamics of reservation.

  19. Estimates of repeatability coefficients and the number of the optimum measure to select superior genotypes in Annona muricata L.

    Science.gov (United States)

    Sanchéz, C F B; Alves, R S; Garcia, A D P; Teodoro, P E; Peixoto, L A; Silva, L A; Bhering, L L; Resende, M D V

    2017-09-21

    The aim of this study was to evaluate repeated measures over the years to estimate repeatability coefficient and the number of the optimum measure to select superior genotypes in Annona muricata L. The fruit production was evaluated over 16 years in 71 genotypes without an experimental design. The estimation of variance components and the prediction of the permanent phenotypic value were performed using REML/BLUP proceedings. The coefficient of determination, accuracy, and selective efficiency increased when measures increased. The coefficient of determination of 80% was reached beyond 8 crop seasons with high accuracy and selective efficiency. Thus, the evaluation of 8 crop seasons can be suitable to select superior genotypes in the A. muricata L. breeding program. Predicted selection gain had a high magnitude for fruit production indicating that it is possible to take a progressive genetic advance for this trait over cycle breeding.

  20. ALIS-FLP: Amplified ligation selected fragment-length polymorphism method for microbial genotyping

    DEFF Research Database (Denmark)

    Brillowska-Dabrowska, A.; Wianecka, M.; Dabrowski, Slawomir

    2008-01-01

    A DNA fingerprinting method known as ALIS-FLP (amplified ligation selected fragment-length polymorphism) has been developed for selective and specific amplification of restriction fragments from TspRI restriction endonuclease digested genomic DNA. The method is similar to AFLP, but differs......RI genomic DNA fragment, and a short, degenerated, oligonucleotide covering the remaining TspRI cohesive ends. Other cohesive ends are covered by a short degenerated oligonucleotide lacking the primer site. The ligation mixture is used as a template for amplification using a single primer corresponding...... for differentiation of the organisms without previous knowledge of their DNA sequence. The usefulness of the method is confirmed by genotyping of 70 previously characterized clinical E. coli isolates. The grouping obtained was identical to the results of REA-PFGE. Versatility of the method is highlighted, i.e. its...

  1. Predicting the impact of selection for scrapie resistance on PRNP genotype frequencies in goats.

    Science.gov (United States)

    Sacchi, Paola; Rasero, Roberto; Ru, Giuseppe; Aiassa, Eleonora; Colussi, Silvia; Ingravalle, Francesco; Peletto, Simone; Perrotta, Maria Gabriella; Sartore, Stefano; Soglia, Dominga; Acutis, Pierluigi

    2018-03-06

    The European Union has implemented breeding programmes to increase scrapie resistance in sheep. A similar approach can be applied also in goats since the K222 allele provides a level of resistance equivalent to that of ARR in sheep. The European Food Safety Authority stated that breeding for resistance could be offered as an option for Member States to control classical scrapie in goats. We assessed the impact of different breeding strategies on PRNP genotype frequencies using a mathematical model that describes in detail the evolution of K222 in two goat breeds, Chamois Coloured and Saanen. Different patterns of age structure and replacement rate were modelled as factors affecting response to selection. Breeding for scrapie resistance can be implemented in goats, even though the initial K222 frequencies in these breeds are not particularly favourable and the rate at which the resistant animals increase, both breeding and slaughtered for meat production, is slow. If the goal is not to achieve the fixation of resistance allele, it is advisable to carry out selection only until a desired frequency of K222-carriers has been attained. Nucleus selection vs. selection on the overall populations is less expensive but takes longer to reach the desired output. The programme performed on the two goat breeds serves as a model of the response the selection could have in other breeds that show different initial frequencies and population structure. In this respect, the model has a general applicability.

  2. Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution

    Directory of Open Access Journals (Sweden)

    Monjane Adérito L

    2011-12-01

    Full Text Available Abstract Background Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae, the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA. Results Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots

  3. Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution.

    Science.gov (United States)

    Monjane, Adérito L; van der Walt, Eric; Varsani, Arvind; Rybicki, Edward P; Martin, Darren P

    2011-12-02

    Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA. Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots - of the breakpoints required to re-create MSV

  4. Physiological characterisation of recombinant Aspergillus nidulans strains with different creA genotypes expressing A-oryzae alpha-amylase

    DEFF Research Database (Denmark)

    Agger, Teit; Petersen, J.B.; O'Connor, S.M.

    2002-01-01

    The physiology of three strains of Aspergillus nidulans was examined-a creA deletion strain, a wild type creA genotype and a strain containing extra copies of the creA gene, all producing Aspergillus oryzae alpha-amylase. The strains were cultured in batch and continuous cultivations and the biom......The physiology of three strains of Aspergillus nidulans was examined-a creA deletion strain, a wild type creA genotype and a strain containing extra copies of the creA gene, all producing Aspergillus oryzae alpha-amylase. The strains were cultured in batch and continuous cultivations...... and the biomass formation and alpha-amylase production was characterised. Overexpression of the creA gene resulted in a lower maximum specific growth rate and a slightly higher repression of the alpha-amylase production during conditions with high glucose concentration. No expression of creA also resulted...... in a decreased maximum specific growth rate, but also in drastic changes in morphology. Furthermore, the expression of alpha-amylase was completely derepressed and creA thus seems to be the only regulatory protein responsible for glucose repression of alpha-amylase expression. The effect of different carbon...

  5. Culturing selects for specific genotypes of Borrelia burgdorferi in an enzootic cycle in Colorado.

    Science.gov (United States)

    Norris, D E; Johnson, B J; Piesman, J; Maupin, G O; Clark, J L; Black, W C

    1997-01-01

    In Colorado, Borrelia burgdorferi sensu stricto, the etiologic agent of Lyme disease, is maintained in an enzootic cycle between Ixodes spinipalpis ticks and Neotoma mexicana rats (27). The frequencies of flagellin (fla), 66-kDa protein (p66), and outer surface protein A (ospA) alleles were examined in 71 B. burgdorferi isolates from samples from Colorado. Approximately two-thirds of these samples were isolates from I. spinipalpis ticks that had been cultured in BSK-H medium prior to DNA extraction. The remaining samples were from total DNA extracted directly from infected I. spinipalpis ticks. A portion of each gene was amplified by PCR and screened for genetic variability by single-strand conformation polymorphism (SSCP) analysis. We identified three alleles in the fla gene, seven in the p66 gene, and seven in the ospA gene. Sequencing verified that the amplified products originated from B. burgdorferi template DNA and indicated 100% sensitivity and specificity of the SSCP analysis. The frequencies of the p66 and ospA alleles were significantly different between cultured and uncultured spirochetes. The number of three-locus genotypes and the genetic diversity of alleles at all loci were consistently lower in cultured spirochetes, suggesting that culturing of B. burgdorferi in BSK-H medium may select for specific genotypes. PMID:9276416

  6. Antagonistic experimental coevolution with a parasite increases host recombination frequency

    Directory of Open Access Journals (Sweden)

    Kerstes Niels AG

    2012-02-01

    Full Text Available Abstract Background One of the big remaining challenges in evolutionary biology is to understand the evolution and maintenance of meiotic recombination. As recombination breaks down successful genotypes, it should be selected for only under very limited conditions. Yet, recombination is very common and phylogenetically widespread. The Red Queen Hypothesis is one of the most prominent hypotheses for the adaptive value of recombination and sexual reproduction. The Red Queen Hypothesis predicts an advantage of recombination for hosts that are coevolving with their parasites. We tested predictions of the hypothesis with experimental coevolution using the red flour beetle, Tribolium castaneum, and its microsporidian parasite, Nosema whitei. Results By measuring recombination directly in the individuals under selection, we found that recombination in the host population was increased after 11 generations of coevolution. Detailed insights into genotypic and phenotypic changes occurring during the coevolution experiment furthermore helped us to reconstruct the coevolutionary dynamics that were associated with this increase in recombination frequency. As coevolved lines maintained higher genetic diversity than control lines, and because there was no evidence for heterozygote advantage or for a plastic response of recombination to infection, the observed increase in recombination most likely represented an adaptive host response under Red Queen dynamics. Conclusions This study provides direct, experimental evidence for an increase in recombination frequency under host-parasite coevolution in an obligatory outcrossing species. Combined with earlier results, the Red Queen process is the most likely explanation for this observation.

  7. Whole-cell biotransformation with recombinant cytochrome P450 for the selective oxidation of Grundmann's ketone.

    Science.gov (United States)

    Hernández-Martín, Alba; von Bühler, Clemens J; Tieves, Florian; Fernández, Susana; Ferrero, Miguel; Urlacher, Vlada B

    2014-10-15

    25-Hydroxy-Grundmann's ketone is a key building block in the chemical synthesis of vitamin D3 and its derivatives through convergent routes. Generally, the chemical synthesis of this compound involves tedious procedures and results in a mixture of several products. Recently, the selective hydroxylation of Grundmann's ketone at position C25 by cytochrome P450 (CYP) 154E1 from Thermobifida fusca YX was described. In this study a recombinant whole-cell biocatalyst was developed and applied for hydroxylation of Grundmann's ketone. Biotransformation was performed by Escherichia coli cells expressing CYP154E1 along with two redox partner systems, Pdx/PdR and YkuN/FdR. The system comprising CYP154E1/Pdx/PdR showed the highest production of 25-hydroxy-Grundmann's ketone and resulted in 1.1mM (300mgL(-1)) product concentration. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Use of FabV-Triclosan Plasmid Selection System for Efficient Expression and Production of Recombinant Proteins in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Syed A Ali

    Full Text Available Maintenance of recombinant plasmid vectors in host bacteria relies on the presence of selection antibiotics in the growth media to suppress plasmid -free segregants. However, presence of antibiotic resistance genes and antibiotics themselves is not acceptable in several applications of biotechnology. Previously, we have shown that FabV-Triclosan selection system can be used to select high and medium copy number plasmid vectors in E. coli. Here, we have extended our previous work and demonstrated that expression vectors containing FabV can be used efficiently to express heterologous recombinant proteins in similar or better amounts in E. coli host when compared with expression vectors containing β-lactamase. Use of small amount of non-antibiotic Triclosan as selection agent in growth medium, enhanced plasmid stability, applicability in various culture media, and compatibility with other selection systems for multiple plasmid maintenance are noteworthy features of FabV-Triclosan selection system.

  9. Use of FabV-Triclosan Plasmid Selection System for Efficient Expression and Production of Recombinant Proteins in Escherichia coli

    Science.gov (United States)

    Ali, Syed A.; Chew, Yik Wei; Omar, Tasyriq Che; Azman, Nizuwan

    2015-01-01

    Maintenance of recombinant plasmid vectors in host bacteria relies on the presence of selection antibiotics in the growth media to suppress plasmid -free segregants. However, presence of antibiotic resistance genes and antibiotics themselves is not acceptable in several applications of biotechnology. Previously, we have shown that FabV-Triclosan selection system can be used to select high and medium copy number plasmid vectors in E. coli. Here, we have extended our previous work and demonstrated that expression vectors containing FabV can be used efficiently to express heterologous recombinant proteins in similar or better amounts in E. coli host when compared with expression vectors containing β-lactamase. Use of small amount of non-antibiotic Triclosan as selection agent in growth medium, enhanced plasmid stability, applicability in various culture media, and compatibility with other selection systems for multiple plasmid maintenance are noteworthy features of FabV-Triclosan selection system. PMID:26642325

  10. SNP calling using genotype model selection on high-throughput sequencing data

    KAUST Repository

    You, Na

    2012-01-16

    Motivation: A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base-calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for.Results: A novel method of consensus and SNP calling, Genotype Model Selection (GeMS), is given which accounts for the errors that occur during the preparation of the genomic sample. Simulations and real data analyses indicate that GeMS has the best performance balance of sensitivity and positive predictive value among the tested SNP callers. © The Author 2012. Published by Oxford University Press. All rights reserved.

  11. Target-selective homologous recombination cloning for high-throughput generation of monoclonal antibodies from single plasma cells.

    Science.gov (United States)

    Kurosawa, Nobuyuki; Yoshioka, Megumi; Isobe, Masaharu

    2011-04-13

    Molecular cloning of functional immunoglobulin genes from single plasma cells is one of the most promising technologies for the rapid development of monoclonal antibody drugs. However, the proper insertion of PCR-amplified immunoglobulin genes into expression vectors remains an obstacle to the high-throughput production of recombinant monoclonal antibodies. We developed a single-step cloning method, target-selective homologous recombination (TS-HR), in which PCR-amplified immunoglobulin variable genes were selectively inserted into vectors, even in the presence of nonspecifically amplified DNA. TS-HR utilizes Red/ET-mediated homologous recombination with a target-selective vector (TS-vector) with unique homology arms on its termini. Using TS-HR, immunoglobulin variable genes were cloned directly into expression vectors by co-transforming unpurified PCR products and the TS-vector into E. coli. Furthermore, the high cloning specificity of TS-HR allowed plasmids to be extracted from pools of transformed bacteria without screening single colonies for correct clones. We present a one-week protocol for the production of recombinant mouse monoclonal antibodies from large numbers of single plasma cells. The time requirements and limitations of traditional cloning procedures for the production of recombinant immunoglobulins have been significantly reduced with the development of the TS-HR cloning technique. © 2011 Kurosawa et al; licensee BioMed Central Ltd.

  12. Target-selective homologous recombination cloning for high-throughput generation of monoclonal antibodies from single plasma cells

    Directory of Open Access Journals (Sweden)

    Isobe Masaharu

    2011-04-01

    Full Text Available Abstract Background Molecular cloning of functional immunoglobulin genes from single plasma cells is one of the most promising technologies for the rapid development of monoclonal antibody drugs. However, the proper insertion of PCR-amplified immunoglobulin genes into expression vectors remains an obstacle to the high-throughput production of recombinant monoclonal antibodies. Results We developed a single-step cloning method, target-selective homologous recombination (TS-HR, in which PCR-amplified immunoglobulin variable genes were selectively inserted into vectors, even in the presence of nonspecifically amplified DNA. TS-HR utilizes Red/ET-mediated homologous recombination with a target-selective vector (TS-vector with unique homology arms on its termini. Using TS-HR, immunoglobulin variable genes were cloned directly into expression vectors by co-transforming unpurified PCR products and the TS-vector into E. coli. Furthermore, the high cloning specificity of TS-HR allowed plasmids to be extracted from pools of transformed bacteria without screening single colonies for correct clones. We present a one-week protocol for the production of recombinant mouse monoclonal antibodies from large numbers of single plasma cells. Conclusion The time requirements and limitations of traditional cloning procedures for the production of recombinant immunoglobulins have been significantly reduced with the development of the TS-HR cloning technique.

  13. A recombinant fusion toxin based on enzymatic inactive C3bot1 selectively targets macrophages.

    Directory of Open Access Journals (Sweden)

    Lydia Dmochewitz

    Full Text Available BACKGROUND: The C3bot1 protein (~23 kDa from Clostridium botulinum ADP-ribosylates and thereby inactivates Rho. C3bot1 is selectively taken up into the cytosol of monocytes/macrophages but not of other cell types such as epithelial cells or fibroblasts. Most likely, the internalization occurs by a specific endocytotic pathway via acidified endosomes. METHODOLOGY/PRINCIPAL FINDINGS: Here, we tested whether enzymatic inactive C3bot1E174Q serves as a macrophage-selective transport system for delivery of enzymatic active proteins into the cytosol of such cells. Having confirmed that C3bot1E174Q does not induce macrophage activation, we used the actin ADP-ribosylating C2I (∼50 kDa from Clostridium botulinum as a reporter enzyme for C3bot1E174Q-mediated delivery into macrophages. The recombinant C3bot1E174Q-C2I fusion toxin was cloned and expressed as GST-protein in Escherichia coli. Purified C3bot1E174Q-C2I was recognized by antibodies against C2I and C3bot and showed C2I-specific enzyme activity in vitro. When applied to cultured cells C3bot1E174Q-C2I ADP-ribosylated actin in the cytosol of macrophages including J774A.1 and RAW264.7 cell lines as well as primary cultured human macrophages but not of epithelial cells. Together with confocal fluorescence microscopy experiments, the biochemical data indicate the selective uptake of a recombinant C3-fusion toxin into the cytosol of macrophages. CONCLUSIONS/SIGNIFICANCE: In summary, we demonstrated that C3bot1E174Q can be used as a delivery system for fast, selective and specific transport of enzymes into the cytosol of living macrophages. Therefore, C3-based fusion toxins can represent valuable molecular tools in experimental macrophage pharmacology and cell biology as well as attractive candidates to develop new therapeutic approaches against macrophage-associated diseases.

  14. Effect of participatory selection of varieties on the identification of outstanding common bean genotypes (Phaseolus vulgaris L.

    Directory of Open Access Journals (Sweden)

    Alexis Lamz Piedra

    2017-10-01

    Full Text Available Among the main factors affecting bean production is poor distribution of varieties for different environmental conditions in which its are grown. The aim of this work was to evaluate the impact of participatory selection of foreign genetic materials and national commercial and pre-commercial common bean in identifying genotypes for their outstanding performance and resistance to common bacteriosis (Xanthomonas campestris pv. phaseoli (Smith Dye (Xcp. In the "El Mulato" farm belonging to the Empowered Cooperative of Credit and Services (CCSF "Orlando Cuellar" in the municipality San José de las Lajas, Mayabeque, two experiments were conducted. In the first one, 15 genotypes were planted in 13 September 2014 (early season in experimental plots to develop a diversity Fair and evaluate the natural incidence of common bean bacteriosis. In the second experiment, they were sown on 25 December (late season the materials selected by farmers with superior agronomic performance (7 genotypes to validate the stability of its performance. Among the results, an effective range of 93,33 % between the selected materials and selective criteria that this diversity was identified were high performance, resistance to common bacteriosis and color of beans. It was found that the selection of the diversity of beans by farmers is not influenced by the origin of materials and participatory selection identified common bean genotypes with high yield potential and stability between planting seasons.

  15. Fatty Acid Content and Some Chemical Properties of Selected Almond (Prunus amygdalus Batsch.) Genotypes in Isparta Province

    OpenAIRE

    YILDIRIM, Adnan N.; KOYUNCU, Fatma; TEKİNTAŞ, Ekmel; AKINCI-YILDIRIM, Fatma

    2008-01-01

    This study was carried out to determine some chemical properties and fatty acid content of selected almond (Prunus amygdalus Batsch.) genotypes in Isparta province. In the study, total oil content, protein content, ash content, humidity, palmitic acid content, palmitoleic acid content, stearic acid content, oleic acid content, and linoleic acid content of the selected genotypes were ranged from 44.25 (ISP 298) to 54.68 % (ISP 66), 21.23 (ISP 66) to 35.2%, 7 (ISP 298) 2.75 (ISP 66) to 3.81% (I...

  16. Selection and characterization of a promoter for expression of single-copy recombinant genes in Gram-positive bacteria

    Directory of Open Access Journals (Sweden)

    Manganelli Riccardo

    2005-01-01

    Full Text Available Abstract Background In the past ten years there has been a growing interest in engineering Gram-positive bacteria for biotechnological applications, including vaccine delivery and production of recombinant proteins. Usually, bacteria are manipulated using plasmid expression vectors. The major limitation of this approach is due to the fact that recombinant plasmids are often lost from the bacterial culture upon removal of antibiotic selection. We have developed a genetic system based on suicide vectors on conjugative transposons allowing stable integration of recombinant DNA into the chromosome of transformable and non-transformable Gram-positive bacteria. Results The aim of this work was to select a strong chromosomal promoter from Streptococcus gordonii to improve this genetic system making it suitable for expression of single-copy recombinant genes. To achieve this task, a promoterless gene encoding a chloramphenicol acetyltransferase (cat, was randomly integrated into the S. gordonii chromosome and transformants were selected for chloramphenicol resistance. Three out of eighteen chloramphenicol resistant transformants selected exhibited 100% stability of the phenotype and only one of them, GP215, carried the cat gene integrated as a single copy. A DNA fragment of 600 base pairs exhibiting promoter activity was isolated from GP215 and sequenced. The 5' end of its corresponding mRNA was determined by primer extention analysis and the putative -10 and a -35 regions were identified. To study the possibility of using this promoter (PP for single copy heterologous gene expression, we created transcriptional fusions of PP with genes encoding surface recombinant proteins in a vector capable of integrating into the conjugative transposon Tn916. Surface recombinant proteins whose expression was controlled by the PP promoter were detected in Tn916-containing strains of S. gordonii and Bacillus subtilis after single copy chromosomal integration of the

  17. Early selection for growth vigor in rubber tree genotypes in northwestern São Paulo State (Brazil

    Directory of Open Access Journals (Sweden)

    Gonçalves Paulo de Souza

    1998-01-01

    Full Text Available Forty-five genotypes (clones of rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss. Müell. Arg.] of different origins were assessed for efficiency of early selection at the Votuporanga Experimental Station in northwestern São Paulo State, Brazil, using a randomized complete block design with three replications and six plants per plot. Girth at 120 cm above the highest point of the grafting union of each tree was taken at ages 12, 24, 36, 48, 60, 72, 84 and 96 months. Highly significant differences in girth were detected among the genotypes at all ages evaluated, except for 12 months. Estimates of genetic variance for two age sets showed a substantial increase with age, while the genotype variation decreased. Selection made at 24 months proved to be the most efficient, giving a superior gain per unit of time.

  18. Neutralizing antibodies induced by recombinant virus-like particles of enterovirus 71 genotype C4 inhibit infection at pre- and post-attachment steps.

    Directory of Open Access Journals (Sweden)

    Zhiqiang Ku

    Full Text Available BACKGROUND: Enterovirus 71 (EV71 is a major causative agent of hand, foot and mouth disease, which has been prevalent in Asia-Pacific regions, causing significant morbidity and mortality in young children. Antibodies elicited by experimental EV71 vaccines could neutralize infection in vitro and passively protect animal models from lethal challenge, indicating that neutralizing antibodies play an essential role in protection. However, how neutralizing antibodies inhibit infection in vitro remains unclear. METHODS/FINDINGS: In the present study, we explored the mechanisms of neutralization by antibodies against EV71 virus-like particles (VLPs. Recombinant VLPs of EV71 genotype C4 were produced in insect cells using baculovirus vectors. Immunization with the VLPs elicited a high-titer, EV71-specific antibody response in mice. Anti-VLP mouse sera potently neutralized EV71 infection in vitro. The neutralizing antibodies in the anti-VLP mouse sera were found to target mainly an extremely conserved epitope (FGEHKQEKDLEYGAC located at the GH loop of the VP1 protein. The neutralizing anti-VLP antisera were able to inhibit virus binding to target cells efficiently. In addition, post-attachment treatment of virus-bound cells with the anti-VLP antisera also neutralized virus infection, although the antibody concentration required was higher than that of the pre-attachment treatment. CONCLUSIONS: Collectively, our findings represent a valuable addition to the understanding of mechanisms of EV71 neutralization and have strong implications for EV71 vaccine development.

  19. Effect of enlarging the reference population with (un)genotyped animals on the accuracy of genomic selection in dairy cattle

    NARCIS (Netherlands)

    Pszczola, M.J.; Mulder, H.A.; Calus, M.P.L.

    2011-01-01

    Genomic selection (GS) permits accurate breeding values to be obtained for young animals, shortening the generation interval and accelerating the genetic gain, thereby leading to reduced costs for proven bulls. Genotyping a large number of animals using high-density single nucleotide polymorphism

  20. Selection and Clonal Propagation of High Artemisinin Genotypes of Artemisia annua

    Directory of Open Access Journals (Sweden)

    Hazel Y. Wetzstein

    2018-03-01

    Full Text Available Artemisinin, produced in the glandular trichomes of Artemisia annua L. is a vital antimalarial drug effective against Plasmodium falciparum resistant to quinine-derived medicines. Although work has progressed on the semi-synthetic production of artemisinin, field production of A. annua remains the principal commercial source of the compound. Crop production of artemisia must be increased to meet the growing worldwide demand for artemisinin combination therapies (ACTs to treat malaria. Grower artemisinin yields rely on plants generated from seeds from open-pollinated parents. Although selection has considerably increased plant artemisinin concentration in the past 15 years, seed-generated plants have highly variable artemisinin content that lowers artemisinin yield per hectare. Breeding efforts to produce improved F1 hybrids have been hampered by the inability to produce inbred lines due to self-incompatibility. An approach combining conventional hybridization and selection with clonal propagation of superior genotypes is proposed as a means to enhance crop yield and artemisinin production. Typical seed-propagated artemisia plants produce less than 1% (dry weight artemisinin with yields below 25 kg/ha. Genotypes were identified producing high artemisinin levels of over 2% and possessing improved agronomic characteristics such as high leaf area and shoot biomass production. Field studies of clonally-propagated high-artemisinin plants verified enhanced plant uniformity and an estimated gross primary productivity of up to 70 kg/ha artemisinin, with a crop density of one plant m-2. Tissue culture and cutting protocols for the mass clonal propagation of A. annua were developed for shoot regeneration, rooting, acclimatization, and field cultivation. Proof of concept studies showed that both tissue culture-regenerated plants and rooted cutting performed better than plants derived from seed in terms of uniformity, yield, and consistently high artemisinin

  1. Activation and Stabilization of Olive Recombinant 13-Hydroperoxide Lyase Using Selected Additives.

    Science.gov (United States)

    Jacopini, Sabrina; Vincenti, Sophie; Mariani, Magali; Brunini-Bronzini de Caraffa, Virginie; Gambotti, Claude; Desjobert, Jean-Marie; Muselli, Alain; Costa, Jean; Tomi, Félix; Berti, Liliane; Maury, Jacques

    2017-07-01

    The stabilization of olive recombinant hydroperoxide lyases (rHPLs) was investigated using selected chemical additives. Two rHPLs were studied: HPL full-length and HPL with its chloroplast transit peptide deleted (matured HPL). Both olive rHPLs are relatively stable at 4 °C, and enzyme activity can be preserved (about 100% of the rHPL activities are maintained) during 5 weeks of storage at -20 or at -80 °C in the presence of glycerol (10%, v/v). Among the additives used in this study, glycine (2.5% w/v), NaCl (0.5 M), and Na 2 SO 4 (0.25 M) provided the highest activation of HPL full-length activity, while the best matured HPL activity was obtained with Na 2 SO 4 (0.25 M) and NaCl (1 M). Although the inactivation rate constants (k) showed that these additives inactivate both rHPLs, their use is still relevant as they strongly increase HPL activity. Results of C6-aldehyde production assays also showed that glycine, NaCl, and Na 2 SO 4 are appropriate additives and that NaCl appears to be the best additive, at least for hexanal production.

  2. Selection of new clones of linalool chemotype from genetic recombination in Lippia alba

    Directory of Open Access Journals (Sweden)

    Elcio Rodrigo Rufino

    2012-01-01

    Full Text Available The aromatic and medicinal species Lippia alba is vigorous and rugged native to the South America (Atlantic Rainforest. Because it is an allogamous and self-incompatible species, natural populations have high morphological and chemical variability. This work had as objective to conduct a preliminary screening to identify new promising clones from a novel (recombinant base population of Lippia alba with regard to its agronomic and phytochemical traits, using the linalool oil or chemotype as model. The two superior linalool clones, obtained by collection, were used as controls. Traits evaluated included: dry mass of leaves (DML, oil yield percentage (EOY%, oil production per plant (OP, and linalool percentage (LN%. Forty linalool chemotype clones were evaluated in three experiments, in a random block design with four replicates and four cuttings (clones per plot. Besides means comparisons, multivariate analysis was used in order to aid in the preliminary selection of clones. There were positive correlations from moderate to strong for DML vs. EOY%, OP vs. EOY% and DML vs. OP. Linalool clones superior or similar to both controls were identified for the DML, EOY%, OP, and LN% traits (univariate analyses, aimed at further validating experimentation. Five distinct groups were defined in the cluster analysis (UPGMA, each containing subgroups as well.

  3. First report of in vitro selection of RNA aptamers targeted to recombinant Loxosceles laeta spider toxins.

    Science.gov (United States)

    Sapag, Amalia; Salinas-Luypaert, Catalina; Constenla-Muñoz, Carlos

    2014-03-26

    Loxoscelism is the envenomation caused by the bite of Loxosceles spp. spiders. It entails severe necrotizing skin lesions, sometimes accompanied by systemic reactions and even death. There are no diagnostic means and treatment is mostly palliative. The main toxin, found in several isoforms in the venom, is sphingomyelinase D (SMD), a phospholipase that has been used to generate antibodies intended for medical applications. Nucleic acid aptamers are a promising alternative to antibodies. Aptamers may be isolated from a combinatorial mixture of oligonucleotides by iterative selection of those that bind to the target. In this work, two Loxosceles laeta SMD isoforms, Ll1 and Ll2, were produced in bacteria and used as targets with the aim of identifying RNA aptamers that inhibit sphingomyelinase activity. Six RNA aptamers capable of eliciting partial but statistically significant inhibitions of the sphingomyelinase activity of recombinant SMD-Ll1 and SMD-Ll2 were obtained: four aptamers exert ~17% inhibition of SMD-Ll1, while two aptamers result in ~25% inhibition of SMD-Ll2 and ~18% cross inhibition of SMD-Ll1. This work is the first attempt to obtain aptamers with therapeutic and diagnostic potential for loxoscelism and provides an initial platform to undertake the development of novel anti Loxosceles venom agents.

  4. First report of in vitro selection of RNA aptamers targeted to recombinant Loxosceles laeta spider toxins

    Directory of Open Access Journals (Sweden)

    Amalia Sapag

    2014-01-01

    Full Text Available BACKGROUND: Loxoscelism is the envenomation caused by the bite of Loxosceles spp. spiders. It entails severe necrotizing skin lesions, sometimes accompanied by systemic reactions and even death. There are no diagnostic means and treatment is mostly palliative. The main toxin, found in several isoforms in the venom, is sphingomyelinase D (SMD, a phospholipase that has been used to generate antibodies intended for medical applications. Nucleic acid aptamers are a promising alternative to antibodies. Aptamers may be isolated from a combinatorial mixture of oligonucleotides by iterative selection of those that bind to the target. In this work, two Loxosceles laeta SMD isoforms, Ll1 and Ll2, were produced in bacteria and used as targets with the aim of identifying RNA aptamers that inhibit sphingomyelinase activity. RESULTS: Six RNA aptamers capable of eliciting partial but statistically significant inhibitions of the sphingomyelinase activity of recombinant SMD-Ll1 and SMD-Ll2 were obtained: four aptamers exert ~17% inhibition of SMD-Ll1, while two aptamers result in ~25% inhibition of SMD-Ll2 and ~18% cross inhibition of SMD-Ll1. CONCLUSIONS: This work is the first attempt to obtain aptamers with therapeutic and diagnostic potential for loxoscelism and provides an initial platform to undertake the development of novel anti Loxoscelesvenom agents.

  5. Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes.

    Science.gov (United States)

    Price, Morgan N; Arkin, Adam P

    2015-12-15

    Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, "background selection" against slightly deleterious alleles should reduce the effective population size (Ne) by orders of magnitude. For example, for a well-mixed population with 10(12) individuals and a typical level of homologous recombination (r/m = 3, i.e., nucleotide changes due to recombination [r] occur at 3 times the mutation rate [m]), we predict that Ne is higher than diversity within a subpopulation, which makes it difficult to estimate Ne correctly. Given an estimate of Ne, standard population genetics models imply that selection should be sufficient to drive evolution if Ne × s is >1, where s is the selection coefficient. We found that this remains approximately correct if background selection is occurring or when population structure is present. Overall, we predict that even for free-living bacteria with enormous populations, natural selection is only a significant force if s is above 10(-7) or so. Because bacteria form huge populations with trillions of individuals, the simplest theoretical prediction is that the better allele at a site would predominate even if its advantage was just 10(-9) per generation. In other words, virtually every nucleotide would be at the local optimum in most individuals. A more sophisticated theory considers that bacterial genomes have millions of sites each and selection events on these many sites could interfere with each other, so that only larger effects would be important. However, bacteria can exchange genetic material, and in principle, this exchange could eliminate the interference between the evolution of the sites. We used simulations to confirm that during multisite evolution with realistic levels of recombination, only larger effects are important. We propose that advantages of less than 10(-7) are effectively neutral

  6. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

    OpenAIRE

    He, Jiangfeng; Zhao, Xiaoqing; Laroche, André; Lu, Zhen-Xiang; Liu, HongKui; Li, Ziqin

    2014-01-01

    Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broad...

  7. Selection of autochthonous sour cherry (Prunus cerasus L. genotypes in Feketić region

    Directory of Open Access Journals (Sweden)

    Radičević Sanja

    2012-01-01

    Full Text Available Autochthonous genotypes of fruit species are very important source of genetic variability and valuable material for breeding work. Fruit Research Institute-Čačak has a long tradition of studying autochthonous genotypes of temperate fruits sporadically spread and preserved in some localities in Serbia. Over 2005-2006, the following properties of nine autochthonous sour cherry genotypes grown in Feketic region were investigated: flowering and ripening time, pomological properties, biochemical composition of fruits and field resistance to causal agents of cherry diseases - cherry leaf spot (Blumeriella jaapii (Rehm. v. Arx., shot-hole (Clasterosporium carpophilum (Lév. Aderh. and brown rot (Monilinia laxa /Ader et Ruhl./ Honey ex Whetz.. The genotypes were tested for the presence of Prune dwarf virus and Prunus necrotic ring spot virus. In majority of genotypes fruits were large, with exceptional organoleptical properties, whereas ripening time was in the first ten or twenty days of June. The highest fruit weight was observed in F-1 genotype (8.1 g. The highest soluble solids and total sugars content were found in F- 4 genotype (17.60% and 14.25%, respectively. As for field resistance to causal agents of diseases and good pomo-technological properties, F-1, F-2, F-3, F-7 and F-8 genotypes were singled out. [Projekat Ministarstva nauke Republike Srbije, br. TR31064

  8. Intermittent hypoxia selects for genotypes and phenotypes that increase survival, invasion, and therapy resistance.

    Directory of Open Access Journals (Sweden)

    Daniel Verduzco

    Full Text Available Hypoxia in tumors correlates with greater risk of metastases, increased invasiveness, and resistance to systemic and radiation therapy. The evolutionary dynamics that links specific adaptations to hypoxia with these observed tumor properties have not been well investigated. While some tumor populations may experience fixed hypoxia, cyclical and stochastic transitions from normoxia to hypoxia are commonly observed in vivo. Although some phenotypic adaptations to this cyclic hypoxia are likely reversible, we hypothesize that some adaptations may become fixed through mutations promoted by hypoxia-induced genomic instability. Here we seek to identify genetic alterations and corresponding stable phenotypes that emerge following cyclic hypoxia. Although these changes may originate as adaptations to this specific environmental stress, their fixation in the tumor genome may result in their observation in tumors from regions of normoxia, a condition known as pseudohypoxia. We exposed several epithelial cell lines to 50 cycles of hypoxia-normoxia, followed by culture in normoxia over a period of several months. Molecular analyses demonstrated permanent changes in expression of several oncogenes and tumor-suppressors, including p53, E-cadherin, and Hif-1α. These changes were associated with increased resistance to multiple cytotoxins, increased survival in hypoxia and increased anchorage-independent growth. These results suggest cycles of hypoxia encountered in early cancers can select for specific and stable genotypic and phenotypic properties that persist even in normoxic conditions, which may promote tumor progression and resistance to therapy.

  9. Adaptability and Stability Study of Selected Sweet Sorghum Genotypes for Ethanol Production under Different Environments Using AMMI Analysis and GGE Biplots

    Directory of Open Access Journals (Sweden)

    Justice Kipkorir Rono

    2016-01-01

    Full Text Available The genotype and environment interaction influences the selection criteria of sorghum (Sorghum bicolor genotypes. Eight sweet sorghum genotypes were evaluated at five different locations in two growing seasons of 2014. The aim was to determine the interaction between genotype and environment on cane, juice, and ethanol yield and to identify best genotypes for bioethanol production in Kenya. The experiments were conducted in a randomized complete block design replicated three times. Sorghum canes were harvested at hard dough stage of grain development and passed through rollers to obtain juice that was then fermented to obtain ethanol. Cane, juice, and ethanol yield was analyzed using the additive main effect and multiplication interaction model (AMMI and genotype plus genotype by environment (GGE biplot. The combined analysis of variance of cane and juice yield of sorghum genotypes showed that sweet sorghum genotypes were significantly (P<0.05 affected by environments (E, genotypes (G and genotype by environment interaction (GEI. GGE biplot showed high yielding genotypes EUSS10, ACFC003/12, SS14, and EUSS11 for cane yield; EUSS10, EUSS11, and SS14 for juice yield; and EUSS10, SS04, SS14, and ACFC003/12 for ethanol yield. Genotype SS14 showed high general adaptability for cane, juice, and ethanol yield.

  10. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding.

    Science.gov (United States)

    He, Jiangfeng; Zhao, Xiaoqing; Laroche, André; Lu, Zhen-Xiang; Liu, HongKui; Li, Ziqin

    2014-01-01

    Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.

  11. Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes

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    Nathalie Kin

    2015-05-01

    Full Text Available Human coronavirus OC43 (HCoV-OC43 is one of five currently circulating human coronaviruses responsible for respiratory infections. Like all coronaviruses, it is characterized by its genome’s high plasticity. The objectives of the current study were to detect genetically distinct genotypes and eventually recombinant genotypes in samples collected in Lower Normandy between 2001 and 2013. To this end, we sequenced complete nsp12, S, and N genes of 15 molecular isolates of HCoV-OC43 from clinical samples and compared them to available data from the USA, Belgium, and Hong-Kong. A new cluster E was invariably detected from nsp12, S, and N data while the analysis of nsp12 and N genes revealed the existence of new F and G clusters respectively. The association of these different clusters of genes in our specimens led to the description of thirteen genetically distinct genotypes, among which eight recombinant viruses were discovered. Identification of these recombinant viruses, together with temporal analysis and tMRCA estimation, provides important information for understanding the dynamics of the evolution of these epidemic coronaviruses.

  12. Somatic homologous recombination in plants is promoted by a geminivirus in a tissue-selective manner.

    Science.gov (United States)

    Richter, K S; Kleinow, T; Jeske, H

    2014-03-01

    Four transgenic Arabidopsis thaliana lines carrying different reporter gene constructs based on split glucuronidase genes were used to monitor the frequency of somatic homologous recombination after geminivirus infections. Euphorbia mosaic virus and Cleome leaf crumple virus were chosen as examples, because they induce only mild symptoms and are expected to induce less general stress responses than other geminiviruses. After comparing the different plant lines and viruses as well as optimizing the infection procedure, Euphorbia mosaic virus enhanced recombination rates significantly in the transgenic reporter line 1445. The effect was tissue-specific in cells of the leaf veins as expected for this phloem-limited virus. The advantage for geminiviruses to activate a general recombination pathway is discussed with reference to an increased fitness by generating virus recombinants which have been observed frequently as an epidemiologic driving force. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

    Science.gov (United States)

    Wang, Jing; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

    2016-03-01

    A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. Copyright © 2016 by the Genetics Society of America.

  14. Selection of lettuce genotypes for phosphorus uptaking efficiency - DOI: 10.4025/actasciagron.v25i1.2348

    OpenAIRE

    Cock, Wallace Rudeck Sthel; UENF; Tardin, Flávio Dessaune; UENF; Amaral Júnior, Antônio Teixeira do; UENF; Scapim, Carlos Alberto; UEM; Amaral, José Francisco Teixeira do; UFES; Cunha, Gláucio de Mello; UFES; Bressan-Smith, Ricardo Enrique; UENF; Pinto, Ronald José Barth; UEM

    2008-01-01

    Nineteen late flowering lettuce genotypes from the UENF horticultural germoplasm bank were evaluated for phosphorus utilization efficiency under a 10 mg.dm-3 P level. A biometrical analysis of genetic parameters and genetic, phenotypic and environment correlations between shoot and root dry matter production, P content in roots and shoot Puptake, P-translocation and P utilization efficiency was undertaken. Genetic variability, which could be promising to obtain positive response to selection,...

  15. Toxoplasma gondii seroprevalence and genotype diversity in select wildlife species from the southeastern United States

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    Richard W. Gerhold

    2017-10-01

    Full Text Available Abstract Background Toxoplasma gondii is a widespread protozoan parasite that infects humans and other animals. Previous studies indicate some genotypes of T. gondii are more frequently isolated in wildlife than agricultural animals, suggesting a wild/feral animal diversity model. To determine seroprevalence and genetic diversity of T. gondii in southeastern US wildlife, we collected sera from 471 wild animals, including 453 mammals and 18 birds, between 2011 and 2014. These serum samples were assayed for T. gondii infection using the modified agglutination test (MAT. Heart or tongue tissues from 66 seropositive animals were bioassayed in mice and 19 isolates were obtained. The isolated parasites were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP method employing 10 genetic markers. Results One hundred and ninety-six of 471 samples (41.6% had a titer ≥1:32 and were considered positive for T. gondii infection. Of 453 mammals, 195 (43% were seropositive, whereas only one (5.6% of 18 birds was seropositive. The seroprevalence in mammals was significantly higher than in the birds. Mammalian hosts with adequate samples size (≥ 20 comprised white-tailed deer (n = 241, feral hogs (n = 100, raccoons (n = 34 and coyotes (n = 22, with seroprevalences of 41.0%, 51.0%, 50.0% and 72.7%, respectively. Coyotes had significantly higher seroprevalence than the white-tailed deer. Genotyping revealed five distinct genotypes, including the ToxoDB PCR-RFLP genotype #5 (a.k.a type 12 for 15 isolates, genotype #3 (a.k.a. type II for 1 isolate, and genotypes #154, #167 and #216, each for 1 isolate. The results showed moderate to high infection rates of T. gondii in white-tailed deer, feral hogs, raccoons and coyotes. Genotyping results indicated limited genetic diversity and a dominance of genotype #5, which has been reported as a major type in wildlife in North America. Conclusions We conclude that T. gondii

  16. Comprehensive characterization of glutamine synthetase-mediated selection for the establishment of recombinant CHO cells producing monoclonal antibodies

    DEFF Research Database (Denmark)

    Noh, Soo Min; Shin, Seunghyeon; Min Lee, Gyun

    2018-01-01

    and GS-knockout CHO). Regardless of the host cell lines used, the clones selected at 50 μM MSX had the lowest average specific growth rate and the highest average specific production rates of toxic metabolic wastes, lactate and ammonia. Unlike CHO-K1, high producing clones could be generated......To characterize a glutamine synthetase (GS)-based selection system, monoclonal antibody (mAb) producing recombinant CHO cell clones were generated by a single round of selection at various methionine sulfoximine (MSX) concentrations (0, 25, and 50 μM) using two different host cell lines (CHO-K1...... in the absence of MSX using GS-knockout CHO with an improved selection stringency. Regardless of the host cell lines used, the clones selected at various MSX concentrations showed no significant difference in the GS, heavy chain, and light chain gene copies (P > 0.05). Furthermore, there was no correlation...

  17. Antioxidant activity of seedling growth in selected soybean genotypes (Glycine max (L.) Merrill) responses of submergence

    Science.gov (United States)

    Damanik, R. I.; Marbun, P.; Sihombing, L.

    2016-08-01

    In order to better understand the physiological and biochemical responses relating to direct seeding establishment in soybeans, the plant growth rate and antioxidative defense responses of seedlings in seven Indonesian soybean genotypes (Anjasmoro, Detam-1, Detam-2, Dieng, Grobogan, Tanggamus, and Willis) at different submergence periods (4, and 8 days) were examined. Twelve-day old seedlings were hydroponically grown in limited oxygen conditions. The results showed that the chlorophyll content in soybean seedlings was reduced beginning as early as 4 d under submerged condition, except for Detam-1, Detam-2, and Grobogan genotypes. The dry weight and protein concentration of seedlings were significantly higher at control condition (0 d) than those in submerged condition. The activities of superoxide dismutase (SOD) increased linearly until 8 d submerged for all genotypes. On the other hand, our results showed that catalase (CAT) and ascorbate peroxidase (APX) activities did not work together, meaning that CAT is activated and APX deactivated, or vice versa, in response to submergence conditions, except for Grobogan and Tanggamus genotypes which had an effect on both CAT and APX activities. Submergence stress led to a significant increase in glutathione reductase (GR) together with APX activity for Detam-2 and Dieng genotypes at 8 d submerged.

  18. Sub-Soiling and Genotype Selection Improves Populus Productivity Grown on a North Carolina Sandy Soil

    Directory of Open Access Journals (Sweden)

    Shawn Dayson Shifflett

    2016-03-01

    Full Text Available This study reports the stem volume of 10 Populus genotypes in a randomized split-plot design with different tillage treatments (disking versus sub-soiling after two years of growth. Height, diameter at breast height (DBH, stem aboveground volume index, survival, Melampsora rust resistance, leaf area index (LAI, chlorophyll content, and foliar nitrogen concentration (Foliar N were measured to identify how tillage treatments might alter poplar growth. Stem volume index and LAI were positively correlated and differed significantly among tillage treatments, taxa, and genotypes. Melampsora rust resistance was also positively correlated with volume index, but significant differences were only detected among taxa and genotypes. Foliar N and chlorophyll did not correlate to stem volume for genotypes or tillage treatments. Overall, sub-soiling yielded 37% more estimated volume compared to disking. Within the sub-soiled treatments, four genotypes (140, 176, 185, and 356 had high survival (>80% and produced substantial stem volume (>32 dm3·tree−1. These findings show that tillage practices do impact poplar stem volumes after two years and that sub-soiling improves productivity for poplar short rotation woody crops on loamy fine-sandy soils.

  19. Nucleotide substitutions in dengue virus serotypes from Asian and American countries: insights into intracodon recombination and purifying selection

    Science.gov (United States)

    2013-01-01

    Background Dengue virus (DENV) infection represents a significant public health problem in many subtropical and tropical countries. Although genetically closely related, the four serotypes of DENV differ in antigenicity for which cross protection among serotypes is limited. It is also believed that both multi-serotype infection as well as the evolution of viral antigenicity may have confounding effects in increased dengue epidemics. Numerous studies have been performed that investigated genetic diversity of DENV, but the precise mechanism(s) of dengue virus evolution are not well understood. Results We investigated genome-wide genetic diversity and nucleotide substitution patterns in the four serotypes among samples collected from different countries in Asia and Central and South America and sequenced as part of the Genome Sequencing Center for Infectious Diseases at the Broad Institute. We applied bioinformatics, statistical and coalescent simulation methods to investigate diversity of codon sequences of DENV samples representing the four serotypes. We show that fixation of nucleotide substitutions is more prominent among the inter-continental isolates (Asian and American) of serotypes 1, 2 and 3 compared to serotype 4 isolates (South and Central America) and are distributed in a non-random manner among the genes encoded by the virus. Nearly one third of the negatively selected sites are associated with fixed mutation sites within serotypes. Our results further show that of all the sites showing evidence of recombination, the majority (~84%) correspond to sites under purifying selection in the four serotypes. The analysis further shows that genetic recombination occurs within specific codons, albeit with low frequency (< 5% of all recombination sites) throughout the DENV genome of the four serotypes and reveals significant enrichment (p < 0.05) among sites under purifying selection in the virus. Conclusion The study provides the first evidence for intracodon

  20. Temporal stability for unpredictable annual climatic variability for Hevea genotype selection

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    Paulo de Souza Gonçalves

    2008-02-01

    Full Text Available The objective of this study was to assess genotype-year interaction and determine temporal stable genotypes across six years of rubber yield evaluation. Stability analyses were performed by Eberhart and Russell method for rubber yield. Twenty-five genotypes were analyzed in a randomized complete block design with three replications. The best genotype in one year was not same always in the other year. The genotype components were partitioned into linear (genotypes within year and nonlinear (pooled deviations components. Significant mean square for linear components was predictable. This indicated that the performance of genotypes across the years for rubber yield could be predicted. Among the analyzed genotypes the IAC 40 also was considered highly productive and vigorous, with suitable adaptation.A interação genótipo x ano em culturas perenes como a seringueira Hevea brasiliensis (Willd. ex Adr. de Juss. Muell.-Arg. representa o diferencial de resposta dos genótipos às mudanças climáticas anuais. O objetivo deste trabalho foi estudar a interação genótipo-ano e determinar genótipos temporalmente estáveis por meio da avaliação de seis anos de produção de borracha. Análises de estabilidade foram realizadas pelo método de Eberhart and Russell para produção de borracha na Estação Experimental de Votuporanga, região Noroeste do Estado de São Paulo, Brasil. Vinte e cinco genótipos foram analisados num delineamento de blocos ao acaso com três repetições. Os resultados mostraram que o melhor genótipo em um ano nem sempre foi o melhor em outro. Os componentes genéticos foram repartidos em lineares (genótipos dentro do ano e não lineares (desvios agrupados. Quadrados médios significativos para os componentes lineares foram previsíveis indicando que o desempenho dos genótipos através dos anos em relação ao rendimento de borracha é passível de previsão. Entre os clones estudados o IAC 40 também foi considerado

  1. Identification of nucleotides in the 5'UTR and amino acids substitutions that are essential for the infectivity of 5'UTR-NS5A recombinant of hepatitis C virus genotype 1b (strain Con1).

    Science.gov (United States)

    Li, Jinqian; Feng, Shengjun; Liu, Xi; Guo, Mingzhe; Chen, Mingxiao; Chen, Yiyi; Rong, Liang; Xia, Jinyu; Zhou, Yuanping; Zhong, Jin; Li, Yi-Ping

    2018-03-14

    Genotype 1b strain Con1 represents an important reference in the study of hepatitis C virus (HCV). Here, we aimed to develop an advanced infectious Con1 recombinant. We found that previously identified mutations A1226G/F1464L/A1672S/Q1773H permitted culture adaption of Con1 Core-NS5A (C-5A) recombinant containing 5'UTR and NS5B-3'UTR from JFH1 (genotype 2a), thus acquired additional mutations L725H/F886L/D2415G. C-5A containing all seven mutations (C-5A_7m) replicated efficiently in Huh7.5 and Huh7.5.1 cells and had an increased infectivity in SEC14L2-expressing Huh7.5.1 cells. Incorporation of Con1 NS5B was deleterious to C-5A_7m, however Con1 5'UTR was permissive but attenuated the virus. Nucleotides G1, A4, and G35 primarily accounted for the viral attenuation without affecting RNA translation. C-5A_7m was inhibited dose-dependently by simeprevir and daclatasvir, and substitutions at A4, A29, A34, and G35 conferred resistance to miR-122 antagonism. The novel Con1 5'UTR-NS5A recombinant, adaptive mutations, and critical nucleotides described here will facilitate future studies of HCV culture systems and virus-host interaction. Copyright © 2018 Elsevier Inc. All rights reserved.

  2. Molecular diversity of Annona species and proximate fruit composition of selected genotypes.

    Science.gov (United States)

    Anuragi, Hirdayesh; Dhaduk, Haresh L; Kumar, Sushil; Dhruve, Jitendra J; Parekh, Mithil J; Sakure, Amar A

    2016-12-01

    Understanding the genetic variation in germplasm is of utmost importance for crop improvement. Therefore, efforts were made to analyse the molecular marker based genetic diversity of 20 Annona genotypes from five different species of family Annonaceae. During analysis, a set of 11 RAPD primers yielded a total of 152 bands with 80.01 % polymorphism and PIC for RAPD ranged from 0.86 to 0.92 with a mean of 0.89. With 93.05 % polymorphism, 12 SSR primers produced 39 amplicons. The PIC for SSRs ranged from 0.169 to 0.694 with of average of 0.339. The dendrogram produced from pooled molecular data of 11 RAPD and 12 SSR primers showed seven clusters at a cutoff value of 0.78. The dendrogram discriminated all the Annona genotypes suggesting that significant genetic diversity was present among the genotypes. Proximate fruit composition study of nine fruiting genotypes of Annona revealed that A. squamosa possessed significantly higher amount of most of studies biochemical which gives an opportunity to fruit breeders to improve the other Annona species. Likewise, A. muricata being rich in seed oil content can be exploited in oil industries.

  3. Multi-Population Selective Genotyping to Identify Soybean [Glycine max (L. Merr.] Seed Protein and Oil QTLs

    Directory of Open Access Journals (Sweden)

    Piyaporn Phansak

    2016-06-01

    Full Text Available Plant breeders continually generate ever-higher yielding cultivars, but also want to improve seed constituent value, which is mainly protein and oil, in soybean [Glycine max (L. Merr.]. Identification of genetic loci governing those two traits would facilitate that effort. Though genome-wide association offers one such approach, selective genotyping of multiple biparental populations offers a complementary alternative, and was evaluated here, using 48 F2:3 populations (n = ∼224 plants created by mating 48 high protein germplasm accessions to cultivars of similar maturity, but with normal seed protein content. All F2:3 progeny were phenotyped for seed protein and oil, but only 22 high and 22 low extreme progeny in each F2:3 phenotypic distribution were genotyped with a 1536-SNP chip (ca. 450 bimorphic SNPs detected per mating. A significant quantitative trait locus (QTL on one or more chromosomes was detected for protein in 35 (73%, and for oil in 25 (52%, of the 48 matings, and these QTL exhibited additive effects of ≥ 4 g kg–1 and R2 values of 0.07 or more. These results demonstrated that a multiple-population selective genotyping strategy, when focused on matings between parental phenotype extremes, can be used successfully to identify germplasm accessions possessing large-effect QTL alleles. Such accessions would be of interest to breeders to serve as parental donors of those alleles in cultivar development programs, though 17 of the 48 accessions were not unique in terms of SNP genotype, indicating that diversity among high protein accessions in the germplasm collection is less than what might ordinarily be assumed.

  4. Does selection in a challenging environment produce Nile tilapia genotypes that can thrive in a range of production systems?

    Science.gov (United States)

    Thoa, Ngo Phu; Ninh, Nguyen Huu; Knibb, Wayne; Nguyen, Nguyen Hong

    2016-02-19

    This study assessed whether selection for high growth in a challenging environment of medium salinity produces tilapia genotypes that perform well across different production environments. We estimated the genetic correlations between trait expressions in saline and freshwater using a strain of Nile tilapia selected for fast growth under salinity water of 15-20 ppt. We also estimated the heritability and genetic correlations for new traits of commercial importance (sexual maturity, feed conversion ratio, deformity and gill condition) in a full pedigree comprising 36,145 fish. The genetic correlations for the novel characters between the two environments were 0.78-0.99, suggesting that the effect of genotype by environment interaction was not biologically important. Across the environments, the heritability for body weight was moderate to high (0.32-0.62), indicating that this population will continue responding to future selection. The estimates of heritability for sexual maturity and survival were low but significant. The additive genetic components also exist for FCR, gill condition and deformity. Genetic correlations of harvest body weight with sexual maturity were positive and those between harvest body weight with FCR were negative. Our results indicate that the genetic line selected under a moderate saline water environment can be cultured successfully in freshwater systems.

  5. SSR markers associated to early leaf spot disease resistance through selective genotyping and single marker analysis in groundnut (Arachis hypogaea L.

    Directory of Open Access Journals (Sweden)

    Adama Zongo

    2017-09-01

    Full Text Available Groundnut (Arachis hypogaea L. is an important oilseed and food crop of the world. Breeding for disease resistance is one of major objectives in groundnut breeding. Early leaf spot (ELS is one of the major destructive diseases worldwide and in West Africa, particularly in Burkina Faso causing significant yield losses. Conventional breeding approaches have been employed to develop improved varieties resistant to ELS. Molecular dissection of resistance traits using QTL analysis can improve the efficiency of resistance breeding. In the present study, an ELS susceptible genotype QH243C and an ELS resistant genotype NAMA were crossed and the F2 population genotypic and F3 progenies phenotypic data were used for marker-trait association analysis. Parents were surveyed with 179 simple sequence repeat (SSR markers out of which 103 SSR markers were found to be polymorphic between the parents. These polymorphic markers were utilized to genotype the F2 population followed by marker-trait analysis through single marker analysis (SMA and selective genotyping of the population using 23 resistant and 23 susceptible genotypes. The SMA revealed 13 markers while the selective genotyping method identified 8 markers associated with ELS resistance. Four markers (GM1911, GM1883, GM1000 and Seq13E09 were found common between the two trait mapping methods. These four markers could be employed in genomics-assisted breeding for selection of ELS resistant genotypes in groundnut breeding.

  6. Selectable high-yield recombinant protein production in human cells using a GFP/YFP nanobody affinity support.

    Science.gov (United States)

    Schellenberg, Matthew J; Petrovich, Robert M; Malone, Christine C; Williams, R Scott

    2018-03-25

    Recombinant protein expression systems that produce high yields of pure proteins and multi-protein complexes are essential to meet the needs of biologists, biochemists, and structural biologists using X-ray crystallography and cryo-electron microscopy. An ideal expression system for recombinant human proteins is cultured human cells where the correct translation and chaperone machinery are present. However, compared to bacterial expression systems, human cell cultures present several technical challenges to their use as an expression system. We developed a method that utilizes a YFP fusion-tag to generate recombinant proteins using suspension-cultured HEK293F cells. YFP is a dual-function tag that enables direct visualization and fluorescence-based selection of high expressing clones for and rapid purification using a high-stringency, high-affinity anti-GFP/YFP nanobody support. We demonstrate the utility of this system by expressing two large human proteins, TOP2α (340 KDa dimer) and a TOP2β catalytic core (260 KDa dimer). This robustly and reproducibly yields >10 mg/L liter of cell culture using transient expression or 2.5 mg/L using stable expression. Published 2018. This article is a US Government work and is in the public domain in the USA.

  7. A genotypic and phenotypic information source for marker-assisted selection of cereals: the CEREALAB database

    Science.gov (United States)

    Milc, Justyna; Sala, Antonio; Bergamaschi, Sonia; Pecchioni, Nicola

    2011-01-01

    The CEREALAB database aims to store genotypic and phenotypic data obtained by the CEREALAB project and to integrate them with already existing data sources in order to create a tool for plant breeders and geneticists. The database can help them in unravelling the genetics of economically important phenotypic traits; in identifying and choosing molecular markers associated to key traits; and in choosing the desired parentals for breeding programs. The database is divided into three sub-schemas corresponding to the species of interest: wheat, barley and rice; each sub-schema is then divided into two sub-ontologies, regarding genotypic and phenotypic data, respectively. Database URL: http://www.cerealab.unimore.it/jws/cerealab.jnlp PMID:21247929

  8. Toona ciliata genotype selection with the use of individual BLUP with repeated measures

    Directory of Open Access Journals (Sweden)

    Rulfe Tavares Ferreira

    2012-06-01

    Full Text Available The increasing demand for raw material for multiple uses of forest products and by-products has attracted the interest for fast growing species, such as the Australian Cedar (Toona ciliata, which presents high productive and economic potential. This study aimed at estimating genotypic parameters and values for the species through the use of the BLUP procedure, at individual level, with repeated measures, by means of the conventional evaluation procedures and the introduction of innovative digitalization of the measurements by digital camera with the images provided by the Imagej software system. The main objective is to subsidize the beginning of a breeding program for the species. The assays were carried out in private properties, in plantations located in the state of Rio de Janeiro, Brazil. The results generated by three evaluations revealed that the image digital analysis is adequate to quantify characteristics of Toona ciliata. It is also an effective and accurate alternative to minimize the costs of data collection in evaluations with the species. There was high accuracy for the characters plant height, diameter at breast height and cylindrical volume. Out of the 90 genotypes evaluated, 38 expressed genotypic values predicted for the diameter at breast height higher than the general average of this character, 33 for the cylindrical volume and 49 for height, allowing gains of up to 24.9 % in average for cylindrical volume. The method of mixed models (REML/BLUP applied via the SELEGEN software system, using the BLUP procedure at individual level and repeated measures in each individual proved to be adequate to estimate the genetic parameters and predict genotypic values in situations of unbalanced data. Therefore, it is very useful and practical for Toona ciliata genetic breeding programs.

  9. Association of molecular markers with polyphenol oxidase activity in selected wheat genotypes

    International Nuclear Information System (INIS)

    Abbas, Z.; Javad, B.; Majeed, N.; Naqvi, S.

    2016-01-01

    Wheat (Triticum aestivum L.), a major staple food for the people of Pakistan and other Asian countries, is used as bread, chapatti, porridge, noodles and many other. It is established that color quality of wheat products depend on chemical and enzymatic factors especially the polyphenol oxidases (PPOs). These are copper containing enzymes which induce browning in wheat-based products. Various procedures for determining PPO activity available and differences in PPO activity among wheat genotypes have been documented. In present study, an attempt was made to establish the association of molecular markers with polyphenol oxidase activity in wheat genotypes having very high or very low PPO activities. Twelve pairs of markers were used out of which only three primer pairs viz. PPO43, PPO30 and WP2-2 yielded specific pattern discriminating high and low PPO genotypes. Cluster analysis for all 12 markers revealed that all the low PPO lline share the same sub cluster, but high PPO lines were dispersed in different clusters. (author)

  10. Phenolics of Selected Cranberry Genotypes (Vaccinium macrocarpon Ait.) and Their Antioxidant Efficacy.

    Science.gov (United States)

    Abeywickrama, Gihan; Debnath, Samir C; Ambigaipalan, Priyatharini; Shahidi, Fereidoon

    2016-12-14

    Free, esterified, and bound phenolic fractions of berries from five different cranberry genotypes and two market samples were evaluated for their total phenolic, flavonoid, and monomeric anthocyanin contents as well as their antioxidant efficacy using TEAC, ORAC, DPPH radical, reducing power, and ferrous ion chelation capacity assays. HPLC-MS/MS analysis was performed for two of the rich sources (Pilgrim and wild clone NL2) of phenolics and high antioxidant activity. Among the genotypes, Pilgrim showed the highest phenolic and flavonoid contents and wild clones NL3 and NL2 showed the highest monomeric anthocyanin and proanthocyanidin content, respectively. Protocatechuic and syringic acids were detected only in Pilgrim, whereas luteolin 7-O-glucoside, quercetin 3-O-rhamnoside, quercetin 3-O-galactoside, proanthocyanidin B-type, and myricetin 3-O-galactoside were found in wild clone NL3 genotype. Moreover, proanthocyanin trimer A-type and dimer B-type predominated in the wild clone NL2, whereas proanthocyanidin dimer B and trimer A were predominant in Pilgrim.

  11. A non-destructive genotyping system from a single seed for marker-assisted selection in watermelon.

    Science.gov (United States)

    Meru, G; McDowell, D; Waters, V; Seibel, A; Davis, J; McGregor, C

    2013-03-11

    Genomic tools for watermelon breeding are becoming increasingly available. A high throughput genotyping system would facilitate the use of DNA markers in marker-assisted selection. DNA extraction from leaf material requires prior seed germination and is often time-consuming and cost prohibitive. In an effort to develop a more efficient system, watermelon seeds of several genotypes and various seed sizes were sampled by removing ⅓ or ½ sections from the distal ends for DNA extraction, while germinating the remaining proximal parts of the seed. Removing ⅓ of the seed from the distal end had no effect on seed germination percentage or seedling vigor. Different DNA extraction protocols were tested to identify a method that could yield DNA of sufficient quality for amplification by polymerase chain reaction. A sodium dodecyl sulfate extraction protocol with 1% polyvinylpyrrolidone yielded DNA that could be amplified with microsatellite primers and was free of pericarp contamination. In this study, an efficient, non-destructive genotyping protocol for watermelon seed was developed.

  12. Genetic diversity in bread wheat (Triticum aestivum L.) genotypes.

    Science.gov (United States)

    Degewione, A; Alamerew, S

    2013-11-01

    Wheat is one most important cereal crops grown in Ethiopia. Yet, keeping in view insufficient information on exotic bread wheat genotypes is limiting the access to useful traits present among the genotypes in the Somali region of Ethiopia. The aim of the study was to assess the extent of genetic diversity among bread wheat genotypes. Twenty six bread wheat (Triticum aestivum L.) genotypes obtained from ICARDA-CIMMYT were tested at Gode and Kelafo research sites at three cropping seasons (2009/10, 2010/11 and 2011/12) under irrigation. The experiment was conducted in randomized complete block design with three replications. Ten agronomic traits were included in the study. The mean values, ranges and the coefficient of variation of the 10 characters indicated the existence of sufficient variability among genotypes. Multivariate techniques were used to classify 26 bread wheat genotypes. Principal component analysis showed that the first six principal components explained about 91.87% of the total variation. D2 analysis showed the 26 bread wheat genotypes grouped into six clusters. This made to become moderate diversity among the genotypes. The crosses between genotypes selected from cluster-III with cluster-VI and cluster V with cluster VI are expected to produce better genetic recombination and segregation in their progenies. Therefore, these bread wheat genotypes need to be crossed and selected to develop high yielding pure line variety.

  13. Comparing the effects of genetic drift and fluctuating selection on genotype frequency changes in the scarlet tiger moth.

    Science.gov (United States)

    O'Hara, R B

    2005-01-22

    One of the recurring arguments in evolutionary biology is whether evolution occurs principally through natural selection or through neutral processes such as genetic drift. A 60-year-long time series of changes in the genotype frequency of a colour polymorphism of the scarlet tiger moth, Callimorpha dominula, was used to compare the relative effects of genetic drift and variable natural selection. The analysis showed that most of the variation in frequency was the result of genetic drift. In addition, although selection was acting, mean fitness barely increased. This supports the 'Red Queen's hypothesis' that long-term improvements in fitness may not occur, because populations have to keep pace with changes in the environment.

  14. Limited protective effect of the CCR5Delta32/CCR5Delta32 genotype on human immunodeficiency virus infection incidence in a cohort of patients with hemophilia and selection for genotypic X4 virus

    DEFF Research Database (Denmark)

    Iversen, Astrid K N; Christiansen, Claus Bohn; Attermann, Jørn

    2003-01-01

    The relationship among CCR5 genotype, cytomegalovirus infection, and disease progression and death was studied among 159 human immunodeficiency virus (HIV)-infected patients with hemophilia. One patient (0.6%) had the CCR5Delta32/CCR5Delta32 genotype (which occurs in approximately 2...... time were seen for CCR5/CCR5 patients. Surprisingly, no protective effect of the CCR5/CCR5Delta32 genotype on disease progression or survival was seen for children but was evident for adults. Age group-related immunologic differences might explain this variation, and transmission route and/or viral...... phenotype variation within donor virus may be related to the limited protection of the CCR5Delta32/CCR5Delta32 genotype. Sequence comparisons indicate that X4 virus can be selected in vivo due to either absence of CCR5 receptors or relative increase of CXCR4 receptors....

  15. Efficient generation of long-distance conditional alleles using recombineering and a dual selection strategy in replicate plates

    Directory of Open Access Journals (Sweden)

    Liang Hong-Erh

    2009-07-01

    Full Text Available Abstract Background Conditional knockout mice are a useful tool to study the function of gene products in a tissue-specific or inducible manner. Classical approaches to generate targeting vectors for conditional alleles are often limited by the availability of suitable restriction sites. Furthermore, plasmid-based targeting vectors can only cover a few kB of DNA which precludes the generation of targeting vectors where the two loxP sites are placed far apart. These limitations have been overcome in the recent past by using homologous recombination of bacterial artificial chromosomes (BACs in Escherichia coli to produce large targeting vector containing two different loxP-flanked selection cassettes so that a single targeting event is sufficient to introduce loxP-sites a great distances into the mouse genome. However, the final targeted allele should be free of selection cassettes and screening for correct removal of selection cassettes can be a laborious task. Therefore, we developed a new strategy to rapidly identify ES cells containing the desired allele. Results Using BAC recombineering we generated a single targeting vector which contained two different selection cassettes that were flanked by loxP-loxP sites or by FRT-FRT/loxP sites so that they could be deleted sequentially by Cre- and FLPe-recombinases, respectively. Transfected ES cells were first selected in the presence of both antibiotics in vitro before correctly targeted clones were identified by Southern blot. After transfection of a Cre recombinase expression plasmid ES cell clones were selected on replicate plates to identify those clones which maintained the FRT-FRT/loxP flanked cassette and lost the loxP-loxP flanked cassette. Using this strategy facilitated the identification of ES cell clones containing the desired allele before blastocyst injection. Conclusion The strategy of ES cell cultures in replicate plates proved to be very efficient in identifying ES cells that had

  16. Fluorescent labeling in semi-solid medium for selection of mammalian cells secreting high-levels of recombinant proteins

    Directory of Open Access Journals (Sweden)

    Garnier Alain

    2009-05-01

    Full Text Available Abstract Background Despite the powerful impact in recent years of gene expression markers like the green fluorescent protein (GFP to link the expression of recombinant protein for selection of high producers, there is a strong incentive to develop rapid and efficient methods for isolating mammalian cell clones secreting high levels of marker-free recombinant proteins. Recently, a method combining cell colony growth in methylcellulose-based medium with detection by a fluorescently labeled secondary antibody or antigen has shown promise for the selection of Chinese Hamster Ovary (CHO cell lines secreting recombinant antibodies. Here we report an extension of this method referred to as fluorescent labeling in semi-solid medium (FLSSM to detect recombinant proteins significantly smaller than antibodies, such as IGF-E5, a 25 kDa insulin-like growth factor derivative. Results CHO cell clones, expressing 300 μg/ml IGF-E5 in batch culture, were isolated more easily and quickly compared to the classic limiting dilution method. The intensity of the detected fluorescent signal was found to be proportional to the amount of IGF-E5 secreted, thus allowing the highest producers in the population to be identified and picked. CHO clones producing up to 9.5 μg/ml of Tissue-Plasminogen Activator (tPA, 67 kDa were also generated using FLSSM. In addition, IGF-E5 high-producers were isolated from 293SF transfectants, showing that cell selection in semi-solid medium is not limited to CHO and lymphoid cells. The best positive clones were collected with a micromanipulator as well as with an automated colony picker, thus demonstrating the method's high throughput potential. Conclusion FLSSM allows rapid visualization of the high secretors from transfected pools prior to picking, thus eliminating the tedious task of screening a high number of cell isolates. Because of its rapidity and its simplicity, FLSSM is a versatile method for the screening of high producers for

  17. L-Lactate-selective microbial sensor based on flavocytochrome b2-enriched yeast cells using recombinant and nanotechnology approaches.

    Science.gov (United States)

    Karkovska, Maria; Smutok, Oleh; Stasyuk, Nataliya; Gonchar, Mykhailo

    2015-11-01

    In the recent years, nanotechnology is the most developing branch due to a wide variety of potential applications in biomedical, biotechnological and agriculture fields. The binding nanoparticles with various biological molecules makes them attractive candidates for using in sensor technologies. The particularly actual is obtaining the bionanomembranes based on biocatalytic elements with improved sensing characteristics. The aim of this investigation is to study the properties of microbial L-lactate-selective sensor based on using the recombinant Hansenula polymorpha yeast cells overproducing flavocytochrome b2 (FC b2), as well as additionally enriched by the enzyme bound with gold nanoparticles (FC b2-nAu). Although, the high permeability of the living cells to nanoparticles is being intensively studied (mostly for delivery of drugs), the idea of using both recombinant technology and nanotechnology to increase the amount of the target enzyme in the biosensing layer is really novel. The FC b2-nAu-enriched living and permeabilized yeast cells were used for construction of a bioselective membrane of microbial L-lactate-selective amperometric biosensor. Phenazine methosulphate was served as a free defusing electron transfer mediator which provides effective electron transfer from the reduced enzyme to the electrode surface. It was shown that the output to L-lactate of FC b2-nAu-enriched permeabilized yeast cells is 2.5-fold higher when compared to the control cells. The obtained results confirm that additional enrichment of the recombinant yeast cell by the enzyme bound with nanoparticles improves the analytical parameters of microbial sensor. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Utilization of Multi-Immunization and Multiple Selection Strategies for Isolation of Hapten-Specific Antibodies from Recombinant Antibody Phage Display Libraries

    Science.gov (United States)

    Tullila, Antti; Nevanen, Tarja K.

    2017-01-01

    Phage display technology provides a powerful tool for the development of novel recombinant antibodies. In this work, we optimized and streamlined the recombinant antibody discovery process for haptens as an example. A multi-immunization approach was used in order to avoid the need for construction of multiple antibody libraries. Selection methods were developed to utilize the full potential of the recombinant antibody library by applying four different elution conditions simultaneously. High-throughput immunoassays were used to analyse the binding properties of the individual antibody clones. Different carrier proteins were used in the immunization, selection, and screening phases to avoid enrichment of the antibodies for the carrier protein epitopes. Novel recombinant antibodies against mycophenolic acid and ochratoxin A, with affinities up to 39 nM and 34 nM, respectively, were isolated from a multi-immunized fragment antigen-binding (Fab) library. PMID:28561803

  19. A novel, lactase-based selection and strain improvement strategy for recombinant protein expression in Kluyveromyces lactis

    Directory of Open Access Journals (Sweden)

    Krijger Jorrit-Jan

    2012-08-01

    Full Text Available Abstract Background The Crabtree-negative yeast species Kluyveromyces lactis has been established as an attractive microbial expression system for recombinant proteins at industrial scale. Its LAC genes allow for utilization of the inexpensive sugar lactose as a sole source of carbon and energy. Lactose efficiently induces the LAC4 promoter, which can be used to drive regulated expression of heterologous genes. So far, strain manipulation of K. lactis by homologous recombination was hampered by the high rate of non-homologous end-joining. Results Selection for growth on lactose was applied to target the insertion of heterologous genes downstream of the LAC4 promoter into the K. lactis genome and found to yield high numbers of positive transformants. Concurrent reconstitution of the β-galactosidase gene indicated the desired integration event of the expression cassette, and β-galactosidase activity measurements were used to monitor gene expression for strain improvement and fermentation optimization. The system was particularly improved by usage of a cell lysis resistant strain, VAK367-D4, which allowed for protein accumulation in long-term fermentation. Further optimization was achieved by increased gene dosage of KlGAL4 encoding the activator of lactose and galactose metabolic genes that led to elevated transcription rates. Pilot experiments were performed with strains expressing a single-chain antibody fragment (scFvox and a viral envelope protein (BVDV-E2, respectively. scFvox was shown to be secreted into the culture medium in an active, epitope-binding form indicating correct processing and protein folding; the E2 protein could be expressed intracellularly. Further data on the influence of protein toxicity on batch fermentation and potential post-transcriptional bottlenecks in protein accumulation were obtained. Conclusions A novel Kluyveromyces lactis host-vector system was developed that places heterologous genes under the control of

  20. Genomic selection strategies in breeding programs: Strong positive interaction between application of genotypic information and intensive use of young bulls on genetic gain

    DEFF Research Database (Denmark)

    Buch, Line Hjortø; Sørensen, Morten Kargo; Berg, Peer

    2012-01-01

    ) a positive interaction exists between the use of genotypic information and a short generation interval on ΔGAG and (iii) the inclusion of an indicator trait in the selection index will only result in a negligible increase in ΔGAG if genotypic information about the breeding goal trait is known. We examined......We tested the following hypotheses: (i) breeding schemes with genomic selection are superior to breeding schemes without genomic selection regarding annual genetic gain of the aggregate genotype (ΔGAG), annual genetic gain of the functional traits and rate of inbreeding per generation (ΔF), (ii...... four breeding schemes with or without genomic selection and with or without intensive use of young bulls using pseudo-genomic stochastic simulations. The breeding goal consisted of a milk production trait and a functional trait. The two breeding schemes with genomic selection resulted in higher ΔGAG...

  1. Female genotype influences the behavioral performance of mice selected for reproductive traits.

    Science.gov (United States)

    Weisker, S M; Barkley, M

    1991-10-01

    The behavioral performance of mice that differ in regularity of the estrous cycle and litter size was studied after female exposure to a male of the same or a different strain. Emotional reactivity was measured using the pole, straightaway and open field tests. Factor interpretations of emotionality included motor discharge, autonomic imbalance and acrophobia. Mice characterized by regular estrous cycles and large litters (line E) were more explorative and emotionally reactive with respect to motor discharge and autonomic imbalance. In contrast, mice with less regular estrous cycles and small litter size (line CN-) were more acrophobic. These strain differences in behavioral performance were influenced by the genotype of the female rather than the cohabitating male.

  2. Testing of Auxotrophic Selection Markers for Use in the Moss Physcomitrella Provides New Insights into the Mechanisms of Targeted Recombination

    Directory of Open Access Journals (Sweden)

    Mikael Ulfstedt

    2017-11-01

    Full Text Available The moss Physcomitrella patens is unique among plants in that homologous recombination can be used to knock out genes, just like in yeast. Furthermore, transformed plasmids can be rescued from Physcomitrella back into Escherichia coli, similar to yeast. In the present study, we have tested if a third important tool from yeast molecular genetics, auxotrophic selection markers, can be used in Physcomitrella. Two auxotrophic moss strains were made by knocking out the PpHIS3 gene encoding imidazoleglycerol-phosphate dehydratase, and the PpTRP1 gene encoding phosphoribosylanthranilate isomerase, disrupting the biosynthesis of histidine and tryptophan, respectively. The resulting PpHIS3Δ and PpTRP1Δ knockout strains were unable to grow on medium lacking histidine or tryptophan. The PpHIS3Δ strain was used to test selection of transformants by complementation of an auxotrophic marker. We found that the PpHIS3Δ strain could be complemented by transformation with a plasmid expressing the PpHIS3 gene from the CaMV 35S promoter, allowing the strain to grow on medium lacking histidine. Both linearized plasmids and circular supercoiled plasmids could complement the auxotrophic marker, and plasmids from both types of transformants could be rescued back into E. coli. Plasmids rescued from circular transformants were identical to the original plasmid, whereas plasmids rescued from linearized transformants had deletions generated by recombination between micro-homologies in the plasmids. Our results show that cloning by complementation of an auxotrophic marker works in Physcomitrella, which opens the door for using auxotrophic selection markers in moss molecular genetics. This will facilitate the adaptation of shuttle plasmid dependent methods from yeast molecular genetics for use in Physcomitrella.

  3. Within-Host Dynamics of the Emergence of Tomato Yellow Leaf Curl Virus Recombinants

    Science.gov (United States)

    Urbino, Cica; Gutiérrez, Serafin; Antolik, Anna; Bouazza, Nabila; Doumayrou, Juliette; Granier, Martine; Martin, Darren P.; Peterschmitt, Michel

    2013-01-01

    Tomato yellow leaf curl virus (TYLCV) is a highly damaging begomovirus native to the Middle East. TYLCV has recently spread worldwide, recombining with other begomoviruses. Recent analysis of mixed infections between TYLCV and Tomato leaf curl Comoros begomovirus (ToLCKMV) has shown that, although natural selection preserves certain co-evolved intra-genomic interactions, numerous and diverse recombinants are produced at 120 days post-inoculation (dpi), and recombinant populations from different tomato plants are very divergent. Here, we investigate the population dynamics that lead to such patterns in tomato plants co-infected with TYLCV and ToLCKMV either by agro-inoculation or using the natural whitefly vector Bemisia tabaci. We monitored the frequency of parental and recombinant genotypes independently in 35 plants between 18 and 330 dpi and identified 177 recombinants isolated at different times. Recombinants were detected from 18 dpi and their frequency increased over time to reach about 50% at 150 dpi regardless of the inoculation method. The distribution of breakpoints detected on 96 fully sequenced recombinants was consistent with a continuous generation of new recombinants as well as random and deterministic effects in their maintenance. A severe population bottleneck of around 10 genomes was estimated during early systemic infection–a phenomenon that could account partially for the heterogeneity in recombinant patterns observed among plants. The detection of the same recombinant genome in six of the thirteen plants analysed beyond 30 dpi supported the influence of selection on observed recombination patterns. Moreover, a highly virulent recombinant genotype dominating virus populations within one plant has, apparently, the potential to be maintained in the natural population according to its infectivity, within-host accumulation, and transmission efficiency - all of which were similar or intermediate to those of the parent genotypes. Our results

  4. Within-host dynamics of the emergence of Tomato yellow leaf curl virus recombinants.

    Directory of Open Access Journals (Sweden)

    Cica Urbino

    Full Text Available Tomato yellow leaf curl virus (TYLCV is a highly damaging begomovirus native to the Middle East. TYLCV has recently spread worldwide, recombining with other begomoviruses. Recent analysis of mixed infections between TYLCV and Tomato leaf curl Comoros begomovirus (ToLCKMV has shown that, although natural selection preserves certain co-evolved intra-genomic interactions, numerous and diverse recombinants are produced at 120 days post-inoculation (dpi, and recombinant populations from different tomato plants are very divergent. Here, we investigate the population dynamics that lead to such patterns in tomato plants co-infected with TYLCV and ToLCKMV either by agro-inoculation or using the natural whitefly vector Bemisia tabaci. We monitored the frequency of parental and recombinant genotypes independently in 35 plants between 18 and 330 dpi and identified 177 recombinants isolated at different times. Recombinants were detected from 18 dpi and their frequency increased over time to reach about 50% at 150 dpi regardless of the inoculation method. The distribution of breakpoints detected on 96 fully sequenced recombinants was consistent with a continuous generation of new recombinants as well as random and deterministic effects in their maintenance. A severe population bottleneck of around 10 genomes was estimated during early systemic infection-a phenomenon that could account partially for the heterogeneity in recombinant patterns observed among plants. The detection of the same recombinant genome in six of the thirteen plants analysed beyond 30 dpi supported the influence of selection on observed recombination patterns. Moreover, a highly virulent recombinant genotype dominating virus populations within one plant has, apparently, the potential to be maintained in the natural population according to its infectivity, within-host accumulation, and transmission efficiency - all of which were similar or intermediate to those of the parent genotypes. Our

  5. Efficient hepatitis c virus genotype 1b core-NS5A recombinants permit efficacy testing of protease and NS5A inhibitors

    DEFF Research Database (Denmark)

    Pham, Long V.; Ramirez Almeida, Santseharay; Carlsen, Thomas H R

    2017-01-01

    cell culture adaptive substitutions A1226G, R1496L, and Q1773H. These viruses spread efficiently in Huh7.5 cells by acquiring additional adaptive substitutions, and final recombinants yielded peak supernatant infectivity titers of 4 to 5 log10 focus-forming units (FFU)/ml. We subsequently succeeded...

  6. Genotype versus phenotype: conflicting results in mapping a lung tumor susceptibility locus to the G7c recombination interval in the mouse MHC class III region

    NARCIS (Netherlands)

    van Kooij, M.; de Groot, K.; van Vugt, H.; Aten, J.; Snoek, M.

    2001-01-01

    Susceptibility to chemically induced lung tumorigenesis has previously been mapped to a genomic interval of 27 kb in the MHC class III region of the mouse using two H2 (a/b) intra- H2 recombinants, B10.A(1R) and B10.A(2R). Three genes are located within this interval, G7e (encoding a viral envelope

  7. Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations.

    Science.gov (United States)

    Petit, Morgane; Astruc, Jean-Michel; Sarry, Julien; Drouilhet, Laurence; Fabre, Stéphane; Moreno, Carole R; Servin, Bertrand

    2017-10-01

    Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and data sets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified ∼50,000 crossover hotspots on the genome, and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting interindividual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly two other loci of smaller effects including the KCNJ15 and FSHR genes. The comparison of these new results to those obtained previously in a distantly related population of domestic sheep (the Soay) revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome. The two data sets were thus combined to create more precise male meiotic recombination maps in Sheep. However, despite their similar recombination maps, Soay and Lacaune males were found to exhibit different heritabilities and QTL effects for interindividual variation in genome-wide recombination rates. This highlights the robustness of recombination patterns to underlying variation in their genetic determinism. Copyright © 2017 by the Genetics Society

  8. Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes

    DEFF Research Database (Denmark)

    Jahn, Leonie Johanna; Munck, Christian; Ellabaan, Mostafa M Hashim

    2017-01-01

    compare the geno- and phenotypes of Escherichia coli after evolution to Amikacin, Piperacillin, and Tetracycline under four different selection regimes. Interestingly, key mutations that confer antibiotic resistance as well as phenotypic changes like collateral sensitivity and cross-resistance emerge...

  9. Soa genotype selectively affects mouse gustatory neural responses to sucrose octaacetate

    Science.gov (United States)

    INOUE, MASASHI; LI, XIA; McCAUGHEY, STUART A.; BEAUCHAMP, GARY K.; BACHMANOV, ALEXANDER A.

    2013-01-01

    In mice, behavioral acceptance of the bitter compound sucrose octaacetate (SOA) depends on allelic variation of a single gene, Soa. The SW.B6-Soab congenic mouse strain has the genetic background of an “SOA taster” SWR/J strain and an Soa-containing donor chromosome fragment from an “SOA nontaster” C57BL/6J strain. Using microsatellite markers polymorphic between the two parental strains, we determined that the donor fragment spans 5–10 cM of distal chromosome 6. The SWR/J mice avoided SOA in two-bottle tests with water and had strong responses to SOA in two gustatory nerves, the chorda tympani (CT) and glossopharyngeal (GL). In contrast, the SW.B6-Soab mice were indifferent to SOA in two-bottle tests and had very weak responses to SOA in both of these nerves. The SWR/J and SW.B6-Soab mice did not differ in responses of either nerve to sucrose, NaCl, HCl, or the bitter-tasting stimuli quinine, denatonium, strychnine, 6-n-propylthiouracil, phenylthiocarbamide, and MgSO4. Thus the effect of the Soa genotype on SOA avoidance is mediated by peripheral taste responsiveness to SOA, involving taste receptor cells innervated by both the CT and GL nerves. PMID:11328963

  10. Digest: Plants adapt under attack: genotypic selection and phenotypic plasticity under herbivore pressure.

    Science.gov (United States)

    Hawkins, Nichola J

    2018-03-31

    Plant species adapt to changing environmental conditions through phenotypic plasticity and natural selection. Agrawal et al. (2018) found that dandelions responded to the presence of insect pests by producing higher levels of defensive compounds. This defensive response resulted both from phenotypic plasticity, with individual plants' defenses triggered by insect attack, and from evolution by natural selection acting on genetic variation in the plant population. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

  11. Co-circulation of multiple subtypes of enterovirus A71 (EV- A71) genotype C, including novel recombinants characterised by use of whole genome sequencing (WGS), Denmark 2016

    DEFF Research Database (Denmark)

    Midgley, Sofie E; Nielsen, Astrid G; Trebbien, Ramona

    2017-01-01

    In Europe, enterovirus A71 (EV-A71) has primarily been associated with sporadic cases of neurological disease. The recent emergence of new genotypes and larger outbreaks with severely ill patients demonstrates a potential for the spread of new, highly pathogenic EV-A71 strains. Detection...

  12. Recombination of hepatitis B virus DNA in patients with HIV.

    Science.gov (United States)

    Fallot, Guillaume; Halgand, Boris; Garnier, Elisabeth; Branger, Michel; Gervais, Anne; Roque-Afonso, Anne-Marie; Thiers, Valérie; Billaud, Eric; Matheron, Sophie; Samuel, Didier; Féray, Cyrille

    2012-08-01

    Hepatitis B is a major cause of death in patients with HIV who usually receive drugs active against hepatitis B virus (HBV). The variability of HBV DNA over time has been little studied. Recombination between different HBV genotypes has been described in many cross-sectional studies, but the frequency of intergenotypic and intragenotypic recombinations in individual patients is unknown. 32 HIV-positive and 11 HIV-negative patients who remained HBV viraemic despite antiviral therapy for at least 1 year were studied. Genotyping was based on line probe assays and genotype-specific PCR. The variability of HBV DNA over time was examined with restriction length and single-strand conformational polymorphism (RFLP-SSCP). HBV DNA sequences obtained by cloning a 2800 bp PCR fragment were analysed for phylogenetic parameters (diversity and selection pressure) and recombination was detected with RDP3 software. Large fragments of HBV DNA could be amplified at two different time points in 33 patients. Marked quasi-species modifications occurred in 14 patients. In seven of these patients and in one patient with no change detectable by RFLP-SSCP, the 2800 bp fragment was cloned at two time points at least. In four (57%) of these seven patients, various intergenotypic or intragenotypic recombination events were detected between subvariants present in the initial quasi-species. Recombinant fragments mostly harboured antiviral resistance determinants and reflected a large increase in diversity and in positive selection pressure on the entire HBV quasi-species. In coinfected patients, HBV DNA recombination events are frequent during antiviral therapy, corresponding to increased positive selection pressure on the HBV quasi-species and to conservation of antiviral resistance mutations. In this population and at the individual level, recombination is a significant source of HBV genetic variability.

  13. Ascites and venous carbon dioxide tensions in juvenile chickens of highly selected genotypes and native strains

    NARCIS (Netherlands)

    Scheele, C.W.; Klis, van der J.D.; Kwakernaak, C.; Dekker, R.A.; Middelkoop, van J.H.; Buyse, J.; Decuypere, E.

    2005-01-01

    A previous study by this group demonstrated that a high carbon dioxide tension in venous blood (pvCO2) of juvenile broiler chickens is a reliable predictor for ascites susceptibility. In a new experiment with five highly selected genetic stocks and two ascites resistant old breeds we studied levels

  14. Spin-selective recombination reactions of radical pairs: Experimental test of validity of reaction operators

    Energy Technology Data Exchange (ETDEWEB)

    Maeda, Kiminori [Department of Chemistry, University of Oxford, Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, Oxford (United Kingdom); Liddell, Paul; Gust, Devens [Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, 85287-1604 (United States); Hore, P. J. [Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, Oxford (United Kingdom)

    2013-12-21

    Spin-selective reactions of radical pairs are conventionally modelled using an approach that dates back to the 1970s [R. Haberkorn, Mol. Phys. 32, 1491 (1976)]. An alternative approach based on the theory of quantum measurements has recently been suggested [J. A. Jones and P. J. Hore, Chem. Phys. Lett. 488, 90 (2010)]. We present here the first experimental attempt to discriminate between the two models. Pulsed electron paramagnetic resonance spectroscopy has been used to investigate intramolecular electron transfer in the radical pair form of a carotenoid-porphyrin-fullerene molecular triad. The rate of spin-spin relaxation of the fullerene radical in the triad was found to be inconsistent with the quantum measurement description of the spin-selective kinetics, and in accord with the conventional model when combined with spin-dephasing caused by rotational modulation of the anisotropic g-tensor of the fullerene radical.

  15. A Genome-Wide Identification of Genes Undergoing Recombination and Positive Selection in Neisseria

    OpenAIRE

    Yu, Dong; Jin, Yuan; Yin, Zhiqiu; Ren, Hongguang; Zhou, Wei; Liang, Long; Yue, Junjie

    2014-01-01

    Currently, there is particular interest in the molecular mechanisms of adaptive evolution in bacteria. Neisseria is a genus of gram negative bacteria, and there has recently been considerable focus on its two human pathogenic species N. meningitidis and N. gonorrhoeae. Until now, no genome-wide studies have attempted to scan for the genes related to adaptive evolution. For this reason, we selected 18 Neisseria genomes (14 N. meningitidis, 3 N. gonorrhoeae and 1 commensal N. lactamics) to cond...

  16. Multivariate analysis of backcross progeny of Passiflora L. (Passifloraceae) for pre-breeding genotype selection.

    Science.gov (United States)

    Melo, C A F; Souza, M M; Sousa, A G R; Viana, A P; Santos, E A

    2015-11-30

    The Ward-MLM procedure was used to evaluate genetic variation in four backcross progenies and in their parents, hybrid F1 HD13 and donor parent Passiflora sublanceolata. Sixteen quantitative descriptors and five qualitative characteristics of relevance to ornamental flower production were assessed. Using the pseudo-F and pseudo-T² criteria, we identified four groups among these plants in two evaluation periods. In both evaluations, the BC1 plants showed greater dissimilarity to their recurrent parent, but showed high genetic similarity with the P. sublanceolata parent. The first two canonical variables produced by the Ward-MLM procedure accounted for over 90% of the variation in both evaluation periods, enabling the representation of diversity through two-dimensional graphics. Groups II and IV were formed in the first assessment period. Groups I and IV formed in the second period and showed plants with selection potential. We found that it was essential to use both qualitative and quantitative variables for this analysis. Assessments of quantitative descriptors indicate that the selection of BC1 plants can be performed in any of the four progenies. Because of the similarities observed for some floral descriptors between BC1 and the P. sublanceolata parent, a second generation backcross was not recommended. However, the selection of BC1 plants for evaluation and direct use as an ornamental cultivar, or as a resource in other breeding programs, can be recommended.

  17. Site-selective conjugation of an anticoagulant aptamer to recombinant albumins and maintenance of neonatal Fc receptor binding

    Science.gov (United States)

    Schmøkel, Julie; Voldum, Anders; Tsakiridou, Georgia; Kuhlmann, Matthias; Cameron, Jason; Sørensen, Esben S.; Wengel, Jesper; Howard, Kenneth A.

    2017-05-01

    Aptamers are an attractive molecular medicine that offers high target specificity. Nucleic acid-based aptamers, however, are prone to nuclease degradation and rapid renal excretion that require blood circulatory half-life extension enabling technologies. The long circulatory half-life, predominately facilitated by engagement with the cellular recycling neonatal Fc receptor (FcRn), and ligand transport properties of albumin promote it as an attractive candidate to improve the pharmacokinetic profile of aptamers. This study investigates the effect of Cys34 site-selective covalent attachment of a factor IXa anticoagulant aptamer on aptamer functionality and human FcRn (hFcRn) engagement using recombinant human albumin (rHA) of either a wild type (WT) or an engineered human FcRn high binding variant (HB). Albumin-aptamer conjugates, connected covalently through a heterobifunctional succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate linker, were successfully prepared and purified by high performance liquid chromatography as confirmed by gel electrophoresis band-shift analysis and matrix-assisted laser desorption/ionization time of flight. Minimal reduction (∼25%) in activity of WT-linked aptamer to that of aptamer alone was found using an anticoagulant activity assay measuring temporal levels of activated partial thrombin. Covalent albumin-aptamer conjugation, however, substantially compromized binding to hFcRn, to 10% affinity of that of non-conjugated WT, determined by biolayer interferometry. Binding could be rescued by aptamer conjugation to recombinant albumin engineered for higher FcRn affinity (HB) that exhibited an 8-fold affinity compared to WT alone. This work describes a novel albumin-based aptamer delivery system whose hFcRn binding can be increased using a HB engineered albumin.

  18. Tagging of four Rf genes with selective genotyping analysis in rice (Oryza sativa L.

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    Yarahmadi Saeid

    2017-01-01

    Full Text Available Wild abortive type of cytoplasmic male sterility (WA-CMS is commercially used for hybrid rice seed production. The linked markers can be used for selection of plants with desirable traits. Tagging of Rf genes was carried out using recessive and dominant class analysis in a large F2 population from the cross IR58025A×IR42686R. Pollen fertility and seed setting were evaluated at the flowering and maturity stages, respectively. Forty-seven highly sterile and 23 fertile homozygous plants were selected from F2 population for molecular marker assay. Four Rf genes identified in a good restorer line with high-quality derived from a random mating composite population at the International Rice Research Institute (IRRI. The genetic distance from Rf3 locus with flanking markers RM443 and RM315 on chromosome 1 was 3.7 and 21.2 cM, respectively. RM258, RM591, RM271 and RM6737 on the long arm of chromosome 10 were linked with the Rf6 gene with distance of 7.4, 22.6, 6 and 2.9 cM, respectively. Rf6 was flanked by RM6737 and RM591. The Rf4 gene located on chromosome 7 was linked with RM6344 at a genetic distance of 10.6 cM. RM519 and RM7003 were linked with other Rf gene on chromosome 12 at a genetic distance of 8.5 and 20.8 cM, respectively. Closely linked markers identified in this study could be used for marker assisted selection in a hybrid rice breeding program. A new Rf locus on chromosome 12 that designated Rf7 was linked with RM7003 and RM519.

  19. Selective Permeation and Organic Extraction of Recombinant Green Fluorescent Protein (gfpuv from Escherichia coli

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    Ishii Marina

    2002-04-01

    Full Text Available Abstract Background Transformed cells of Escherichia coli DH5-α with pGFPuv, induced by IPTG (isopropyl-β-d-thiogalactopyranoside, express the green fluorescent protein (gfpuv during growth phases. E. coli subjected to the combination of selective permeation by freezing/thawing/sonication cycles followed by the three-phase partitioning extraction (TPP method were compared to the direct application of TPP to the same culture of E. coli on releasing gfpuv from the over-expressing cells. Material and Methods Cultures (37°C/100 rpm/ 24 h; μ = 0.99 h-1 - 1.10 h-1 of transformed (pGFP Escherichia coli DH5-α, expressing the green fluorescent protein (gfpuv, absorbance at 394 nm and emission at 509 nm were sonicated in successive intervals of sonication (25 vibrations/pulse to determine the maximum amount of gfpuv released from the cells. For selective permeation, the transformed previously frozen (-75°C cells were subjected to three freeze/thaw (-20°C/ 0.83°C/min cycles interlaid by sonication (3 pulses/ 6 seconds/ 25 vibrations. The intracellular permeate with gfpuv in extraction buffer (TE solution (25 mM Tris-HCl, pH 8.0, 1 mM β-mercaptoethanol β-ME, 0.1 mM PMSF was subjected to the three-phase partitioning (TPP method with t-butanol and 1.6 M ammonium sulfate. Sonication efficiency was verified on the application to the cells previously treated by the TPP method. The intra-cell releases were mixed and eluted through methyl HIC column with a buffer solution (10 mM Tris-HCl, 10 mM EDTA, pH 8.0. Results The sonication maximum released amount obtained from the cells was 327.67 μg gfpuv/mL (20.73 μg gfpuv/mg total proteins – BSA, after 9 min of treatment. Through the selective permeation by three repeated freezing/thawing/sonication cycles applied to the cells, a close content of 241.19 μg gfpuv/mL (29.74 μg gfpuv/mg BSA was obtained. The specific mass range of gfpuv released from the same cultures, by the three-phase partitioning (TPP

  20. Selection-Based Instruction with Touch-Screen Video and the Emergence of Exact, Recombinative, and Novel Topography-Based Responses to Interview Questions

    Science.gov (United States)

    O'Neill, John; Rehfeldt, Ruth Anne

    2016-01-01

    The purpose of the present experiment was to replicate and extend the literature on using selection-based instruction to teach responses to interview questions by (a) evaluating the emergence of recombinative (i.e., combinations of taught) and novel (i.e., untaught) topography-based intraverbal responses, in addition to exact repetitions of taught…

  1. Three vibrio-resistance related EST-SSR markers revealed by selective genotyping in the clam Meretrix meretrix.

    Science.gov (United States)

    Nie, Qing; Yue, Xin; Chai, Xueliang; Wang, Hongxia; Liu, Baozhong

    2013-08-01

    The clam Meretrix meretrix is an important commercial bivalve distributed in the coastal areas of South and Southeast Asia. In this study, marker-trait association analyses were performed based on the stock materials of M. meretrix with different vibrio-resistance profile obtained by selective breeding. Forty-eight EST-SSR markers were screened and 27 polymorphic SSRs of them were genotyped in the clam stocks with different resistance to Vibrio parahaemolyticus (11-R and 11-S) and to Vibrio harveyi (09-R and 09-C). Allele frequency distributions of the SSRs among different stocks were compared using Pearson's Chi-square test, and three functional EST-SSR markers (MM959, MM4765 and MM8364) were found to be associated with vibrio-resistance trait. The 140-bp allele of MM959 and 128-bp allele of MM4765 had significantly higher frequencies in resistant groups (11-R and 09-R) than in susceptive/control groups (11-S and 09-C) (P markers were consistent with the three subgroups distinctions. The putative functions of contig959, contig4765 and contig8364 also suggested that the three SSR-involved genes might play important roles in immunity of M. meretrix. All these results supported that EST-SSR markers MM959, MM4765 and MM8364 were associated with vibrio-resistance and would be useful for marker-assisted selection (MAS) in M. meretrix genetic breeding. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Multivariate analysis and determination of the best indirect selection criteria to genetic improvement the biological nitrogen fixation ability in common bean genotypes (Phaseolus vulgaris L.

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    Golparvar Reza Ahmad

    2012-01-01

    Full Text Available In order to determine the best indirect selection criteria for genetic improvement of biological nitrogen fixation, sixty four common bean genotypes were cultivated in two randomized complete block design. Genotypes were inoculated with bacteria Rhizobium legominosarum biovar Phaseoli isolate L-109 only in one of the experiments. The second experiment was considered as check for the first. Correlation analysis showed positive and highly significant correlation of majority of the traits with percent of nitrogen fixation. Step-wise regression designated that traits percent of total nitrogen of shoot, number of nodule per plant and biological yield accounted for 92.3 percent of variation exist in percent of nitrogen fixation. Path analysis indicated that these traits have direct and positive effect on percent of nitrogen fixation. Hence, these traits are promising indirect selection criteria for genetic improvement of nitrogen fixation capability in common bean genotypes especially in early generations.

  3. Sibling genes as environment: Sibling dopamine genotypes and adolescent health support frequency dependent selection.

    Science.gov (United States)

    Rauscher, Emily; Conley, Dalton; Siegal, Mark L

    2015-11-01

    While research consistently suggests siblings matter for individual outcomes, it remains unclear why. At the same time, studies of genetic effects on health typically correlate variants of a gene with the average level of behavioral or health measures, ignoring more complicated genetic dynamics. Using National Longitudinal Study of Adolescent Health data, we investigate whether sibling genes moderate individual genetic expression. We compare twin variation in health-related absences and self-rated health by genetic differences at three locations related to dopamine regulation and transport to test sibship-level cross-person gene-gene interactions. Results suggest effects of variation at these genetic locations are moderated by sibling genes. Although the mechanism remains unclear, this evidence is consistent with frequency dependent selection and suggests much genetic research may violate the stable unit treatment value assumption. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Path analysis and canonical correlations for indirect selection of Jatropha genotypes with higher oil yield.

    Science.gov (United States)

    Silva, L A; Peixoto, L A; Teodoro, P E; Rodrigues, E V; Laviola, B G; Bhering, L L

    2017-03-22

    Jatropha is a species with great potential for biodiesel production, and the knowledge on how the main agronomic traits are correlated will contribute to its improvement. Therefore, the objectives of this study were to estimate the genetic parameters of the traits: plant height at 12 and 40 months, canopy projection on the row at 12 and 40 months, canopy projection between the row at 12 and 40 months, number of branches at 40 months, grain yield, and oil yield; to verify the existence of phenotypic correlation between these traits; to verify the influence of the morphological traits on oil yield by means of path analysis; and to evaluate the relationship between the productive traits in Jatropha and the morphological traits measured at different ages. Sixty-seven half-sib families were evaluated using a completely randomized block design with two replications and five plants per plot. Analysis of variance was used to estimate the genetic value. Phenotypic correlations were given by the Pearson correlation between traits. For the canonical correlation analysis, two groups of traits were established: group I, consisting of traits of economic importance for the culture, and group II, consisting of morphological traits. Path analysis was carried out considering oil yield as the main dependent variable. Genetic variability was observed among Jatropha families. Productive traits can be indirectly selected via morphological traits due to the correlation between these two groups of traits. Therefore, canonical correlations and path analysis are two strategies that may be useful in Jatropha-breeding program when the objective is to select productive traits via morphological traits.

  5. Recombinant Expression and Functional Characterization of Martentoxin: A Selective Inhibitor for BK Channel (α + β4

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    Jie Tao

    2014-04-01

    Full Text Available Martentoxin (MarTX, a 37-residue peptide purified from the venom of East-Asian scorpion (Buthus martensi Karsch, was capable of blocking large-conductance Ca2+-activated K+ (BK channels. Here, we report an effective expression and purification approach for this toxin. The cDNA encoding martentoxin was expressed by the prokaryotic expression system pGEX-4T-3 which was added an enterokinase cleavage site by PCR. The fusion protein (GST-rMarTX was digested by enterokinase to release hetero-expressed toxin and further purified via reverse-phase HPLC. The molecular weight of the hetero-expressed rMarTX was 4059.06 Da, which is identical to that of the natural peptide isolated from scorpion venom. Functional characterization through whole-cell patch clamp showed that rMarTX selectively and potently inhibited the currents of neuronal BK channels (α + β4 (IC50 = 186 nM, partly inhibited mKv1.3, but hardly having any significant effect on hKv4.2 and hKv3.1a even at 10 μM. Successful expression of martentoxin lays basis for further studies of structure-function relationship underlying martentoxin or other potassium-channel specific blockers.

  6. Selecting sagebrush seed sources for restoration in a variable climate: ecophysiological variation among genotypes

    Science.gov (United States)

    Germino, Matthew J.

    2012-01-01

    Big sagebrush (Artemisia tridentata) communities dominate a large fraction of the United States and provide critical habitat for a number of wildlife species of concern. Loss of big sagebrush due to fire followed by poor restoration success continues to reduce ecological potential of this ecosystem type, particularly in the Great Basin. Choice of appropriate seed sources for restoration efforts is currently unguided due to knowledge gaps on genetic variation and local adaptation as they relate to a changing landscape. We are assessing ecophysiological responses of big sagebrush to climate variation, comparing plants that germinated from ~20 geographically distinct populations of each of the three subspecies of big sagebrush. Seedlings were previously planted into common gardens by US Forest Service collaborators Drs. B. Richardson and N. Shaw, (USFS Rocky Mountain Research Station, Provo, Utah and Boise, Idaho) as part of the Great Basin Native Plant Selection and Increase Project. Seed sources spanned all states in the conterminous Western United States. Germination, establishment, growth and ecophysiological responses are being linked to genomics and foliar palatability. New information is being produced to aid choice of appropriate seed sources by Bureau of Land Management and USFS field offices when they are planning seed acquisitions for emergency post-fire rehabilitation projects while considering climate variability and wildlife needs.

  7. Improving the phenotypic expression of rice genotypes: Rethinking “intensification” for production systems and selection practices for rice breeding

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    Norman Uphoff

    2015-06-01

    expression of rice plants' genetic potential, thereby creating more productive and robust phenotypes from given rice genotypes. Data indicate that increased plant density does not necessarily enhance crop yield potential, as classical breeding methods suggest. Developing cultivars that can achieve their higher productivity under a wide range of plant densities—breeding for density-neutral cultivars using alternative selection strategies—will enable more effective exploitation of available crop growth resources. Density-neutral cultivars that achieve high productivity under ample environmental growth resources can also achieve optimal productivity under limited resources, where lower densities can avert crop failure due to overcrowding. This will become more important to the extent that climatic and other factors become more adverse to crop production. Focusing more on which management practices can evoke the most productive and robust phenotypes from given genotypes is important for rice breeding and improvement programs since it is phenotypes that feed our human populations.

  8. Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

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    Vaishali P. Waman

    2016-08-01

    Full Text Available Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae. There are four serotypes of Dengue Virus (DENV-1 to DENV-4, each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. Methods Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. Results DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. Discussion Complete genome-based analysis

  9. A novel Gateway®-compatible binary vector allows direct selection of recombinant clones in Agrobacterium tumefaciens

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    Traore Sy

    2011-12-01

    Full Text Available Abstract Background Cloning genes into plasmid vectors is one of the key steps for studying gene function. Recently, Invitrogen™ developed a convenient Gateway® cloning system based on the site-specific DNA recombination properties of bacteriophage lambda and the cytotoxic protein ccdB, which is lethal to most E. coli strains. The ccdB protein, however, is not toxic to Agrobacterium tumefaciens, an important player often used for studying gene function in planta. This limits the direct application of the Gateway® cloning system in plant transformation-mediated research. Results In this study, we constructed a novel Gateway®-compatible destination vector, pEG101-SacB/R, by replacing the ccdB gene with a SacB-SacR gene cassette as the negative selectable marker. Conclusion Our results demonstrate that the new pEG101-SacB/R destination vector can be used for Gateway® cloning in Agrobacterium tumefaciens. pEG101-SacB/R will be a valuable tool for high-throughput functional analysis of genes in planta.

  10. Selective blockade of trypanosomatid protein synthesis by a recombinant antibody anti-Trypanosoma cruzi P2β protein.

    Science.gov (United States)

    Ayub, Maximiliano Juri; Nyambega, Benson; Simonetti, Leandro; Duffy, Tomas; Longhi, Silvia A; Gómez, Karina A; Hoebeke, Johan; Levin, Mariano J; Smulski, Cristian R

    2012-01-01

    The ribosomal P proteins are located on the stalk of the ribosomal large subunit and play a critical role during the elongation step of protein synthesis. The single chain recombinant antibody C5 (scFv C5) directed against the C-terminal region of the Trypanosoma cruzi P2β protein (TcP2β) recognizes the conserved C-terminal end of all T. cruzi ribosomal P proteins. Although this region is highly conserved among different species, surface plasmon resonance analysis showed that the scFv C5 possesses very low affinity for the corresponding mammalian epitope, despite having only one single amino-acid change. Crystallographic analysis, in silico modelization and NMR assays support the analysis, increasing our understanding on the structural basis of epitope specificity. In vitro protein synthesis experiments showed that scFv C5 was able to specifically block translation by T. cruzi and Crithidia fasciculata ribosomes, but virtually had no effect on Rattus norvegicus ribosomes. Therefore, we used the scFv C5 coding sequence to make inducible intrabodies in Trypanosoma brucei. Transgenic parasites showed a strong decrease in their growth rate after induction. These results strengthen the importance of the P protein C terminal regions for ribosomal translation activity and suggest that trypanosomatid ribosomal P proteins could be a possible target for selective therapeutic agents that could be derived from structural analysis of the scFv C5 antibody paratope.

  11. Selective blockade of trypanosomatid protein synthesis by a recombinant antibody anti-Trypanosoma cruzi P2β protein.

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    Maximiliano Juri Ayub

    Full Text Available The ribosomal P proteins are located on the stalk of the ribosomal large subunit and play a critical role during the elongation step of protein synthesis. The single chain recombinant antibody C5 (scFv C5 directed against the C-terminal region of the Trypanosoma cruzi P2β protein (TcP2β recognizes the conserved C-terminal end of all T. cruzi ribosomal P proteins. Although this region is highly conserved among different species, surface plasmon resonance analysis showed that the scFv C5 possesses very low affinity for the corresponding mammalian epitope, despite having only one single amino-acid change. Crystallographic analysis, in silico modelization and NMR assays support the analysis, increasing our understanding on the structural basis of epitope specificity. In vitro protein synthesis experiments showed that scFv C5 was able to specifically block translation by T. cruzi and Crithidia fasciculata ribosomes, but virtually had no effect on Rattus norvegicus ribosomes. Therefore, we used the scFv C5 coding sequence to make inducible intrabodies in Trypanosoma brucei. Transgenic parasites showed a strong decrease in their growth rate after induction. These results strengthen the importance of the P protein C terminal regions for ribosomal translation activity and suggest that trypanosomatid ribosomal P proteins could be a possible target for selective therapeutic agents that could be derived from structural analysis of the scFv C5 antibody paratope.

  12. A novel Gateway®-compatible binary vector allows direct selection of recombinant clones in Agrobacterium tumefaciens.

    Science.gov (United States)

    Traore, Sy Mamadou; Zhao, Bingyu

    2011-12-07

    Cloning genes into plasmid vectors is one of the key steps for studying gene function. Recently, Invitrogen™ developed a convenient Gateway® cloning system based on the site-specific DNA recombination properties of bacteriophage lambda and the cytotoxic protein ccdB, which is lethal to most E. coli strains. The ccdB protein, however, is not toxic to Agrobacterium tumefaciens, an important player often used for studying gene function in planta. This limits the direct application of the Gateway® cloning system in plant transformation-mediated research. In this study, we constructed a novel Gateway®-compatible destination vector, pEG101-SacB/R, by replacing the ccdB gene with a SacB-SacR gene cassette as the negative selectable marker. Our results demonstrate that the new pEG101-SacB/R destination vector can be used for Gateway® cloning in Agrobacterium tumefaciens. pEG101-SacB/R will be a valuable tool for high-throughput functional analysis of genes in planta.

  13. Marker-assisted selection for recognizing wheat mutant genotypes carrying HMW glutenin alleles related to baking quality.

    Science.gov (United States)

    Zamani, Mohammad Javad; Bihamta, Mohammad Reza; Naserian Khiabani, Behnam; Tahernezhad, Zahra; Hallajian, Mohammad Taher; Shamsi, Marzieh Varasteh

    2014-01-01

    Allelic diversity of HMW glutenin loci in several studies revealed that allelic combinations affect dough quality. Dx5 + Dy10 subunits are related to good baking quality and Dx2 + Dy12 are related to undesirable baking quality. One of the most regular methods to evaluate the baking quality is SDS-PAGE which is used to improve baking quality labs. Marker-assisted selection is the method which can recognize the alleles related to baking quality and this method is based on polymerase chain reaction. 10 pairs of specific primers related to Dx2, Dx2.1, Dx5, Dy10, and Dy12 subunits were used for recognizing baking quality of some wheat varieties and some mutant genotypes. Only 5 pairs of them could show the specific bands. All subunits were recognized by the primers except Dx2.1. Some of the primers were extracted from previous studies and the others were designed based on D genome subunits of wheat. SDS-PAGE method accomplished having confidence in these marker's results. To realize the effect of mutation, seed storage proteins were measured. It showed that mutation had effect on the amount of seed storage protein on the mutant seeds (which showed polymorphism).

  14. Validating a probe from GhSERK1 gene for selection of cotton genotypes with somatic embryogenic capacity.

    Science.gov (United States)

    da Cunha Soares, Taiza; da Silva, Carliane Rebeca Coelho; Chagas Carvalho, Julita Maria Frota; Cavalcanti, José Jaime Vasconcelos; de Lima, Liziane Maria; de Albuquerque Melo Filho, Péricles; Severino, Liv Soares; Dos Santos, Roseane Cavalcanti

    2018-03-20

    Substantial progress is being reported in the techniques for plant transformation, but successful regeneration of some genotypes remains a challenging step in the attempts to transform some recalcitrant species. GhSERK1 gene is involved on embryo formation, and its overexpression enhances the embryogenic competence. In this study we validate a short GhSERK1 probe in order to identify embryogenic cotton genotypes using RT-qPCR and blotting assays. Cotton genotypes with contrasting somatic embryogenic capacity were tested using in vitro procedures. High expression of transcripts was found in embryogenic genotypes, and the results were confirmed by the RT-PCR-blotting using a non-radioactive probe. The regeneration ability was confirmed in embryogenic genotypes. We confirmed that GhSERK1 can be used as marker for estimating the somatic embryogenesis ability of cotton plants. Copyright © 2018. Published by Elsevier B.V.

  15. Quasispecies theory for horizontal gene transfer and recombination

    Science.gov (United States)

    Muñoz, Enrique; Park, Jeong-Man; Deem, Michael W.

    2008-12-01

    We introduce a generalization of the parallel, or Crow-Kimura, and Eigen models of molecular evolution to represent the exchange of genetic information between individuals in a population. We study the effect of different schemes of genetic recombination on the steady-state mean fitness and distribution of individuals in the population, through an analytic field theoretic mapping. We investigate both horizontal gene transfer from a population and recombination between pairs of individuals. Somewhat surprisingly, these nonlinear generalizations of quasispecies theory to modern biology are analytically solvable. For two-parent recombination, we find two selected phases, one of which is spectrally rigid. We present exact analytical formulas for the equilibrium mean fitness of the population, in terms of a maximum principle, which are generally applicable to any permutation invariant replication rate function. For smooth fitness landscapes, we show that when positive epistatic interactions are present, recombination or horizontal gene transfer introduces a mild load against selection. Conversely, if the fitness landscape exhibits negative epistasis, horizontal gene transfer or recombination introduces an advantage by enhancing selection towards the fittest genotypes. These results prove that the mutational deterministic hypothesis holds for quasispecies models. For the discontinuous single sharp peak fitness landscape, we show that horizontal gene transfer has no effect on the fitness, while recombination decreases the fitness, for both the parallel and the Eigen models. We present numerical and analytical results as well as phase diagrams for the different cases.

  16. Empirical evaluation of selective DNA pooling to map QTL in dairy cattle using a half-sib design by comparison to individual genotyping and interval mapping

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    Robinson Nicholas

    2007-04-01

    Full Text Available Abstract This study represents the first attempt at an empirical evaluation of the DNA pooling methodology by comparing it to individual genotyping and interval mapping to detect QTL in a dairy half-sib design. The findings indicated that the use of peak heights from the pool electropherograms without correction for stutter (shadow product and preferential amplification performed as well as corrected estimates of frequencies. However, errors were found to decrease the power of the experiment at every stage of the pooling and analysis. The main sources of errors include technical errors from DNA quantification, pool construction, inconsistent differential amplification, and from the prevalence of sire alleles in the dams. Additionally, interval mapping using individual genotyping gains information from phenotypic differences between individuals in the same pool and from neighbouring markers, which is lost in a DNA pooling design. These errors cause some differences between the markers detected as significant by pooling and those found significant by interval mapping based on individual selective genotyping. Therefore, it is recommended that pooled genotyping only be used as part of an initial screen with significant results to be confirmed by individual genotyping. Strategies for improving the efficiency of the DNA pooling design are also presented.

  17. Influence of Changing Rainfall Patterns on the Yield of Rambutan (Nephelium lappaceum L. and Selection of Genotypes in Known Drought-tolerant Fruit Species for Climate Change Adaptation

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    Pablito M. Magdalita

    2015-06-01

    Full Text Available In fruit crop production, rainfall, water stress, temperature, and wind are key variables for success, and the present changes in rainfall patterns could affect the flowering and yield of the rambutan (Nephelium lappaceum L. Other fruit species like macopa (Syzygium samarangense, siniguelas (Spondias purpurea, and native santol or cotton fruit (Sandoricum koetjape remain productive despite extreme climatic changes. This study assessed the influence of rainfall on rambutan yield and evaluated and selected tree genotypes of known drought-tolerant fruit species. Rambutan yield in a selected farm in Calauan, Laguna, Philippines, dropped remarkably from 152.2 kg/tree in 2008 to 8.6 kg/tree in 2009. This reduction could be attributed to the high rainfall in April 2009 at 334.4 mm, and possibly other environmental factors like temperature, relative humidity, solar radiation, and strong wind. Furthermore, wet months in 2009 also inhibited the flowering of rambutan. However, a low yield obtained in 2010 at 45.5 kg/tree could be partly attributed to the very low rainfall in May 2010 at only 9.1 mm. On the other hand, in relation to changing climate, selection of tree genotypes for use as varieties in known drought- and flood-tolerant fruit species based on important fruit qualities like sweetness, juiciness, and high edible portion was done. Among 103 macopa genotypes, Mc-13, 43, and 91 were selected and the best (i.e. , Mc-13 had sweet (7.15 °Brix and crispy fruits weighing 49.44 g, creamy white (RHCC 155 A, and had high edible portion (EP, 93.22%. Among 114 siniguelas genotypes, Sg-41, 42 and 105 were selected and the best selection (i.e., Sg-41, had sweet (12.50 °Brix and juicy fruit weighing 20.42 g, ruby red (RHCC 59 A, and had high EP (83.27%. Among 101 native santol genotypes, Sn-47, 59, and 74 were selected and the best selection (i.e. , Sn-59 had relatively sweet (5.56 °Brix and juicy fruits weighing 51.96 g, maize yellow (RHCC 21 B, and had

  18. Accounting for Genotype-by-Environment Interactions and Residual Genetic Variation in Genomic Selection for Water-Soluble Carbohydrate Concentration in Wheat.

    Science.gov (United States)

    Ovenden, Ben; Milgate, Andrew; Wade, Len J; Rebetzke, Greg J; Holland, James B

    2018-04-16

    Abiotic stress tolerance traits are often complex and recalcitrant targets for conventional breeding improvement in many crop species. This study evaluated the potential of genomic selection to predict water-soluble carbohydrate concentration (WSCC), an important drought tolerance trait, in wheat under field conditions. A panel of 358 varieties and breeding lines constrained for maturity was evaluated under rainfed and irrigated treatments across two locations and two years. Whole-genome marker profiles and factor analytic mixed models were used to generate genomic estimated breeding values (GEBVs) for specific environments and environment groups. Additive genetic variance was smaller than residual genetic variance for WSCC, such that genotypic values were dominated by residual genetic effects rather than additive breeding values. As a result, GEBVs were not accurate predictors of genotypic values of the extant lines, but GEBVs should be reliable selection criteria to choose parents for intermating to produce new populations. The accuracy of GEBVs for untested lines was sufficient to increase predicted genetic gain from genomic selection per unit time compared to phenotypic selection if the breeding cycle is reduced by half by the use of GEBVs in off-season generations. Further, genomic prediction accuracy depended on having phenotypic data from environments with strong correlations with target production environments to build prediction models. By combining high-density marker genotypes, stress-managed field evaluations, and mixed models that model simultaneously covariances among genotypes and covariances of complex trait performance between pairs of environments, we were able to train models with good accuracy to facilitate genetic gain from genomic selection. Copyright © 2018, G3: Genes, Genomes, Genetics.

  19. Using artificial neural networks to select upright cowpea (Vigna unguiculata) genotypes with high productivity and phenotypic stability.

    Science.gov (United States)

    Barroso, L M A; Teodoro, P E; Nascimento, M; Torres, F E; Nascimento, A C C; Azevedo, C F; Teixeira, F R F

    2016-11-03

    Cowpea (Vigna unguiculata) is grown in three Brazilian regions: the Midwest, North, and Northeast, and is consumed by people on low incomes. It is important to investigate the genotype x environment (GE) interaction to provide accurate recommendations for farmers. The aim of this study was to identify cowpea genotypes with high adaptability and phenotypic stability for growing in the Brazilian Cerrado, and to compare the use of artificial neural networks with the Eberhart and Russell (1966) method. Six trials with upright cowpea genotypes were conducted in 2005 and 2006 in the States of Mato Grosso do Sul and Mato Grosso. The data were subjected to adaptability and stability analysis by the Eberhart and Russell (1966) method and artificial neural networks. The genotypes MNC99-537F-4 and EVX91-2E-2 provided grain yields above the overall environment means, and exhibited high stability according to both methods. Genotype IT93K-93-10 was the most suitable for unfavorable environments. There was a high correlation between the results of both methods in terms of classifying the genotypes by their adaptability and stability. Therefore, this new approach would be effective in quantifying the GE interaction in upright cowpea breeding programs.

  20. Effects of acute dopamine precusor depletion on immediate reward selection bias and working memory depend on catechol-O-methyltransferase genotype.

    Science.gov (United States)

    Kelm, Mary Katherine; Boettiger, Charlotte A

    2013-12-01

    Little agreement exists as to acute dopamine (DA) manipulation effects on intertemporal choice in humans. We previously found that catechol-O-methyltransferase (COMT) Val158Met genotype predicts individual differences in immediate reward selection bias among adults. Moreover, we and others have shown that the relationship between COMT genotype and immediate reward bias is inverted in adolescents. No previous pharmacology studies testing DA manipulation effects on intertemporal choice have accounted for COMT genotype, and many have included participants in the adolescent age range (18-21 years) as adults. Moreover, many studies have included female participants without strict cycle phase control, although recent evidence demonstrates that cyclic estradiol elevations interact with COMT genotype to affect DA-dependent cognition. These factors may have interacted with DA manipulations in past studies, potentially occluding detection of effects. Therefore, we predicted that, among healthy male adults (ages 22-40 years), frontal DA tone, as indexed by COMT genotype, would interact with acute changes in DA signaling to affect intertemporal choice. In a double-blind, placebo-controlled design, we decreased central DA via administration of an amino acid beverage deficient in the DA precursors, phenylalanine and tyrosine, and tested effects on immediate reward bias in a delay-discounting (DD) task and working memory (WM) in an n-back task. We found no main effect of beverage on DD or WM performance but did find significant beverage*genotype effects. These results suggest that the effect of DA manipulations on DD depends on individual differences in frontal DA tone, which may have impeded some past efforts to characterize DA's role in immediate reward bias in humans.

  1. Multiple genomic recombination events in the evolution of saffold cardiovirus.

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    Lili Ren

    Full Text Available BACKGROUND: Saffold cardiovirus (SAFV is a new human cardiovirus with 11 identified genotypes. Little is known about the natural history and pathogenicity of SAFVs. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced the genome of five SAFV-1 strains which were identified from fecal samples taken from children with viral diarrhea in Beijing, China between March 2006 and November 2007, and analyzed the phylogenetic and phylodynamic properties of SAFVs using the genome sequences of every known SAFV genotypes. We identified multiple recombination events in our SAFV-1 strains, specifically recombination between SAFV-2, -3, -4, -9, -10 and the prototype SAFV-1 strain in the VP4 region and recombination between SAFV-4, -6, -8, -10, -11 and prototype SAFV-1 in the VP1/2A region. Notably, recombination in the structural gene VP4 is a rare event in Cardiovirus. The ratio of nonsynonymous substitutions to synonymous substitutions indicates a purifying selection of the SAFV genome. Phylogenetic and molecular clock analysis indicates the existence of at least two subclades of SAFV-1 with different origins. Subclade 1 includes two strains isolated from Pakistan, whereas subclade 2 includes the prototype strain and strains isolated in China, Pakistan, and Afghanistan. The most recent common ancestor of all SAFV genotypes dates to the 1710s, and SAFV-1, -2, and -3 to the 1940s, 1950s, and 1960s, respectively. No obvious relationship between variation and pathogenicity exists in the critical domains of the CD and EF loops of viral capsid proteins or the multi-functional proteins L based on amino acid sequence identity comparison between SAFV genotypes. CONCLUSIONS/SIGNIFICANCE: Our findings suggest that intertypic recombination plays an important role in the diversity of SAFVs, highlighting the diversity of the five strains with the previously described SAFV-1 strains.

  2. Sex in a test tube: testing the benefits of in vitro recombination.

    Science.gov (United States)

    Pesce, Diego; Lehman, Niles; de Visser, J Arjan G M

    2016-10-19

    The origin and evolution of sex, and the associated role of recombination, present a major problem in biology. Sex typically involves recombination of closely related DNA or RNA sequences, which is fundamentally a random process that creates but also breaks up beneficial allele combinations. Directed evolution experiments, which combine in vitro mutation and recombination protocols with in vitro or in vivo selection, have proved to be an effective approach for improving functionality of nucleic acids and enzymes. As this approach allows extreme control over evolutionary conditions and parameters, it also facilitates the detection of small or position-specific recombination benefits and benefits associated with recombination between highly divergent genotypes. Yet, in vitro approaches have been largely exploratory and motivated by obtaining improved end products rather than testing hypotheses of recombination benefits. Here, we review the various experimental systems and approaches used by in vitro studies of recombination, discuss what they say about the evolutionary role of recombination, and sketch their potential for addressing extant questions about the evolutionary role of sex and recombination, in particular on complex fitness landscapes. We also review recent insights into the role of 'extracellular recombination' during the origin of life.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).

  3. Selection individual on mutant genotype of soybean (Glycine maxl.merrill) in m5 generation based on resistance of stem rot disease Athelia rolfsii (curzi)

    Science.gov (United States)

    Rahmah, M.; Hanafiah, D. S.; Siregar, L. A. M.; Safni, I.

    2018-02-01

    This study was aimed to obtain selected individuals on soybean plant Glycine max L. (Merrill) in M5 generation based on high production character and tolerance of stem rot disease Athelia rolfsii (Curzi). This research was conducted in Plant Disease Laboratory and experimental field Faculty of Agriculture Universitas Sumatera Utara Medan, Indonesia. This research was conducted from December 2016 to June 2017. The treatments were 15 mutant lines genotypes and Anjasmoro variety. The results showed that some lines mutant genotypes can gave the good agronomic appearance character than Anjasmoro variety on inoculation treatment of stem rot disease. Selection performed on population M5 producesselected individuals with tolerance of stem rot disease from 100 and 200 Gy population.

  4. Evidence of recombination in natural populations of hepatitis A virus

    International Nuclear Information System (INIS)

    Costa-Mattioli, Mauro; Ferre, Virginie; Casane, Didier; Perez-Bercoff, Raoul; Coste-Burel, Marianne; Imbert-Marcille, Berthe-Marie; Andre, Elisabeth Claude Monique; Bressollette-Bodin, Celine; Billaudel, Sylviane; Cristina, Juan

    2003-01-01

    Genetic analysis of selected genome regions of hepatitis A virus (HAV) suggested that distinct genotypes of HAV could be found in different geographical regions. At least seven HAV genotypes have been identified all over the world, including four human genotypes (I, II, III, and VII) and three simian strains (IV, V, and VI). Phylogenetic analysis using full-length VP1 sequences revealed that human strain 9F94 has a close genetic relation with strain SLF-88 (sub-genotype VII). Nevertheless, the same analysis using full-length VP2 or VP3 sequences revealed that strain 9F94 has a close genetic relation with strain MBB (sub-genotype IB). To test the possibility of genetic recombination, phylogenetic studies were carried out, revealing that a crossing over had taken place in the VP1 capsid protein. These findings indicate that capsid-recombination can play a significant role in shaping the genetic diversity of HAV and, as such, can have important implications for its evolution, biology, and control

  5. The promastigote surface antigen gene family of the Leishmania parasite: differential evolution by positive selection and recombination.

    Science.gov (United States)

    Devault, Alain; Bañuls, Anne-Laure

    2008-10-24

    PSA (promastigote surface antigen) is one of the major classes of membrane proteins present at the surface of the parasitic protozoan Leishmania. While it harbours leucine rich repeats, which are suggestive of its involvement in parasite-to-host physical interactions, its exact role is largely unknown. Furthermore, the extent of diversity of this gene family, both in copy number and sequence has not been established. From the newly available complete genome sequences of L. major, L. infantum and L. braziliensis, we have established the complete list of PSA genes, based on the conservation of specific domain architecture. The latter includes an array of leucine rich repeats of unique signature flanked by conserved cysteine-rich domains. All PSA genes code either for secreted or membrane-anchored surface proteins. Besides the few previously identified PSA genes, which are shown here to be part of a relatively large subclass of PSA genes located on chromosome 12, this study identifies seven other PSA subtypes. The latter, whose genes lie on chromosomes 5, 9, 21 and 31 in all three species, form single gene (two genes in one instance) subfamilies, which phylogenetically cluster as highly related orthologs. On the other hand, genes found on chromosome 12 generally show high diversification, as reflected in greater sequence divergence between species, and in an extended set of divergent paralogs. Moreover, we show that the latter genes are submitted to strong positive selection. We also provide evidence that evolution of these genes is driven by intra- and intergenic recombination, thereby modulating the number of LRRs in protein and generating chimeric genes. PSA is a Leishmania family of membrane-bound or secreted proteins, whose main signature consists in a specific LRR sequence. All PSA genes found in the genomes of three sequenced Leishmania species unambiguously distribute into eight subfamilies of orthologs. Seven of these are evolving relatively slowly and could

  6. The promastigote surface antigen gene family of the Leishmania parasite: differential evolution by positive selection and recombination

    Directory of Open Access Journals (Sweden)

    Bañuls Anne-Laure

    2008-10-01

    Full Text Available Abstract Background PSA (promastigote surface antigen is one of the major classes of membrane proteins present at the surface of the parasitic protozoan Leishmania. While it harbours leucine rich repeats, which are suggestive of its involvement in parasite-to-host physical interactions, its exact role is largely unknown. Furthermore, the extent of diversity of this gene family, both in copy number and sequence has not been established. Results From the newly available complete genome sequences of L. major, L. infantum and L. braziliensis, we have established the complete list of PSA genes, based on the conservation of specific domain architecture. The latter includes an array of leucine rich repeats of unique signature flanked by conserved cysteine-rich domains. All PSA genes code either for secreted or membrane-anchored surface proteins. Besides the few previously identified PSA genes, which are shown here to be part of a relatively large subclass of PSA genes located on chromosome 12, this study identifies seven other PSA subtypes. The latter, whose genes lie on chromosomes 5, 9, 21 and 31 in all three species, form single gene (two genes in one instance subfamilies, which phylogenetically cluster as highly related orthologs. On the other hand, genes found on chromosome 12 generally show high diversification, as reflected in greater sequence divergence between species, and in an extended set of divergent paralogs. Moreover, we show that the latter genes are submitted to strong positive selection. We also provide evidence that evolution of these genes is driven by intra- and intergenic recombination, thereby modulating the number of LRRs in protein and generating chimeric genes. Conclusion PSA is a Leishmania family of membrane-bound or secreted proteins, whose main signature consists in a specific LRR sequence. All PSA genes found in the genomes of three sequenced Leishmania species unambiguously distribute into eight subfamilies of orthologs

  7. Evaluation of the Abbott realtime HCV genotype II RUO (GT II) assay with reference to 5'UTR, core and NS5B sequencing.

    Science.gov (United States)

    Mallory, Melanie A; Lucic, Danijela X; Sears, Mitchell T; Cloherty, Gavin A; Hillyard, David R

    2014-05-01

    HCV genotyping is a critical tool for guiding initiation of therapy and selecting the most appropriate treatment regimen. To evaluate the concordance between the Abbott GT II assay and genotyping by sequencing subregions of the HCV 5'UTR, core and NS5B. The Abbott assay was used to genotype 127 routine patient specimens and 35 patient specimens with unusual subtypes and mixed infection. Abbott results were compared to genotyping by 5'UTR, core and NS5B sequencing. Sequences were genotyped using the NCBI non-redundant database and the online genotyping tool COMET. Among routine specimens, core/NS5B sequencing identified 93 genotype 1s, 13 genotype 2s, 15 genotype 3s, three genotype 4s, two genotype 6s and one recombinant specimen. Genotype calls by 5'UTR, core, NS5B sequencing and the Abbott assay were 97.6% concordant. Core/NS5B sequencing identified two discrepant samples as genotype 6 (subtypes 6l and 6u) while Abbott and 5'UTR sequencing identified these samples as genotype 1 with no subtype. The Abbott assay subtyped 91.4% of genotype 1 specimens. Among the 35 rare specimens, the Abbott assay inaccurately genotyped 3k, 6e, 6o, 6q and one genotype 4 variant; gave indeterminate results for 3g, 3h, 4r, 6m, 6n, and 6q specimens; and agreed with core/NS5B sequencing for mixed specimens. The Abbott assay is an automated HCV genotyping method with improved accuracy over 5'UTR sequencing. Samples identified by the Abbott assay as genotype 1 with no subtype may be rare subtypes of other genotypes and thus require confirmation by another method. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Selection of Wheat Mutant Genotypes Carrying HMW Glutenin Alleles Related to Baking Quality by Using PCR (STS Method)

    International Nuclear Information System (INIS)

    Zamani, M.J.; Bihamta, M.R.; Khiabani, B.N.; Hallajian, M.T.

    2009-01-01

    This study was performed in the Agriculture, Medicine and Industry Research School, Nuclear Science and Technology Research Institute of Iran in 2005-2006, through Polymerase Chain Reaction by using Sequence Tagged Site (STS) method, to characterize in terms of bread quality of some wheat mutant genotypes (Roshan, Omid, Tabasi, Azar and Azadi), their parents and other cultivars such as Chamran, Enia, Bezostaya, Tajan, Pishtaz and Chinese spring. Twelve pairs of primers were used in this study; seven of them were extracted from the literature and the others were designed from the D genome subunites sequences of wheat. Some studies on drought resistance, salt resistance, etc., have been done for these mutant genotypes, some of them showing good results. However, their baking quality has not been studied before. The alleles Dx2+Dy12 (with negative effect on bread quality) and Dx2*, Dx5+Dy10 (with positive effect on bread quality) had the main effect on wheat bread quality. Special primers of these subunits were used to amplify these alleles. Except for the cultivars that had Dx5+Dx10, six mutant genotypes whose parents did not have these alleles (T-66-58-60, Ro-5, Ro-4, Ro-3, Ro-1 and O-64-1-10), showed Dx5+Dx10. SDS-PAGE analyses showed no contradictory results with molecular experiments. Significant differences were seen on protein percentage for polymorphic mutant genotypes, Ro-1 , Ro-3 and Ro-5 with Roshan (their parent), at 1% probability level. (author)

  9. Recombination in hepatitis C virus.

    Science.gov (United States)

    González-Candelas, Fernando; López-Labrador, F Xavier; Bracho, María Alma

    2011-10-01

    Hepatitis C virus (HCV) is a Flavivirus with a positive-sense, single-stranded RNA genome of about 9,600 nucleotides. It is a major cause of liver disease, infecting almost 200 million people all over the world. Similarly to most RNA viruses, HCV displays very high levels of genetic diversity which have been used to differentiate six major genotypes and about 80 subtypes. Although the different genotypes and subtypes share basic biological and pathogenic features they differ in clinical outcomes, response to treatment and epidemiology. The first HCV recombinant strain, in which different genome segments derived from parentals of different genotypes, was described in St. Petersburg (Russia) in 2002. Since then, there have been only a few more than a dozen reports including descriptions of HCV recombinants at all levels: between genotypes, between subtypes of the same genotype and even between strains of the same subtype. Here, we review the literature considering the reasons underlying the difficulties for unequivocally establishing recombination in this virus along with the analytical methods necessary to do it. Finally, we analyze the potential consequences, especially in clinical practice, of HCV recombination in light of the coming new therapeutic approaches against this virus.

  10. Epigenetic silencing of V(DJ recombination is a major determinant for selective differentiation of mucosal-associated invariant t cells from induced pluripotent stem cells.

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    Yutaka Saito

    Full Text Available Mucosal-associated invariant T cells (MAITs are innate-like T cells that play a pivotal role in the host defense against infectious diseases, and are also implicated in autoimmune diseases, metabolic diseases, and cancer. Recent studies have shown that induced pluripotent stem cells (iPSCs derived from MAITs selectively redifferentiate into MAITs without altering their antigen specificity. Such a selective differentiation is a prerequisite for the use of MAITs in cell therapy and/or regenerative medicine. However, the molecular mechanisms underlying this phenomenon remain unclear. Here, we performed methylome and transcriptome analyses of MAITs during the course of differentiation from iPSCs. Our multi-omics analyses revealed that recombination-activating genes (RAG1 and RAG2 and DNA nucleotidylexotransferase (DNTT were highly methylated with their expression being repressed throughout differentiation. Since these genes are essential for V(DJ recombination of the T cell receptor (TCR locus, this indicates that nascent MAITs are kept from further rearrangement that may alter their antigen specificity. Importantly, we found that the repression of RAGs was assured in two layers: one by the modulation of transcription factors for RAGs, and the other by DNA methylation at the RAG loci. Together, our study provides a possible explanation for the unaltered antigen specificity in the selective differentiation of MAITs from iPSCs.

  11. Number of recombinations and genetic properties of a maize population undergoing recurrent selection Número de recombinações e as propriedades genéticas de uma população de milho sob seleção recorrente

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    Francisco Pinheiro Lima Neto

    2009-02-01

    Full Text Available In maize recurrent selection programs, selected genotypes were recombined once to generate genetic variability for the next selection cycle. Selection generates negative gametic phase disequilibrium which reduces genetic variances, and this disequilibrium is not significantly reduced with only one generation of recombination. The objective of this research was to assess the effects of one additional generation of recombination on phenotypic and genotypic parameters in a maize population undergoing recurrent selection. Selected progenies of the EPB-4 population were subjected to one and two generations of recombination, and from each generation half- and full-sib progenies were developed and evaluated at three environments for grain yield, plant and ear heights, prolificacy, and ear placement. There were no significant changes between each progeny type with one and two generations of recombination for the means, ranges, phenotypic distribution of the traits, genetic variances, heritability coefficients, and genetic correlations for the traits assessed. The results suggest that an additional generation of recombination will not increase the effectiveness of maize recurrent selection programs.Nos programas de seleção recorrente, os genótipos selecionados são recombinados uma vez para gerar variabilidade genética para o próximo ciclo de seleção. A seleção gera desequilíbrio negativo na fase gamética, reduzindo as variâncias genéticas, e este desequilíbrio não é significantemente reduzido com apenas uma geração de recombinação. O objetivo desta pesquisa foi avaliar os efeitos de uma geração adicional de recombinação sobre parâmetros fenotípicos e genéticos em uma população de milho submetida à seleção recorrente. Progênies selecionadas da população EPB-4 foram recombinadas por uma e duas gerações, e de cada geração foram obtidas progênies de meios-irmãos e de irmãos germanos, as quais foram avaliadas em tr

  12. A novel prokaryotic vector for identification and selection of recombinants: Direct use of the vector for expression studies in E. coli

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    Apte-Deshpande Anjali

    2010-05-01

    Full Text Available Abstract Background The selection of bacterial recombinants that harbour a desired insert, has been a key factor in molecular cloning and a series of screening procedures need to be performed for selection of clones carrying the genes of interest. The conventional cloning techniques are reported to have problems such as screening high number of colonies, generation of false positives, setting up of control ligation mix with vector alone etc. Results We describe the development of a novel dual cloning/expression vector, which enables to screen the recombinants directly and expression of the gene of interest. The vector contains Green fluorescence protein (GFP as the reporter gene and is constructed in such a way that the E. coli cells upon transformation with this vector does not show any fluorescence, but readily fluoresce upon insertion of a foreign gene of interest. The same construct could be easily used for screening of the clones and expression studies by mere switching to specific hosts. Conclusions This is the first vector reported that takes the property of colour or fluorescence to be achieved only upon cloning while all the other vectors available commercially show loss of colour or loss of fluorescence upon cloning. As the fluorescence of GFP depends on the solubility of the protein, the intensity of the fluorescence would also indicate the extent of solubility of the expressed target protein.

  13. Proteomic analysis of CHO cell lines producing high and low quantities of a recombinant antibody before and after selection with methotrexate.

    Science.gov (United States)

    Hausmann, Ruth; Chudobová, Ivana; Spiegel, Holger; Schillberg, Stefan

    2018-01-10

    High levels of recombinant protein production in Chinese hamster ovary (CHO) cells can be achieved by amplification of transgenes using the dihydrofolate reductase/methotrexate (DHFR/MTX) system. With the aim to identify predictive markers enabling the preselection of suitable high producing clones we investigated the impact of MTX-based gene amplification on two CHO cells lines producing different levels of a human monoclonal antibody by carrying out a comparative proteome analysis. The difference in antibody yield between the high and low producer was 15-fold before and 245-fold after MTX selection. Difference in-gel electrophoresis of samples from before and after MTX selection revealed 17 unique proteins that were differentially expressed between the high and low productivity lines. Of these, five proteins were differently expressed before MTX selection, representing potential markers for productivity prior to selection and for engineering processes to generate novel CHO cell line with the desirable high productivity phenotype. Fifteen proteins were differently expressed between high and low producer after MTX selection. We further found that MTX selection induced more changes in the proteome of the low producer compared to the high producer. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Influence of genotype, cultivation system and irrigation regime on antioxidant capacity and selected phenolics of blueberries (Vaccinium corymbosum L.).

    Science.gov (United States)

    Cardeñosa, Vanessa; Girones-Vilaplana, Amadeo; Muriel, José Luis; Moreno, Diego A; Moreno-Rojas, José M

    2016-07-01

    Demand for and availability of blueberries has increased substantially over recent years, driven in part by their health-promoting properties. Three blueberry varieties ('Rocío', V2, and V3) were grown under two cultivation systems (open-field and plastic tunnels) and subjected to two irrigations regimes (100% and 80% of crop evapotranspiration) in two consecutive years (2011-2012). They were evaluated for their phytochemical composition and antioxidant capacity. Genotype influenced the antioxidant capacity and the content of the three groups of phenolics in the blueberries. The antioxidant activity and total flavonols content increased when the blueberries were grown under open-field conditions. Deficit irrigation conditions led to additional positive effects on their phenolics (delphinidn-3-acetilhexoside content was increased under plastic tunnel with deficit irrigation). In conclusion, the amount of phenolic compounds and the antioxidant capacity of blueberries were not negatively affected by water restriction; Moreover, several changes were recorded due to growing system and genotype. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. The HLA-DQ2 genotype selects for early intestinal microbiota composition in infants at high risk of developing coeliac disease.

    Science.gov (United States)

    Olivares, M; Neef, A; Castillejo, G; Palma, G De; Varea, V; Capilla, A; Palau, F; Nova, E; Marcos, A; Polanco, I; Ribes-Koninckx, C; Ortigosa, L; Izquierdo, L; Sanz, Y

    2015-03-01

    Intestinal dysbiosis has been associated with coeliac disease (CD), but whether the alterations are cause or consequence of the disease is unknown. This study investigated whether the human leukocyte antigen (HLA)-DQ2 genotype is an independent factor influencing the early gut microbiota composition of healthy infants at family risk of CD. As part of a larger prospective study, a subset (n=22) of exclusively breastfed and vaginally delivered infants with either high genetic risk (HLA-DQ2 carriers) or low genetic risk (non-HLA-DQ2/8 carriers) of developing CD were selected from a cohort of healthy infants with at least one first-degree relative with CD. Infant faecal microbiota was analysed by 16S rRNA gene pyrosequencing and real time quantitative PCR. Infants with a high genetic risk had significantly higher proportions of Firmicutes and Proteobacteria and lower proportions of Actinobacteria compared with low-risk infants. At genus level, high-risk infants had significantly less Bifidobacterium and unclassified Bifidobacteriaceae proportions and more Corynebacterium, Gemella, Clostridium sensu stricto, unclassified Clostridiaceae, unclassified Enterobacteriaceae and Raoultella proportions. Quantitative real time PCR also revealed lower numbers of Bifidobacterium species in infants with high genetic risk than in those with low genetic risk. In high-risk infants negative correlations were identified between Bifidobacterium species and several genera of Proteobacteria (Escherichia/Shigella) and Firmicutes (Clostridium). The genotype of infants at family risk of developing CD, carrying the HLA-DQ2 haplotypes, influences the early gut microbiota composition. This finding suggests that a specific disease-biased host genotype may also select for the first gut colonisers and could contribute to determining disease risk. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  16. Genetic variability, associations, and path analysis of chemical and morphological traits in Indian ginseng [Withania somnifera (L. Dunal] for selection of higher yielding genotypes

    Directory of Open Access Journals (Sweden)

    Abhilasha Srivastava

    2018-04-01

    Full Text Available Background: The study was carried out to assess the genetic variability present in ashwagandha and to examine the nature of associations of various traits to the root yield of the plant. Methods: Fifty-three diverse genetic stocks of ashwagandha (Withania somnifera were evaluated for 14 quantitative characteristics. Analysis of variance, correlation, and path coefficient analysis were performed using the mean data of 2 years. Results: Analysis of variance revealed that the genotypes differed significantly for all characteristics studied. High heritability in conjunction with high genetic advance was observed for fresh root weight, 12 deoxywithastramonolide in roots, and plant height, which indicated that selection could be effective for these traits. Dry root weight has a tight linkage with plant height and fresh root weight. Further, in path coefficient analysis, fresh root weight, total alkaloid (% in leaves, and 12 deoxywithastramonolide (% in roots had the highest positive direct effect on dry root weight. Conclusion: Therefore, these characteristics can be exploited to improve dry root weight in ashwagandha genotypes and there is also scope for the selection of promising and specific chemotypes (based on the alkaloid content from the present germplasm. Keywords: ashwagandha, direct effect, genetic advance, heritability, path coefficient

  17. Phenotypic and genotypic screening of rice genotypes at seedling ...

    African Journals Online (AJOL)

    Selection for salinity tolerance genotypes of rice based on phenotypic performance alone is less reliable and will delay progress in breeding. Recent advent of molecular markers, microsatellites or simple sequence repeats (SSRs) are used to find out salt tolerant rice genotypes. Three selected SSR markers; RM7075, ...

  18. pheS*, an effective host-genotype-independent counter-selectable marker for marker-free chromosome deletion in Bacillus amyloliquefaciens.

    Science.gov (United States)

    Zhou, Chaoyang; Shi, Lingling; Ye, Bin; Feng, Haichao; Zhang, Ji; Zhang, Ruifu; Yan, Xin

    2017-01-01

    Aside from applications in the production of commercial enzymes and metabolites, Bacillus amyloliquefaciens is also an important group of plant growth-promoting rhizobacteria that supports plant growth and suppresses phytopathogens. A host-genotype-independent counter-selectable marker would enable rapid genetic manipulation and metabolic engineering, accelerating the study of B. amyloliquefaciens and its development as both a microbial cell factory and plant growth-promoting rhizobacteria. Here, a host-genotype-independent counter-selectable marker pheS * was constructed through a point mutation of the gene pheS, which encodes the α-subunit of phenylalanyl-tRNA synthetase in Bacillus subtilis strain 168. In the presence of 5 mM p-chloro-phenylalanine, 100 % of B. amyloliquefaciens strain SQR9 cells carrying pheS * were killed, whereas the wild-type strain SQR9 showed resistance to p-chloro-phenylalanine. A simple pheS * and overlap-PCR-based strategy was developed to create the marker-free deletion of the amyE gene as well as a 37-kb bmy cluster in B. amyloliquefaciens SQR9. The effectiveness of pheS * as a counter-selectable marker in B. amyloliquefaciens was further confirmed through the deletion of amyE genes in strains B. amyloliquefaciens FZB42 and NJN-6. In addition, the potential use of pheS * in other Bacillus species was preliminarily assessed. The expression of PheS * in B. subtilis strain 168 and B. cereus strain ATCC 14579 caused pronounced sensitivity of both hosts to p-chloro-phenylalanine, indicating that pheS * could be used as a counter-selectable marker (CSM) in these strains.

  19. Quick survey for detection, identification and characterization of Acanthamoeba genotypes from some selected soil and water samples in Pakistan

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    Tania Tanveer

    2015-05-01

    Full Text Available Acanthamoeba is an opportunistic protozoan pathogen which is widely distributed in nature and plays a pivotal role in ecosystem. Acanthamoeba species may cause blinding keratitis and fatal granulomatous encephalitis involving central nervous system. In this study, we investigated the presence of Acanthamoeba in soil and water resources of Pakistan. Here, Acanthamoeba were recovered on non-nutrient agar plate lawn with E.coli and identified by morphological characteristics of the cyst. Furthermore PCR was performed with genus-specific primers followed by direct sequencing of the PCR product for molecular identification. Overall our PCR and sequencing results confirmed pathogenic genotypes including T4 and T15 from both soil and water samples. This is our first report of Acanthamoeba isolation from both soil and water resources of Pakistan which may serve as a potential treat to human health across the country.

  20. Quick survey for detection, identification and characterization of Acanthamoeba genotypes from some selected soil and water samples across Pakistan.

    Science.gov (United States)

    Tanveer, Tania; Hameed, Abdul; Gul, Asma; Matin, Abdul

    2015-01-01

    Acanthamoeba is an opportunistic protozoan pathogen which is widely distributed in nature and plays a pivotal role in ecosystem. Acanthamoeba species may cause blinding keratitis and fatal granulomatous encephalitis involving central nervous system. In this study, we investigated the presence of Acanthamoeba in soil and water resources of Pakistan. Here, Acanthamoeba were recovered on non-nutrient agar plate lawn with E. coli and identified by morphological characteristics of the cyst. Furthermore PCR was performed with genus-specific primers followed by direct sequencing of the PCR product for molecular identification. Overall our PCR and sequencing results confirmed pathogenic genotypes including T4 and T15 from both soil and water samples. This is our first report of Acanthamoeba isolation from both soil and water resources of Pakistan which may serve as a potential treat to human health across the country.

  1. Characterization of a recombinant humanized anti-cocaine monoclonal antibody produced from multiple clones for the selection of a master cell bank candidate.

    Science.gov (United States)

    Wetzel, Hanna N; Webster, Rose P; Saeed, Fatima O; Kirley, Terence L; Ball, William J; Norman, Andrew B

    2017-06-03

    We have generated a humanized anti-cocaine monoclonal antibody (mAb), which is at an advanced stage of pre-clinical development. We report here in vitro binding affinity studies, and in vivo pharmacokinetic and efficacy studies of the recombinant mAb. The overall aim was to characterize the recombinant antibody from each of the three highest producing transfected clones and to select one to establish a master cell bank. In mAb pharmacokinetic studies, after injection with h2E2 (120 mg/kg iv) blood was collected from the tail tip of mice over 28 days. Antibody concentrations were quantified using ELISA. The h2E2 concentration as a function of time was fit using a two-compartment pharmacokinetic model. To test in vivo efficacy, mice were injected with h2E2 (120 mg/kg iv), then one hour later injected with an equimolar dose of cocaine. Blood and brain were collected 5 min after cocaine administration. Cocaine concentrations were quantified using LC/MS. The affinity of the antibody for cocaine was determined using a [ 3 H] cocaine binding assay. All three antibodies had long elimination half-lives, 2-5 nM Kd for cocaine, and prevented cocaine's entry into the brain by sequestering it in the plasma. Pharmacokinetic and radioligand binding assays supported designation of the highest producing clone 85 as the master cell bank candidate. Overall, the recombinant h2E2 showed favorable binding properties, pharmacokinetics, and in vivo efficacy. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Cydia pomonella granulovirus Genotypes Overcome Virus Resistance in the Codling Moth and Improve Virus Efficiency by Selection against Resistant Hosts▿

    Science.gov (United States)

    Berling, Marie; Blachere-Lopez, Christine; Soubabere, Olivier; Lery, Xavier; Bonhomme, Antoine; Sauphanor, Benoît; Lopez-Ferber, Miguel

    2009-01-01

    Cydia pomonella granulovirus (CpGV) has been used for 15 years as a bioinsecticide in codling moth (Cydia pomonella) control. In 2004, some insect populations with low susceptibility to the virus were detected for the first time in southeast France. RGV, a laboratory colony of codling moths resistant to the CpGV-M isolate used in the field, was established with collection of resistant insects in the field followed by an introgression of the resistant trait into a susceptible colony (Sv). The resistance level (based on the 50% lethal concentrations [LC50s]) of the RGV colony to the CpGV-M isolate, the active ingredient in all commercial virus formulations in Europe, appeared to be over 60,000-fold compared to the Sv colony. The efficiency of CpGV isolates from various other regions was tested on RGV. Among them, two isolates (I12 and NPP-R1) presented an increased pathogenicity on RGV. I12 had already been identified as effective against a resistant C. pomonella colony in Germany and was observed to partially overcome the resistance in the RGV colony. The recently identified isolate NPP-R1 showed an even higher pathogenicity on RGV than other isolates, with an LC50 of 166 occlusion bodies (OBs)/μl, compared to 1.36 × 106 OBs/μl for CpGV-M. Genetic characterization showed that NPP-R1 is a mixture of at least two genotypes, one of which is similar to CpGV-M. The 2016-r4 isolate obtained from four successive passages of NPP-R1 in RGV larvae had a sharply reduced proportion of the CpGV-M-like genotype and an increased pathogenicity against insects from the RGV colony. PMID:19114533

  3. Cydia pomonella granulovirus genotypes overcome virus resistance in the codling moth and improve virus efficiency by selection against resistant hosts.

    Science.gov (United States)

    Berling, Marie; Blachere-Lopez, Christine; Soubabere, Olivier; Lery, Xavier; Bonhomme, Antoine; Sauphanor, Benoît; Lopez-Ferber, Miguel

    2009-02-01

    Cydia pomonella granulovirus (CpGV) has been used for 15 years as a bioinsecticide in codling moth (Cydia pomonella) control. In 2004, some insect populations with low susceptibility to the virus were detected for the first time in southeast France. RGV, a laboratory colony of codling moths resistant to the CpGV-M isolate used in the field, was established with collection of resistant insects in the field followed by an introgression of the resistant trait into a susceptible colony (Sv). The resistance level (based on the 50% lethal concentrations [LC(50)s]) of the RGV colony to the CpGV-M isolate, the active ingredient in all commercial virus formulations in Europe, appeared to be over 60,000-fold compared to the Sv colony. The efficiency of CpGV isolates from various other regions was tested on RGV. Among them, two isolates (I12 and NPP-R1) presented an increased pathogenicity on RGV. I12 had already been identified as effective against a resistant C. pomonella colony in Germany and was observed to partially overcome the resistance in the RGV colony. The recently identified isolate NPP-R1 showed an even higher pathogenicity on RGV than other isolates, with an LC(50) of 166 occlusion bodies (OBs)/microl, compared to 1.36 x 10(6) OBs/microl for CpGV-M. Genetic characterization showed that NPP-R1 is a mixture of at least two genotypes, one of which is similar to CpGV-M. The 2016-r4 isolate obtained from four successive passages of NPP-R1 in RGV larvae had a sharply reduced proportion of the CpGV-M-like genotype and an increased pathogenicity against insects from the RGV colony.

  4. Genetic Recombination

    Science.gov (United States)

    Whitehouse, H. L. K.

    1973-01-01

    Discusses the mechanisms of genetic recombination with particular emphasis on the study of the fungus Sordaria brevicollis. The study of recombination is facilitated by the use of mutants of this fungus in which the color of the ascospores is affected. (JR)

  5. Seletividade de herbicidas a genótipos de cana-de-açúcar Herbicide selectivity to sugarcane genotypes

    Directory of Open Access Journals (Sweden)

    L Galon

    2009-12-01

    a variation between sugarcane genotypes regarding herbicide tolerance. This work evaluated the tolerance of three genotypes to the herbicides ametryn, trifloxysulfuron-sodium and their commercial formulated mixture in 0.0, 0.5, 1.0 and 3.0 times the recommended commercial dose. The experiment was conducted under protected environmental conditions. A completely randomized design was used, with four replications. The treatments were composed by genotypes SP80-1816, RB855113, RB867515 associated to herbicides ametryn, trifloxysulfuron-sodium and sodium-ametryn + trifloxysulfuron, at doses of 0, 0.5, 1.0 and 3.0 times the recommended commercial dose. Intoxication of the plants (% was assessed at 14, 28 and 42 days after application of the herbicides (DAT. The other variables measured at 80 days after crop emergence were leaf area and shoot dry matter. In general, the genotypes SP80-1816 and RB855113 were less tolerant to the herbicides ametryn, trifloxysulfuron- sodium and the mixture ametryn + trifloxysulfuron-sodium than the RB867515 at all tested doses. They showed high intoxication levels at 14, 28 and 42 days after herbicide application. It was concluded that genotype RB855113 was the most sensitive to the herbicides, followed by SP80-1816, with RB867515 being the most tolerant.

  6. Seasonal Malaria Chemoprevention with Sulphadoxine-Pyrimethamine and Amodiaquine Selects Pfdhfr-dhps Quintuple Mutant Genotype in Mali.

    Directory of Open Access Journals (Sweden)

    Hamma Maiga

    Full Text Available Seasonal malaria chemoprevention (SMC with sulphadoxine-pyrimethamine (SP plus amodiaquine (AQ is being scaled up in Sahelian countries of West Africa. However, the potential development of Plasmodium falciparum resistance to the respective component drugs is a major concern.Two cross-sectional surveys were conducted before (August 2012 and after (June 2014 a pilot implementation of SMC in Koutiala, Mali. Children aged 3-59 months received 7 rounds of curative doses of SP plus AQ over two malaria seasons. Genotypes of P. falciparum Pfdhfr codons 51, 59 and 108; Pfdhps codons 437 and 540, Pfcrt codon 76 and Pfmdr1codon 86 were analyzed by PCR on DNA from samples collected before and after SMC, and in non-SMC patient population as controls (November 2014.In the SMC population 191/662 (28.9% and 85/670 (12.7% of children were P. falciparum positive by microscopy and were included in the molecular analysis before (2012 and after SMC implementation (2014, respectively. In the non-SMC patient population 220/310 (71% were successfully PCR analyzed. In the SMC children, the prevalence of all molecular markers of SP resistance increased significantly after SMC including the Pfdhfr-dhps quintuple mutant genotype, which was 1.6% before but 7.1% after SMC (p = 0.02. The prevalence of Pfmdr1-86Y significantly decreased from 26.7% to 15.3% (p = 0.04 while no significant change was seen for Pfcrt 76T. In 2014, prevalence of all molecular markers of SP resistance were significantly higher among SMC children compared to the non-SMC population patient (p < 0.01. No Pfdhfr-164 mutation was found neither at baseline nor post SMC.SMC increased the prevalence of molecular markers of P. falciparum resistance to SP in the treated children. However, there was no significant increase of these markers of resistance in the general parasite population after 2 years and 7 rounds of SMC.

  7. Limited protective effect of the CCR5Δ32/CCR5Δ32 genotype on human immunodeficiency virus infection incidence in a cohort of patients with hemophilia and selection for genotypic X4 virus

    DEFF Research Database (Denmark)

    Iversen, Astrid K. N.; Christiansen, Claus Bohn; Attermann, Jørn

    2003-01-01

    The relationship among CCR5 genotype, cytomegalovirus infection, and disease progression and death was studied among 159 human immunodeficiency virus (HIV)–infected patients with hemophilia. One patient (0.6%) had the CCR5Δ32/CCR5Δ32 genotype (which occurs in ∼2% of the Scandinavian population...

  8. Homologous recombination is a force in the evolution of canine distemper virus.

    Science.gov (United States)

    Yuan, Chaowen; Liu, Wenxin; Wang, Yingbo; Hou, Jinlong; Zhang, Liguo; Wang, Guoqing

    2017-01-01

    Canine distemper virus (CDV) is the causative agent of canine distemper (CD) that is a highly contagious, lethal, multisystemic viral disease of receptive carnivores. The prevalence of CDV is a major concern in susceptible animals. Presently, it is unclear whether intragenic recombination can contribute to gene mutations and segment reassortment in the virus. In this study, 25 full-length CDV genome sequences were subjected to phylogenetic and recombinational analyses. The results of phylogenetic analysis, intragenic recombination, and nucleotide selection pressure indicated that mutation and recombination occurred in the six individual genes segment (H, F, P, N, L, M) of the CDV genome. The analysis also revealed pronounced genetic diversity in the CDV genome according to the geographically distinct lineages (genotypes), namely Asia-1, Asia-2, Asia-3, Europe, America-1, and America-2. The six recombination events were detected using SimPlot and RDP programs. The analysis of selection pressure demonstrated that a majority of the nucleotides in the CDV individual gene were under negative selection. Collectively, these data suggested that homologous recombination acts as a key force driving the genetic diversity and evolution of canine distemper virus.

  9. A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection

    Directory of Open Access Journals (Sweden)

    Tetreau Guillaume

    2008-10-01

    Full Text Available Abstract Background For most organisms, developing hundreds of genetic markers spanning the whole genome still requires excessive if not unrealistic efforts. In this context, there is an obvious need for methodologies allowing the low-cost, fast and high-throughput genotyping of virtually any species, such as the Diversity Arrays Technology (DArT. One of the crucial steps of the DArT technique is the genome complexity reduction, which allows obtaining a genomic representation characteristic of the studied DNA sample and necessary for subsequent genotyping. In this article, using the mosquito Aedes aegypti as a study model, we describe a new genome complexity reduction method taking advantage of the abundance of miniature inverted repeat transposable elements (MITEs in the genome of this species. Results Ae. aegypti genomic representations were produced following a two-step procedure: (1 restriction digestion of the genomic DNA and simultaneous ligation of a specific adaptor to compatible ends, and (2 amplification of restriction fragments containing a particular MITE element called Pony using two primers, one annealing to the adaptor sequence and one annealing to a conserved sequence motif of the Pony element. Using this protocol, we constructed a library comprising more than 6,000 DArT clones, of which at least 5.70% were highly reliable polymorphic markers for two closely related mosquito strains separated by only a few generations of artificial selection. Within this dataset, linkage disequilibrium was low, and marker redundancy was evaluated at 2.86% only. Most of the detected genetic variability was observed between the two studied mosquito strains, but individuals of the same strain could still be clearly distinguished. Conclusion The new complexity reduction method was particularly efficient to reveal genetic polymorphisms in Ae. egypti. Overall, our results testify of the flexibility of the DArT genotyping technique and open new

  10. Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution

    Science.gov (United States)

    Peabody, George; Winkler, James; Fountain, Weston; Castro, David A.; Leiva-Aravena, Enzo

    2016-01-01

    ABSTRACT Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of Escherichia coli engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load. IMPORTANCE Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual Escherichia coli and determine if a sexual strain of E. coli can become an effective tool for strain development. PMID:27613685

  11. REPEATABILITY OF FRUITS AND SEEDS PRODUCTION AND SELECTION OF BRAZIL NUT GENOTYPES IN NATIVE POPULATIONS IN RORAIMA1

    Directory of Open Access Journals (Sweden)

    Cássia Ângela Pedrozo

    2015-10-01

    Full Text Available ABSTRACT This study estimates the repeatability coefficients of two production traits in two native populations of Brazil nut trees. It determines the number of years of suitable evaluations for an efficient selection process, determines the permanent phenotypic correlation between production traits and also the selection of promising trees in these populations. Populations, located in the Itã region (ITA and in the in the Cujubim region (CUJ, are both belonging to the municipality of Caracaraí, state of Roraima - Brazil, and consist of 85 and 51 adult trees, respectively. Each tree was evaluated regarding the number of fruits per plant (NFP and fresh seed weight per plant (SWP, for eight (ITA and five consecutive years (CUJ. Statistical analyses were performed according to the mixed model methodology, using Software Selegen-REML/BLUP (RESENDE, 2007. The repeatability coefficients were low for NFP (0.3145 and 0.3269 for ITA and CUJ, respectively and also for SWP (0.2957 and 0.3436 for ITA and CUJ, respectively. It on average takes nine evaluation years to reach coefficients of determination higher than 80%. Permanent phenotypic correlation values higher than 0.95 were obtained for NFP and SWP in both populations. Although trees with a high number of fruits and seed weight were identified, more evaluation years are needed to perform the selection process more efficiently.

  12. Evaluating the possibility of detecting evidence of positive selection across Asia with sparse genotype data from the HUGO Pan-Asian SNP Consortium.

    Science.gov (United States)

    Liu, Xuanyao; Saw, Woei-Yuh; Ali, Mohammad; Ong, Rick Twee-Hee; Teo, Yik-Ying

    2014-05-02

    , suggesting a strong need for high-density population-level genotyping data or sequencing data in order to achieve a comprehensive survey of positive selection in Asian populations.

  13. Interleukin-1 interaction with neuroregulatory systems: selective enhancement by recombinant human and mouse interleukin-1 of in vitro opioid peptide receptor binding in rat brain

    Energy Technology Data Exchange (ETDEWEB)

    Wiedermann, C.J.

    1989-02-01

    Interleukin-1 (IL-1) exerts a wide variety of biological effects on various cell types and may be regarded as a pleiotropic peptide hormone. Biological evidence suggests that IL-1 participates in the modulation of central nervous system physiology and behavior in a fashion characteristic of neuroendocrine hormones. In this investigation, recombinant (r) human (h) IL-1 and r mouse (m) IL-1 were examined for their modulation of opioid peptide receptor binding in vitro. Experiments were performed on frozen sections of rat brain. Receptor binding of radiolabeled substance P and of radiolabeled neurotensin were not significantly affected by the presence of rIL-1s. Recombinant IL-1s, however, significantly enhanced specific binding of 125I-beta-endorphin (125I-beta-END) and of D-ala2-(tyrosyl-3,5-3H)enkephalin-(5-D-leucine) (3H-D-ALA), equipotently and in a concentration-dependent manner with maximal activity occurring at a concentration of 10 LAF units/ml. The increased binding of 125I-beta-END and 3H-D-ALA was blocked steroselectively by (-)-naloxone and by etorphine, suggesting detection of opiate receptors. In addition, brain distribution patterns of receptors labeled in the presence of rIL-1s corresponded to patterns previously published for opiate receptors. Autoradiographic visualization of receptors revealed that rIL-1s in the different areas of the brain exert their effect on opioid binding with comparable potencies. The data suggest that certain central nervous system effects of IL-1s may be mediated by their selective interaction with opiatergic systems at the receptor level.

  14. Seasonal cycle of inbreeding and recombination of the parasitic mite Varroa destructor in honeybee colonies and its implications for the selection of acaricide resistance.

    Science.gov (United States)

    Beaurepaire, Alexis L; Krieger, Klemens J; Moritz, Robin F A

    2017-06-01

    Varroa destructor is the most devastating parasite of the Western honeybee, Apis mellifera. In the light of the arm race opposing the host and its parasite, the population dynamics and genetic diversity of these organisms are key parameters. However, the life cycle of V. destructor is characterized by extreme inbreeding due to full sibling mating in the host brood cells. We here present an equation reflecting the evolution of inbreeding in such a clonal system, and compare our predictions with empirical data based on the analysis of seven microsatellite markers. This comparison revealed that the mites perform essentially incestuous mating in the beginning of the brood season. However, this pattern changes with the development of mite infestation. Despite the fact that the overall level of genetic diversity of the mites remained low through the season, multiple inbred lineages were identified in the mites we sampled in June. As a response to the decrease of brood availability and the increase of the parasite population in parallel in the colonies, these lineages recombined towards the end of the season as mites co-infest brood cells. Our results suggest that the ratio of the number of mite per brood cell in the colony determines the genetic structure of the populations of V. destructor. This intracolonial population dynamics has great relevance for the selection of acaricide resistance in V. destructor. If chemical treatments occur before the recombination phase, inbreeding will greatly enhance the fixation of resistance alleles at the colony level. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Site-selective conjugation of an anticoagulant aptamer to recombinant albumins and maintenance of neonatal Fc receptor binding

    DEFF Research Database (Denmark)

    Schmøkel, Julie; Voldum, Anders; Tsakiridou, Georgia

    2017-01-01

    -life, predominately facilitated by engagement with the cellular recycling neonatal Fc receptor (FcRn), and ligand transport properties of albumin promote it as an attractive candidate to improve the pharmacokinetic profile of aptamers. This study investigates the effect of Cys34 site-selective covalent attachment......Aptamers are an attractive molecular medicine that offers high target specificity. Nucleic acid-based aptamers, however, are prone to nuclease degradation and rapid renal excretion that require blood circulatory half-life extension enabling technologies. The long circulatory half...

  16. Binary and ternary recombination of para-H3(+) and ortho-H3(+) with electrons: state selective study at 77-200 K.

    Science.gov (United States)

    Dohnal, Petr; Hejduk, Michal; Varju, Jozef; Rubovič, Peter; Roučka, Štěpán; Kotrík, Tomáš; Plašil, Radek; Glosík, Juraj; Johnsen, Rainer

    2012-06-28

    Measurements in H(3)(+) afterglow plasmas with spectroscopically determined relative abundances of H(3)(+) ions in the para-nuclear and ortho-nuclear spin states provide clear evidence that at low temperatures (77-200 K) para-H(3)(+) ions recombine significantly faster with electrons than ions in the ortho state, in agreement with a recent theoretical prediction. The cavity ring-down absorption spectroscopy used here provides an in situ determination of the para/ortho abundance ratio and yields additional information on the translational and rotational temperatures of the recombining ions. The results show that H(3)(+) recombination with electrons occurs by both binary recombination and third-body (helium) assisted recombination, and that both the two-body and three-body rate coefficients depend on the nuclear spin states. Electron-stabilized (collisional-radiative) recombination appears to make only a small contribution.

  17. Binary and ternary recombination of para-H3+ and ortho-H3+ with electrons: State selective study at 77-200 K

    Science.gov (United States)

    Dohnal, Petr; Hejduk, Michal; Varju, Jozef; Rubovič, Peter; Roučka, Štěpán; Kotrík, Tomáš; Plašil, Radek; Glosík, Juraj; Johnsen, Rainer

    2012-06-01

    Measurements in H_3^+ afterglow plasmas with spectroscopically determined relative abundances of H_3^+ ions in the para-nuclear and ortho-nuclear spin states provide clear evidence that at low temperatures (77-200 K) para-H_3^+ ions recombine significantly faster with electrons than ions in the ortho state, in agreement with a recent theoretical prediction. The cavity ring-down absorption spectroscopy used here provides an in situ determination of the para/ortho abundance ratio and yields additional information on the translational and rotational temperatures of the recombining ions. The results show that H_3^+ recombination with electrons occurs by both binary recombination and third-body (helium) assisted recombination, and that both the two-body and three-body rate coefficients depend on the nuclear spin states. Electron-stabilized (collisional-radiative) recombination appears to make only a small contribution.

  18. Mortality selection during the 2003 European heat wave in three-spined sticklebacks: effects of parasites and MHC genotype

    Directory of Open Access Journals (Sweden)

    Milinski Manfred

    2008-04-01

    Full Text Available Abstract Background Ecological interaction strength may increase under environmental stress including temperature. How such stress enhances and interacts with parasite selection is almost unknown. We studied the importance of resistance genes of the major histocompatibility complex (MHC class II in 14 families of three-spined sticklebacks Gasterosteus aculeatus exposed to their natural macroparasites in field enclosures in the extreme summer of 2003. Results After a mass die-off during the 2003-European heat wave killing 78% of 277 experimental fish, we found strong differences in survival among and within families. In families with higher average parasite load fewer individuals survived. Multivariate analysis revealed that the composition of the infecting parasite fauna was family specific. Within families, individuals with an intermediate number of MHC class IIB sequence variants survived best and had the lowest parasite load among survivors, suggesting a direct functional link between MHC diversity and fitness. The within family MHC effects were, however, small compared to between family effects, suggesting that other genetic components or non-genetic effects were also important. Conclusion The correlation between parasite load and mortality that we found at both individual and family level might have appeared only in the extraordinary heatwave of 2003. Due to global warming the frequency of extreme climatic events is predicted to increase, which might intensify costs of parasitism and enhance selection on immune genes.

  19. Utilisation of antibody microarrays for the selection of specific and informative antibodies from recombinant library binders of unknown quality

    DEFF Research Database (Denmark)

    Kibat, Janek; Schirrmann, Thomas; Knape, Matthias J

    2016-01-01

    reducing the effort of antibody characterisation by concentrating on relevant molecules. In a pilot scheme, a library of 456 single-chain variable fragment (scFv) binders to 134 antigens was used. They were arranged in a microarray format and incubated with the protein content of clinical tissue samples...... isolated from pancreatic ductal adenocarcinoma and healthy pancreas, as well as recurrent and non-recurrent bladder tumours. We observed significant variation in the expression of the E3 ubiquitin-protein ligase (CHFR) as well as the glutamate receptor interacting protein 2 (GRIP2), for example, always...... with more than one of the scFvs binding to these targets. Only the relevant antibodies were then characterised further on antigen microarrays and by surface plasmon resonance experiments so as to select the most specific and highest affinity antibodies. These binders were in turn used to confirm...

  20. Host–symbiont recombination versus natural selection in the response of coral–dinoflagellate symbioses to environmental disturbance

    Science.gov (United States)

    LaJeunesse, Todd C.; Smith, Robin; Walther, Mariana; Pinzón, Jorge; Pettay, Daniel T.; McGinley, Michael; Aschaffenburg, Matthew; Medina-Rosas, Pedro; Cupul-Magaña, Amilcar L.; Pérez, Andrés López; Reyes-Bonilla, Hector; Warner, Mark E.

    2010-01-01

    Mutualisms between reef-building corals and endosymbiotic dinoflagellates are particularly sensitive to environmental stress, yet the ecosystems they construct have endured major oscillations in global climate. During the winter of 2008, an extreme cold-water event occurred in the Gulf of California that bleached corals in the genus Pocillopora harbouring a thermally ‘sensitive’ symbiont, designated Symbiodinium C1b-c, while colonies possessing Symbiodinium D1 were mostly unaffected. Certain bleached colonies recovered quickly while others suffered partial or complete mortality. In most colonies, no appreciable change was observed in the identity of the original symbiont, indicating that these partnerships are stable. During the initial phases of recovery, a third species of symbiont B1Aiptasia, genetically identical to that harboured by the invasive anemone, Aiptasia sp., grew opportunistically and was visible as light-yellow patches on the branch tips of several colonies. However, this symbiont did not persist and was displaced in all cases by C1b-c several months later. Colonies with D1 were abundant at inshore habitats along the continental eastern Pacific, where seasonal turbidity is high relative to offshore islands. Environmental conditions of the central and southern coasts of Mexico were not sufficient to explain the exclusivity of D1 Pocillopora in these regions. It is possible that mass mortalities associated with major thermal disturbances during the 1997–1998 El Niño Southern Oscillation eliminated C1b-c holobionts from these locations. The differential loss of Pocillopora holobionts in response to thermal stress suggests that natural selection on existing variation can cause rapid and significant shifts in the frequency of particular coral–algal partnerships. However, coral populations may take decades to recover following episodes of severe selection, thereby raising considerable uncertainty about the long-term viability of these communities

  1. Testing the effect of paraquat exposure on genomic recombination rates in queens of the western honey bee, Apis mellifera.

    Science.gov (United States)

    Langberg, Kurt; Phillips, Matthew; Rueppell, Olav

    2018-04-01

    The rate of genomic recombination displays evolutionary plasticity and can even vary in response to environmental factors. The western honey bee (Apis mellifera L.) has an extremely high genomic recombination rate but the mechanistic basis for this genome-wide upregulation is not understood. Based on the hypothesis that meiotic recombination and DNA damage repair share common mechanisms in honey bees as in other organisms, we predicted that oxidative stress leads to an increase in recombination rate in honey bees. To test this prediction, we subjected honey bee queens to oxidative stress by paraquat injection and measured the rates of genomic recombination in select genome intervals of offspring produced before and after injection. The evaluation of 26 genome intervals in a total of over 1750 offspring of 11 queens by microsatellite genotyping revealed several significant effects but no overall evidence for a mechanistic link between oxidative stress and increased recombination was found. The results weaken the notion that DNA repair enzymes have a regulatory function in the high rate of meiotic recombination of honey bees, but they do not provide evidence against functional overlap between meiotic recombination and DNA damage repair in honey bees and more mechanistic studies are needed.

  2. Evaluation of common bean (Phaseolus vulgaris L. genotypes for drought stress adaptation in Ethiopia

    Directory of Open Access Journals (Sweden)

    Kwabena Darkwa

    2016-10-01

    Full Text Available Drought stress linked with climate change is one of the major constraints faced by common bean farmers in Africa and elsewhere. Mitigating this constraint requires the selection of resilient varieties that withstand drought threats to common bean production. This study assessed the drought response of 64 small red-seeded genotypes of common bean grown in a lattice design replicated twice under contrasting moisture regimes, terminal drought stress and non-stress, in Ethiopia during the dry season from November 2014 to March 2015. Multiple plant traits associated with drought were assessed for their contribution to drought adaptation of the genotypes. Drought stress determined by a drought intensity index was moderate (0.3. All the assessed traits showed significantly different genotypic responses under drought stress and non-stress conditions. Eleven genotypes significantly (P ≤ 0.05 outperformed the drought check cultivar under both drought stress and non-stress conditions in seed yielding potential. Seed yield showed positive and significant correlations with chlorophyll meter reading, vertical root pulling resistance force, number of pods per plant, and seeds per pod under both soil moisture regimes, indicating their potential use in selection of genotypes yielding well under drought stress and non-stress conditions. Clustering analysis using Mahalanobis distance grouped the genotypes into four groups showing high and significant inter-cluster distance, suggesting that hybridization between drought-adapted parents from the groups will provide the maximum genetic recombination for drought tolerance in subsequent generations.

  3. ReCombine: a suite of programs for detection and analysis of meiotic recombination in whole-genome datasets.

    Directory of Open Access Journals (Sweden)

    Carol M Anderson

    Full Text Available In meiosis, the exchange of DNA between chromosomes by homologous recombination is a critical step that ensures proper chromosome segregation and increases genetic diversity. Products of recombination include reciprocal exchanges, known as crossovers, and non-reciprocal gene conversions or non-crossovers. The mechanisms underlying meiotic recombination remain elusive, largely because of the difficulty of analyzing large numbers of recombination events by traditional genetic methods. These traditional methods are increasingly being superseded by high-throughput techniques capable of surveying meiotic recombination on a genome-wide basis. Next-generation sequencing or microarray hybridization is used to genotype thousands of polymorphic markers in the progeny of hybrid yeast strains. New computational tools are needed to perform this genotyping and to find and analyze recombination events. We have developed a suite of programs, ReCombine, for using short sequence reads from next-generation sequencing experiments to genotype yeast meiotic progeny. Upon genotyping, the program CrossOver, a component of ReCombine, then detects recombination products and classifies them into categories based on the features found at each location and their distribution among the various chromatids. CrossOver is also capable of analyzing segregation data from microarray experiments or other sources. This package of programs is designed to allow even researchers without computational expertise to use high-throughput, whole-genome methods to study the molecular mechanisms of meiotic recombination.

  4. Increased expression and secretion of recombinant hIFNγ through amino acid starvation-induced selective pressure on the adjacent HIS4 gene in Pichia pastoris

    Directory of Open Access Journals (Sweden)

    Razaghi Ali

    2015-12-01

    Full Text Available Transcriptional co-regulation of adjacent genes has been observed for prokaryotic and eukaryotic organisms, alike. High levels of gene adjacency were also found in a wide variety of yeast species with a high frequency of co-regulated gene sets. The aim of this research was to study how selective pressure on the Histidinol dehydrogenase gene (HIS4, using amino acid starvation, affects the level of expression and secretion of the adjacent human interferon gamma gene (hIFNγ in the recombinant Pichia pastoris GS115 strain, a histidine-deficient mutant. hIFNγ was cloned into the pPIC9 vector adjacent to the HIS4 gene, a gene essential for histidine biosynthesis, which was then transformed into P. pastoris. The transformed P. pastoris was cultured under continuous amino acid starvation in amino acid-free minimal medium for ten days, with five inoculations into unspent medium every second day. Under these conditions, only successfully transformed cells (hIFNγ -HIS4+ are able to synthesise histidine and therefore thrive. As shown by ELISA, amino acid starvation-induced selective pressure on HIS4 improved expression and secretion of the adjacent hIFNγ by 55% compared to unchallenged cells. RT-qPCR showed that there was also a positive correlation between duration of amino acid starvation and increased levels of the hIFNγ RNA transcripts. According to these results, it is suggested that these adjacent genes (hIFNγ and HIS4 in the transformed P. pastoris are transcriptionally co-regulated and their expression is synchronised. To the best of the knowledge of the authors; this is the first study demonstrating that amino acid starvationinduced selective pressure on HIS4 can alter the regulation pattern of adjacent genes in P. pastoris.

  5. Genotypic variability and relationships between mite infestation levels, mite damage, grooming intensity, and removal of Varroa destructor mites in selected strains of worker honey bees (Apis mellifera L.).

    Science.gov (United States)

    Guzman-Novoa, Ernesto; Emsen, Berna; Unger, Peter; Espinosa-Montaño, Laura G; Petukhova, Tatiana

    2012-07-01

    The objective of this study was to demonstrate genotypic variability and analyze the relationships between the infestation levels of the parasitic mite Varroa destructor in honey bee (Apis mellifera) colonies, the rate of damage of fallen mites, and the intensity with which bees of different genotypes groom themselves to remove mites from their bodies. Sets of paired genotypes that are presumably susceptible and resistant to the varroa mite were compared at the colony level for number of mites falling on sticky papers and for proportion of damaged mites. They were also compared at the individual level for intensity of grooming and mite removal success. Bees from the "resistant" colonies had lower mite population rates (up to 15 fold) and higher percentages of damaged mites (up to 9 fold) than bees from the "susceptible" genotypes. At the individual level, bees from the "resistant" genotypes performed significantly more instances of intense grooming (up to 4 fold), and a significantly higher number of mites were dislodged from the bees' bodies by intense grooming than by light grooming (up to 7 fold) in all genotypes. The odds of mite removal were high and significant for all "resistant" genotypes when compared with the "susceptible" genotypes. The results of this study strongly suggest that grooming behavior and the intensity with which bees perform it, is an important component in the resistance of some honey bee genotypes to the growth of varroa mite populations. The implications of these results are discussed. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. The κB transcriptional enhancer motif and signal sequences of V(DJ recombination are targets for the zinc finger protein HIVEP3/KRC: a site selection amplification binding study

    Directory of Open Access Journals (Sweden)

    Wu Lai-Chu

    2002-08-01

    Full Text Available Abstract Background The ZAS family is composed of proteins that regulate transcription via specific gene regulatory elements. The amino-DNA binding domain (ZAS-N and the carboxyl-DNA binding domain (ZAS-C of a representative family member, named κB DNA binding and recognition component (KRC, were expressed as fusion proteins and their target DNA sequences were elucidated by site selection amplification binding assays, followed by cloning and DNA sequencing. The fusion proteins-selected DNA sequences were analyzed by the MEME and MAST computer programs to obtain consensus motifs and DNA elements bound by the ZAS domains. Results Both fusion proteins selected sequences that were similar to the κB motif or the canonical elements of the V(DJ recombination signal sequences (RSS from a pool of degenerate oligonucleotides. Specifically, the ZAS-N domain selected sequences similar to the canonical RSS nonamer, while ZAS-C domain selected sequences similar to the canonical RSS heptamer. In addition, both KRC fusion proteins selected oligonucleoties with sequences identical to heptamer and nonamer sequences within endogenous RSS. Conclusions The RSS are cis-acting DNA motifs which are essential for V(DJ recombination of antigen receptor genes. Due to its specific binding affinity for RSS and κB-like transcription enhancer motifs, we hypothesize that KRC may be involved in the regulation of V(DJ recombination.

  7. High efficiency recombineering in lactic acid bacteria

    OpenAIRE

    van Pijkeren, Jan-Peter; Britton, Robert A.

    2012-01-01

    The ability to efficiently generate targeted point mutations in the chromosome without the need for antibiotics, or other means of selection, is a powerful strategy for genome engineering. Although oligonucleotide-mediated recombineering (ssDNA recombineering) has been utilized in Escherichia coli for over a decade, the successful adaptation of ssDNA recombineering to Gram-positive bacteria has not been reported. Here we describe the development and application of ssDNA recombineering in lact...

  8. Application of NIR - CRDS for state selective study of recombination of para and ortho H3+ ions with electrons in low temperature plasma

    Science.gov (United States)

    Varju, J.; Roučka, Š.; Kotrík, T.; Plašil, R.; Glosík, J.

    2010-05-01

    We present a study of H3+ recombination performed at 77 K on the two lowest rotational levels of this ion, which belong to its two different nuclear spin states of the studied ion. A near infrared cavity ring-down spectrometer (~1381 nm, CRDS arrangement) has been used to obtain the time evolution of concentration of both states. From the overall ion density decay during the afterglow we obtained the binary recombination rate coefficient αbin (77 K) = 1.2×10-7 cm3s-1. We have also observed ternary helium assisted recombination of both para and ortho H3+. The process is very slow (at 77 K) and the obtained ternary recombination rate coefficient is in contradiction with the theoretical prediction. It is the first time that the binary and ternary H3+ recombination rate coefficient was measured at a known population of para and ortho H3+ ions in decaying plasma.

  9. Application of NIR - CRDS for state selective study of recombination of para and ortho H3+ ions with electrons in low temperature plasma

    International Nuclear Information System (INIS)

    Varju, J; Roucka, S; KotrIk, T; Plasil, R; Glosik, J

    2010-01-01

    We present a study of H 3 + recombination performed at 77 K on the two lowest rotational levels of this ion, which belong to its two different nuclear spin states of the studied ion. A near infrared cavity ring-down spectrometer (∼1381 nm, CRDS arrangement) has been used to obtain the time evolution of concentration of both states. From the overall ion density decay during the afterglow we obtained the binary recombination rate coefficient α bin (77 K) = 1.2x10 -7 cm 3 s -1 . We have also observed ternary helium assisted recombination of both para and ortho H 3 + . The process is very slow (at 77 K) and the obtained ternary recombination rate coefficient is in contradiction with the theoretical prediction. It is the first time that the binary and ternary H 3 + recombination rate coefficient was measured at a known population of para and ortho H 3 + ions in decaying plasma.

  10. HBV Genotypic Variability in Cuba

    Science.gov (United States)

    Loureiro, Carmen L.; Aguilar, Julio C.; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H.

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions. PMID:25742179

  11. Recombinant cells and organisms having persistent nonstandard amino acid dependence and methods of making them

    Science.gov (United States)

    Church, George M.; Mandell, Daniel J.; Lajoie, Marc J.

    2017-12-05

    Recombinant cells and recombinant organisms persistently expressing nonstandard amino acids (NSAAs) are provided. Methods of making recombinant cells and recombinant organisms dependent on persistently expressing NSAAs for survival are also provided. These methods may be used to make safe recombinant cells and recombinant organisms and/or to provide a selective pressure to maintain one or more reassigned codon functions in recombinant cells and recombinant organisms.

  12. Positive selection and intragenic recombination contribute to high allelic diversity in effector genes of Mycosphaerella fijiensis, causal agent of the black leaf streak disease of banana.

    Science.gov (United States)

    Stergiopoulos, Ioannis; Cordovez, Viviane; Okmen, Bilal; Beenen, Henriek G; Kema, Gert H J; de Wit, Pierre J G M

    2014-06-01

    Previously, we have determined the nonhost-mediated recognition of the MfAvr4 and MfEcp2 effector proteins from the banana pathogen Mycosphaerella fijiensis in tomato, by the cognate Cf-4 and Cf-Ecp2 resistance proteins, respectively. These two resistance proteins could thus mediate resistance against M. fijiensis if genetically transformed into banana (Musa spp.). However, disease resistance controlled by single dominant genes can be overcome by mutated effector alleles, whose products are not recognized by the cognate resistance proteins. Here, we surveyed the allelic variation within the MfAvr4, MfEcp2, MfEcp2-2 and MfEcp2-3 effector genes of M. fijiensis in a global population of the pathogen, and assayed its impact on recognition by the tomato Cf-4 and Cf-Ecp2 resistance proteins, respectively. We identified a large number of polymorphisms that could reflect a co-evolutionary arms race between host and pathogen. The analysis of nucleotide substitution patterns suggests that both positive selection and intragenic recombination have shaped the evolution of M. fijiensis effectors. Clear differences in allelic diversity were observed between strains originating from South-East Asia relative to strains from other banana-producing continents, consistent with the hypothesis that M. fijiensis originated in the Asian-Pacific region. Furthermore, transient co-expression of the MfAvr4 effector alleles and the tomato Cf-4 resistance gene, as well as of MfEcp2, MfEcp2-2 and MfEcp2-3 and the putative Cf-Ecp2 resistance gene, indicated that effector alleles able to overcome these resistance genes are already present in natural populations of the pathogen, thus questioning the durability of resistance that can be provided by these genes in the field. © 2013 BSPP AND JOHN WILEY & SONS LTD.

  13. Industrial case study: evaluation of a mixed-mode resin for selective capture of a human growth factor recombinantly expressed in E. coli.

    Science.gov (United States)

    Kaleas, Kimberly A; Schmelzer, Charles H; Pizarro, Shelly A

    2010-01-08

    Mixed-mode chromatography resins are gaining popularity as effective purification tools for challenging feedstocks. This study presents the development of an industrial application to selectively capture recombinant human vascular endothelial growth factor (rhVEGF) on Capto MMC from an alkaline feedstock. Capto MMC resin contains a ligand that has the potential to participate in ionic, hydrophobic, and hydrogen boding interactions with proteins and is coupled to a highly cross-linked agarose bead matrix. VEGF is a key growth factor involved in angiogenesis and has therapeutic applications for wound healing. In this process, it is expressed in Escherichia coli as inclusion bodies. Solids are harvested from the cell lysate, and the rhVEGF is solubilized and refolded at pH 9.8 in the presence of urea and redox reagents. The unique mixed-mode characteristics of Capto MMC enabled capture of this basic protein with minimal load conditioning and delivered a concentrated pool for downstream processing with >95% yields while reducing host cell protein content to study explores the impact of loading conditions and residence time on the dynamic binding capacity as well as the development of elution conditions for optimal purification performance. After evaluating various elution buffers, l-arginine HCl was shown to be an effective eluting agent for rhVEGF desorption from the Capto MMC mixed-mode resin since it successfully disrupted the multiple interactions between the resin and rhVEGF. The lab scale effort produced a robust chromatography step that was successfully implemented at commercial manufacturing scale. Copyright 2009 Elsevier B.V. All rights reserved.

  14. Recombinant renewable polyclonal antibodies.

    Science.gov (United States)

    Ferrara, Fortunato; D'Angelo, Sara; Gaiotto, Tiziano; Naranjo, Leslie; Tian, Hongzhao; Gräslund, Susanne; Dobrovetsky, Elena; Hraber, Peter; Lund-Johansen, Fridtjof; Saragozza, Silvia; Sblattero, Daniele; Kiss, Csaba; Bradbury, Andrew R M

    2015-01-01

    Only a small fraction of the antibodies in a traditional polyclonal antibody mixture recognize the target of interest, frequently resulting in undesirable polyreactivity. Here, we show that high-quality recombinant polyclonals, in which hundreds of different antibodies are all directed toward a target of interest, can be easily generated in vitro by combining phage and yeast display. We show that, unlike traditional polyclonals, which are limited resources, recombinant polyclonal antibodies can be amplified over one hundred million-fold without losing representation or functionality. Our protocol was tested on 9 different targets to demonstrate how the strategy allows the selective amplification of antibodies directed toward desirable target specific epitopes, such as those found in one protein but not a closely related one, and the elimination of antibodies recognizing common epitopes, without significant loss of diversity. These recombinant renewable polyclonal antibodies are usable in different assays, and can be generated in high throughput. This approach could potentially be used to develop highly specific recombinant renewable antibodies against all human gene products.

  15. The Effects of Bean Leafroll Virus on Life History Traits and Host Selection Behavior of Specialized Pea Aphid (Acyrthosiphon pisum, Hemiptera: Aphididae) Genotypes.

    Science.gov (United States)

    Davis, T S; Wu, Y; Eigenbrode, S D

    2017-02-01

    Intraspecific specialization by insect herbivores on different host plant species contributes to the formation of genetically distinct "host races," but the effects of plant virus infection on interactions between specialized herbivores and their host plants have barely been investigated. Using three genetically and phenotypically divergent pea aphid clones (Acyrthosiphon pisum L.) adapted to either pea (Pisum sativum L.) or alfalfa (Medicago sativa L.), we tested how infection of these hosts by an insect-borne phytovirus (Bean leafroll virus; BLRV) affects aphid performance and preference. Four important findings emerged: 1) mean aphid survival rate and intrinsic rate of population growth (Rm) were increased by 15% and 14%, respectively, for aphids feeding on plants infected with BLRV; 2) 34% of variance in survival rate was attributable to clone × host plant interactions; 3) a three-way aphid clone × host plant species × virus treatment significantly affected intrinsic rates of population growth; and 4) each clone exhibited a preference for either pea or alfalfa when choosing between noninfected host plants, but for two of the three clones tested these preferences were modestly reduced when selecting among virus-infected host plants. Our studies show that colonizing BLRV-infected hosts increased A. pisum survival and rates of population growth, confirming that the virus benefits A. pisum. BLRV transmission affected aphid discrimination of host plant species in a genotype-specific fashion, and we detected three unique "virus-association phenotypes," with potential consequences for patterns of host plant use by aphid populations and crop virus epidemiology. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. Application of NIR - CRDS for state selective study of recombination of para and ortho H{sub 3}{sup +} ions with electrons in low temperature plasma

    Energy Technology Data Exchange (ETDEWEB)

    Varju, J; Roucka, S; KotrIk, T; Plasil, R; Glosik, J, E-mail: Juraj.Glosik@mff.cuni.c [Charles University, Faculty of Mathematics and Physics, Department of Surface and Plasma Science, V Holesovickach 2, Prague 8 (Czech Republic)

    2010-05-01

    We present a study of H{sub 3}{sup +} recombination performed at 77 K on the two lowest rotational levels of this ion, which belong to its two different nuclear spin states of the studied ion. A near infrared cavity ring-down spectrometer ({approx}1381 nm, CRDS arrangement) has been used to obtain the time evolution of concentration of both states. From the overall ion density decay during the afterglow we obtained the binary recombination rate coefficient {alpha}{sub bin} (77 K) = 1.2x10{sup -7} cm{sup 3}s{sup -1}. We have also observed ternary helium assisted recombination of both para and ortho H{sub 3}{sup +}. The process is very slow (at 77 K) and the obtained ternary recombination rate coefficient is in contradiction with the theoretical prediction. It is the first time that the binary and ternary H{sub 3}{sup +} recombination rate coefficient was measured at a known population of para and ortho H{sub 3}{sup +} ions in decaying plasma.

  17. Genetic diversity in Australian Cedar genotypes selected by mixed models Diversidade genética em genótipos de Cedro Australiano selecionados via modelos mistos

    Directory of Open Access Journals (Sweden)

    Rulfe Tavares

    2012-04-01

    Full Text Available The increasing demand for raw material for multiple uses of forest products and by-products has attracted the interest for fast growing species, such as the Australian Cedar (Toona ciliata, which presents high productive and economic potential. The present work aimed at estimating genetic diversity by DNA markers and morphological traits supported for the mixed models. The following traits were measured and genotypes were sampled randomly in different areas: diameter at breast height, height, cylindrical volume, diameter, distance between nodes and crown diameter. Twelve RAPD primers were used and generated a total of 91 marks, 82 of which were polymorphic. The high percentage of polymorphic markers, 90.10%, demonstrated that discrimination in this species is efficient, but it yet little studied, for this case we can find the extent of the genetic basis for the application of technical improvement. The assessment of genetic diversity by the UPGMA method using the binary and morphological data provided the expression of genetic dissimilarities among the accessions evaluated, optimizing the perception of this divergence. The use of mixed models was efficient to assess combined genetic diversity to optimize the selection of genotypes with divergent genetic values for diameter at breast height.A crescente demanda por matéria-prima para múltiplos usos dos produtos florestais e subprodutos tem despertado o interesse para espécies de crescimento rápido, como o cedro australiano (Toona ciliata, que apresenta potencial produtivo e econômico. Neste trabalho, objetivou-se estimar a diversidade genética por marcadores de DNA e caracteres morfológicos com o uso dos modelos mistos. Os seguintes caracteres foram medidos e os genótipos foram amostrados aleatoriamente em diferentes áreas de plantio: diâmetro à altura do peito, altura, volume cilíndrico, distância entre nós e diâmetro de copa. Doze primers RAPD foram utilizados e geraram um total

  18. Agrobacterium tumefaciens-mediated transformation for investigation of somatic recombination in the fungal pathogen Armillaria mellea.

    Science.gov (United States)

    Baumgartner, Kendra; Fujiyoshi, Phillip; Foster, Gary D; Bailey, Andy M

    2010-12-01

    Armillaria root disease is one of the most damaging timber and fruit tree diseases in the world. Despite its economic importance, many basic questions about the biology of the causal fungi, Armillaria spp., are unanswered. For example, Armillaria undergoes matings between diploid and haploid mycelia, which can result in a recombinant diploid without meiosis. Evidence of such somatic recombination in natural populations suggests that this reproductive mode may affect the pathogen's ecology. Investigations of the mechanisms and adaptive consequences of somatic recombination are, however, hampered by the lack of a method to reliably synthesize somatic recombinants. Here we report the first genetic transformation system for the genus Armillaria. We transformed A. mellea with selective markers for use in diploid-haploid matings to reliably synthesize somatic recombinants. This was accomplished with Agrobacterium tumefaciens carrying pBGgHg, which carries the hygromycin phosphotransferase gene (hph). hph was integrated into transformants, as evidenced by serial transfer to selective media, PCR, reverse transcription-PCR (RT-PCR), and Southern hybridization. Nuclear and mitochondrial markers were developed to genotype synthesized mycelia. In matings between a wild-type diploid and hygromycin-resistant haploids (transgenic), we identified recombinant, hygromycin-resistant diploids and, additionally, hygromycin-resistant triploids, all with the mitochondrial haplotype of the haploid partner. Our approach created no mycelium in which the haploid nucleus was replaced by the diploid nucleus, the typical outcome of diploid-haploid matings in Armillaria. This genetic transformation system, in combination with new markers to track chromosomal and cytoplasmic inheritance in A. mellea, will advance research aimed at characterizing the significance of somatic recombination in the ecology of this important fungus.

  19. Agrobacterium tumefaciens-Mediated Transformation for Investigation of Somatic Recombination in the Fungal Pathogen Armillaria mellea▿

    Science.gov (United States)

    Baumgartner, Kendra; Fujiyoshi, Phillip; Foster, Gary D.; Bailey, Andy M.

    2010-01-01

    Armillaria root disease is one of the most damaging timber and fruit tree diseases in the world. Despite its economic importance, many basic questions about the biology of the causal fungi, Armillaria spp., are unanswered. For example, Armillaria undergoes matings between diploid and haploid mycelia, which can result in a recombinant diploid without meiosis. Evidence of such somatic recombination in natural populations suggests that this reproductive mode may affect the pathogen's ecology. Investigations of the mechanisms and adaptive consequences of somatic recombination are, however, hampered by the lack of a method to reliably synthesize somatic recombinants. Here we report the first genetic transformation system for the genus Armillaria. We transformed A. mellea with selective markers for use in diploid-haploid matings to reliably synthesize somatic recombinants. This was accomplished with Agrobacterium tumefaciens carrying pBGgHg, which carries the hygromycin phosphotransferase gene (hph). hph was integrated into transformants, as evidenced by serial transfer to selective media, PCR, reverse transcription-PCR (RT-PCR), and Southern hybridization. Nuclear and mitochondrial markers were developed to genotype synthesized mycelia. In matings between a wild-type diploid and hygromycin-resistant haploids (transgenic), we identified recombinant, hygromycin-resistant diploids and, additionally, hygromycin-resistant triploids, all with the mitochondrial haplotype of the haploid partner. Our approach created no mycelium in which the haploid nucleus was replaced by the diploid nucleus, the typical outcome of diploid-haploid matings in Armillaria. This genetic transformation system, in combination with new markers to track chromosomal and cytoplasmic inheritance in A. mellea, will advance research aimed at characterizing the significance of somatic recombination in the ecology of this important fungus. PMID:20952653

  20. Evidence of a recombinant wild-type human astrovirus strain from a Kenyan child with gastroenteritis.

    Science.gov (United States)

    Wolfaardt, Marianne; Kiulia, Nicholas M; Mwenda, Jason M; Taylor, Maureen B

    2011-02-01

    A human astrovirus (HAstV) strain from Kenya was characterized by nucleotide sequence analysis. Sequences from open reading frame 1a (ORF1a) clustered with genotype 6/7, those from ORF1b clustered with genotype 3, and those from ORF2 clustered with genotype 2. A recombination point in the ORF1b-ORF2 junction was identified, with a second possible recombination point within the ORF1a region.

  1. Evaluation of Diversity Based on Morphological Variabilities and ISSR Molecular Markers in Iranian Cynodon dactylon (L.) Pers. Accessions to Select and Introduce Cold-Tolerant Genotypes.

    Science.gov (United States)

    Akbari, M; Salehi, H; Niazi, A

    2018-04-01

    , Naein, Aligoudarz, and the foreign cultivar. This study may provide useful information for further breeding programs on common bermudagrass. Selected genotypes can be evaluated for other abiotic stresses such as drought and salinity.

  2. Serendipitous identification of natural intergenotypic recombinants of hepatitis C in Ireland.

    LENUS (Irish Health Repository)

    Moreau, Isabelle

    2006-01-01

    BACKGROUND: Recombination between hepatitis C single stranded RNA viruses is a rare event. Natural viable intragenotypic and intergenotypic recombinants between 1b-1a, 1a-1c and 2k-1b, 2i-6p, respectively, have been reported. Diagnostically recombinants represent an intriguing challenge. Hepatitis C genotype is defined by interrogation of the sequence composition of the 5\\' untranslated region [5\\'UTR]. Occasionally, ambiguous specimens require further investigation of the genome, usually by interrogation of the NS5B region. The original purpose of this study was to confirm the existence of a suspected mixed genotype infection of genotypes 2 and 4 by clonal analysis at the NS5B region of the genome in two specimens from two separate individuals. This initial identification of genotype was based on analysis of the 5\\'UTR of the genome by reverse line probe hybridisation [RLPH]. RESULTS: The original diagnosis of a mixed genotype infection was not confirmed by clonal analysis of the NS5B region of the genome. The phylogenetic analysis indicated that both specimens were natural intergenotypic recombinant forms of HCV. The recombination was between genotypes 2k and 1b for both specimens. The recombination break point was identified as occurring within the NS2 region of the genome. CONCLUSION: The viral recombinants identified here resemble the recombinant form originally identified in Russia. The RLPH pattern observed in this study may be a signature indicative of this particular type of intergenotype recombinant of hepatitis C meriting clonal analysis of NS2.

  3. Performance comparison of the versant HCV genotype 2.0 assay (LiPA) and the abbott realtime HCV genotype II assay for detecting hepatitis C virus genotype 6.

    Science.gov (United States)

    Yang, Ruifeng; Cong, Xu; Du, Shaocai; Fei, Ran; Rao, Huiying; Wei, Lai

    2014-10-01

    The Versant HCV genotype 2.0 assay (line probe assay [LiPA] 2.0), based on reverse hybridization, and the Abbott Realtime HCV genotype II assay (Realtime II), based on genotype-specific real-time PCR, have been widely used to analyze hepatitis C virus (HCV) genotypes. However, their performances for detecting HCV genotype 6 infections have not been well studied. Here, we analyzed genotype 6 in 63 samples from the China HCV Genotyping Study that were originally identified as genotype 6 using the LiPA 2.0. The genotyping results were confirmed by nonstructural 5B (NS5B) or core sequence phylogenetic analysis. A total of 57 samples were confirmed to be genotype 6 (51 genotype 6a, 5 genotype 6n, and 1 genotype 6e). Four samples identified as a mixture of genotypes 6 and 4 by the LiPA 2.0 were confirmed to be genotype 3b. The remaining two samples classified as genotype 6 by the LiPA 2.0 were confirmed to be genotype 1b, which were intergenotypic recombinants and excluded from further comparison. In 57 genotype 6 samples detected using the Realtime II version 2.00 assay, 47 genotype 6a samples were identified as genotype 6, one 6e sample was misclassified as genotype 1, and four 6a and five 6n samples yielded indeterminate results. Nine nucleotide profiles in the 5' untranslated region affected the performances of both assays. Therefore, our analysis shows that both assays have limitations in identifying HCV genotype 6. The LiPA 2.0 cannot distinguish some 3b samples from genotype 6 samples. The Realtime II assay fails to identify some 6a and all non-6a subtypes, and it misclassifies genotype 6e as genotype 1. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  4. The genetic architecture of disease resistance in plants and the maintenance of recombination by parasites.

    Science.gov (United States)

    Kover, P X; Caicedo, A L

    2001-01-01

    Parasites represent strong selection on host populations because they are ubiquitous and can drastically reduce host fitness. It has been hypothesized that parasite selection could explain the widespread occurrence of recombination because it is a coevolving force that favours new genetic combinations in the host. A review of deterministic models for the maintenance of recombination reveals that for recombination to be favoured, multiple genes that interact with each other must be under selection. To evaluate whether parasite selection can explain the maintenance of recombination, we review 85 studies that investigated the genetic architecture of plant disease resistance and discuss whether they conform to the requirements that emerge from theoretical models. General characteristics of disease resistance in plants and problems in evaluating resistance experimentally are also discussed. We found strong evidence that disease resistance in plants is determined by multiple loci. Furthermore, in most cases where loci were tested for interactions, epistasis between loci that affect resistance was found. However, we found weak support for the idea that specific allelic combinations determine resistance to different host genotypes and there was little data on whether epistasis between resistance genes is negative or positive. Thus, the current data indicate that it is possible that parasite selection can favour recombination, but more studies in natural populations that specifically address the nature of the interactions between resistance genes are necessary. The data summarized here suggest that disease resistance is a complex trait and that environmental effects and fitness trade-offs should be considered in future models of the coevolutionary dynamics of host and parasites.

  5. Selection index and molecular markers in reciprocal recurrent selection in maize

    Directory of Open Access Journals (Sweden)

    Flávio Dessaune Tardin

    2007-01-01

    Full Text Available Reciprocal recurrent selection among full-sib families is one of the outstanding methodologies of maizeimprovement, since gains are possible in the per se and/or in cross populations. Here the selection index proposed by Smithand Hazel was used in the cited methodology; besides, an additional phase involving RAPD markers was introduced topreserve the genetic variability of the selected genotypes and identify contaminants before their recombination. Multivariatetechniques of grouping and discriminant analyses were used for this purpose, to assure the continuance of the improvementprogram and amplify the genetic distance between the populations Cimmyt and Piranão, which were used for an intervarietalhybrid. The molecular technique proved useful to identify contaminants and helpful in the choice of the genotypes to berecombined to maximize heterosis among populations. The technique can be included in recurrent selection programs, mainlythose that target the development of hybrids.

  6. Sex recombination, and reproductive fitness: an experimental study using Paramecium

    Energy Technology Data Exchange (ETDEWEB)

    Nyberg, D.

    1982-08-01

    The effect of sex and recombination on reproductive fitness are measured using five wild stocks of Paramecium primaurelia. Among the wild stocks there were highly significant differences in growth rates. No hybrid had as low a fitness as the least fit parental stock. Recombination produced genotypes of higher fitness than those of either parent only in the cross between the two stocks of lowest fitness. The increase in variance of fitness as a result of recombination was almost exclusively attributable to the generation lines with low fitness. The fitness consequences of sexuality and mate choice were stock specific; some individuals leaving the most descendants by inbreeding, others by outcrossing. For most crosses the short-term advantage of sex, if any, accrue from the fusion of different gametes (hybrid vigor) and not from recombination. Since the homozygous genotype with the highest fitnes left the most progeny by inbreeding (no recombination), the persistence of conjugation in P. primaurelia is paradoxical. (JMT)

  7. A novel complex A/C/G intergenotypic recombinant of hepatitis B virus isolated in southern China.

    Directory of Open Access Journals (Sweden)

    Heling Su

    Full Text Available Hepatitis B virus (HBV genotypes and subgenotypes may vary in geographical distribution and virological features. Previous investigations, including ours, showed that HBV genotypes B and C were respectively predominant in South and North China, while genotypes A and D were infrequently detected and genotype G was not found. In this study, a novel A/C/G intergenotype was identified in patients with chronic HBV infection in Guilin, a city in southern China. Initial phylogenetic analysis based on the S gene suggested the HBV recombinant to be genotype G. However, extended genotyping based on the entire HBV genome indicated it to be an A/C/G intergenotype with a closer relation to genotype C. Breakpoint analysis using the SIMPLOT program revealed that the recombinant had a recombination with a arrangement of genotypes A, G, A and C fragments. Compared with the HBV recombinants harboring one or two genotype G fragments found in Asian countries, this Guilin recombinant was highly similar to the Vietnam (98-99% and Long An recombinants (96-99%, but had a relatively low similarity to the Thailand one (89%. Unlike those with the typical genotype G of HBV, the patients with the Guilin recombinant were seropositive for HBeAg. Moreover, a relatively high HBV DNA viral load (>2 × 10(6 IU/ml was detected in the patients, and the analysis of viral replication capacity showed that the Guilin recombinant strains had a competent replication capacity similar to genotypes B and C strains. These findings can aid in not only the clarification of the phylogenetic origin of the HBV recombinants with the genotype G fragment found in Asian countries, but also the understanding of the virological properties of these complicated HBV recombinants.

  8. A novel complex A/C/G intergenotypic recombinant of hepatitis B virus isolated in southern China.

    Science.gov (United States)

    Su, Heling; Liu, Yan; Xu, Zhihui; Cheng, Shuquan; Ye, Haiyan; Xu, Qing; Liu, Qingbo; Tan, Shuhong; Xu, Dongping; Liu, Yongming

    2014-01-01

    Hepatitis B virus (HBV) genotypes and subgenotypes may vary in geographical distribution and virological features. Previous investigations, including ours, showed that HBV genotypes B and C were respectively predominant in South and North China, while genotypes A and D were infrequently detected and genotype G was not found. In this study, a novel A/C/G intergenotype was identified in patients with chronic HBV infection in Guilin, a city in southern China. Initial phylogenetic analysis based on the S gene suggested the HBV recombinant to be genotype G. However, extended genotyping based on the entire HBV genome indicated it to be an A/C/G intergenotype with a closer relation to genotype C. Breakpoint analysis using the SIMPLOT program revealed that the recombinant had a recombination with a arrangement of genotypes A, G, A and C fragments. Compared with the HBV recombinants harboring one or two genotype G fragments found in Asian countries, this Guilin recombinant was highly similar to the Vietnam (98-99%) and Long An recombinants (96-99%), but had a relatively low similarity to the Thailand one (89%). Unlike those with the typical genotype G of HBV, the patients with the Guilin recombinant were seropositive for HBeAg. Moreover, a relatively high HBV DNA viral load (>2 × 10(6) IU/ml) was detected in the patients, and the analysis of viral replication capacity showed that the Guilin recombinant strains had a competent replication capacity similar to genotypes B and C strains. These findings can aid in not only the clarification of the phylogenetic origin of the HBV recombinants with the genotype G fragment found in Asian countries, but also the understanding of the virological properties of these complicated HBV recombinants.

  9. Immunization with a Recombinant Expression Vector Encoding NS3/NS4A of Hepatitis C Virus Genotype 3a Elicits Cell-Mediated Immune Responses in C57BL/6 Mice.

    Science.gov (United States)

    Behzadi, Mohammad Amin; Alborzi, Abdolvahab; Kalani, Mehdi; Pouladfar, Gholamreza; Dianatpour, Mehdi; Ziyaeyan, Mazyar

    2016-04-01

    Today, hepatitis C virus (HCV) infection is considered as one of the most significant international health concerns. Although novel therapeutic regimens against the infection have shown satisfactory results, no approved vaccine exists yet. This study aimed to evaluate the immunogenicity of a DNA vaccine candidate for HCV-3a, based on nonstructural proteins NS3/NS4A, in C57BL/6 mice. Immunogenicity effect of pDisplay-NS3/NS4A was analyzed through immunization with 100 and 200 μg concentrations of the construct with complete Freund's adjuvant, monophosphoryl lipid A (MPL), or without adjuvant. The frequencies of different splenic mononuclear cells were measured using the Mouse Th1/Th2/Th17 Phenotyping Kit. Moreover, the number of T-CD8(+) cells was determined using conjugated anti-CD8a and anti-CD3e antibodies by flow cytometry. As observed, the frequencies of Th1, T-CD8(+), and Th2 cells increased in all the experimental groups, compared with the controls. The highest levels of the respective cells were seen in the group immunized with 200 μg of the construct with MPL. Also, there were positive correlations between the frequency of Th1 cells and those of Th2 and T-CD8(+) cells in all the immunized groups, but were significant in those receiving adjuvants. The frequency of Th17 cells did not statistically change among the groups. Taken together, our findings revealed that the constructed DNA vaccine encoding HCV-3a NS3/NS4A gene induces the cell-mediated immune responses significantly. However, its coadministration with adjuvants exhibits more efficient results than the recombinant plasmid alone. Further study is currently underway to evaluate the specific immune responses and recognize the responsible antigenic epitopes.

  10. Genotype by environment interactions and yield stability of stem ...

    African Journals Online (AJOL)

    In a maize breeding program, potential genotypes are usually evaluated in different environments before desirable ones are selected. Genotype x environment (G x E) interaction is associated with the differential performance of genotypes tested at different locations and in different years, and influences selection and ...

  11. Genotyping-by-Sequencing and Its Exploitation for Forage and Cool-Season Grain Legume Breeding

    Science.gov (United States)

    Annicchiarico, Paolo; Nazzicari, Nelson; Wei, Yanling; Pecetti, Luciano; Brummer, Edward C.

    2017-01-01

    Genotyping-by-Sequencing (GBS) may drastically reduce genotyping costs compared with single nucleotide polymorphism (SNP) array platforms. However, it may require optimization for specific crops to maximize the number of available markers. Exploiting GBS-generated markers may require optimization, too (e.g., to cope with missing data). This study aimed (i) to compare elements of GBS protocols on legume species that differ for genome size, ploidy, and breeding system, and (ii) to show successful applications and challenges of GBS data on legume species. Preliminary work on alfalfa and Medicago truncatula suggested the greater interest of ApeKI over PstI:MspI DNA digestion. We compared KAPA and NEB Taq polymerases in combination with primer extensions that were progressively more selective on restriction sites, and found greater number of polymorphic SNP loci in pea, white lupin and diploid alfalfa when adopting KAPA with a non-selective primer. This protocol displayed a slight advantage also for tetraploid alfalfa (where SNP calling requires higher read depth). KAPA offered the further advantage of more uniform amplification than NEB over fragment sizes and GC contents. The number of GBS-generated polymorphic markers exceeded 6,500 in two tetraploid alfalfa reference populations and a world collection of lupin genotypes, and 2,000 in different sets of pea or lupin recombinant inbred lines. The predictive ability of GBS-based genomic selection was influenced by the genotype missing data threshold and imputation, as well as by the genomic selection model, with the best model depending on traits and data sets. We devised a simple method for comparing phenotypic vs. genomic selection in terms of predicted yield gain per year for same evaluation costs, whose application to preliminary data for alfalfa and pea in a hypothetical selection scenario for each crop indicated a distinct advantage of genomic selection. PMID:28536584

  12. Genotyping-by-Sequencing and Its Exploitation for Forage and Cool-Season Grain Legume Breeding

    Directory of Open Access Journals (Sweden)

    Paolo Annicchiarico

    2017-05-01

    Full Text Available Genotyping-by-Sequencing (GBS may drastically reduce genotyping costs compared with single nucleotide polymorphism (SNP array platforms. However, it may require optimization for specific crops to maximize the number of available markers. Exploiting GBS-generated markers may require optimization, too (e.g., to cope with missing data. This study aimed (i to compare elements of GBS protocols on legume species that differ for genome size, ploidy, and breeding system, and (ii to show successful applications and challenges of GBS data on legume species. Preliminary work on alfalfa and Medicago truncatula suggested the greater interest of ApeKI over PstI:MspI DNA digestion. We compared KAPA and NEB Taq polymerases in combination with primer extensions that were progressively more selective on restriction sites, and found greater number of polymorphic SNP loci in pea, white lupin and diploid alfalfa when adopting KAPA with a non-selective primer. This protocol displayed a slight advantage also for tetraploid alfalfa (where SNP calling requires higher read depth. KAPA offered the further advantage of more uniform amplification than NEB over fragment sizes and GC contents. The number of GBS-generated polymorphic markers exceeded 6,500 in two tetraploid alfalfa reference populations and a world collection of lupin genotypes, and 2,000 in different sets of pea or lupin recombinant inbred lines. The predictive ability of GBS-based genomic selection was influenced by the genotype missing data threshold and imputation, as well as by the genomic selection model, with the best model depending on traits and data sets. We devised a simple method for comparing phenotypic vs. genomic selection in terms of predicted yield gain per year for same evaluation costs, whose application to preliminary data for alfalfa and pea in a hypothetical selection scenario for each crop indicated a distinct advantage of genomic selection.

  13. Linkage of human cytomegalovirus glycoprotein gO variant groups identified from worldwide clinical isolates with gN genotypes, implications for disease associations and evidence for N-terminal sites of positive selection

    International Nuclear Information System (INIS)

    Mattick, C.; Dewin, D.; Polley, S.; Sevilla-Reyes, E.; Pignatelli, S.; Rawlinson, W.; Wilkinson, G.; Dal Monte, P.; Gompels, U.A.

    2004-01-01

    Previously, we identified the glycoprotein gO gene, UL74, as a hypervariable locus in the human cytomegalovirus (HCMV) genome [Virology 293 (2002) 281]. Here, we analyze gO from 50 isolates from congenitally infected newborns, transplant recipients, and HIV/AIDS patients from Italy, Australia, and UK. These are compared to four gO groups described from USA transplantation patients [J. Virol. 76 (2002) 10841]. Phylogenetic analyses identified seven genotypes. Divergence between genotypes was up to 55% and within 3%. Discrete linkage was shown between seven hypervariable gO and gN genotypes, but not with gB. This suggests interactions, while gN and gO are known to form complexes with distinct conserved glycoproteins gM, gH/gL, respectively, both are involved in fusogenic entry and exit. Codon-based maximum likelihood models showed evidence for sites of positive selection. Further analyses of disease relationships should take into account these newly defined gO/gN groups

  14. RNA recombination in Hepatitis delta virus: Identification of a novel naturally occurring recombinant

    Directory of Open Access Journals (Sweden)

    Chia-Chi Lin

    2017-12-01

    Full Text Available Background/Purpose: Hepatitis delta virus (HDV is the only animal RNA virus that has an unbranched rod-like genome with ribozyme activity. It replicates in the nucleus by host RNA polymerase via a rolling circle mechanism. Similar to many RNA viruses encoding their own RNA-dependent RNA polymerases, homologous recombination of HDV occurs in mixed-genotype infections and in cultured cells cotransfected with two HDV sequences, as demonstrated by molecular analyses. Methods: Among 237 published complete genomic sequences, 34 sequences were reported from the small and isolated Miyako Island, Japan, and belonged to the Asia-specific genotypes, HDV-2 and HDV-4 (the majority of them belonged to the known Miyako Island-specific subgroup, HDV-4M. We investigated the presence of naturally occurring HDV recombinant in Miyako Island using phylogenetic and recombination analyses. Results: We identified a two-switch HDV-4/4M intersubtype recombinant with an unbranched rod-like RNA genome. Conclusion: Our data suggest that RNA recombination plays an important role in the rapid evolution of HDV, allowing the production of new HDV strains with correct genomic structures. Keywords: hepatitis delta virus, RNA recombination

  15. β-Lactamase Production in Prevotella intermedia, Prevotella nigrescens, and Prevotella pallens Genotypes and In Vitro Susceptibilities to Selected Antimicrobial Agents

    Science.gov (United States)

    Mättö, Jaana; Asikainen, Sirkka; Väisänen, Marja-Liisa; Von Troil-Lindén, Birgitta; Könönen, Eija; Saarela, Maria; Salminen, Kari; Finegold, Sydney M.; Jousimies-Somer, Hannele

    1999-01-01

    The present study investigated the β-lactamase production of 73 Prevotella intermedia, 84 Prevotella nigrescens, and 14 Prevotella pallens isolates and their in vitro susceptibilities to six antimicrobial agents. The P. intermedia and P. nigrescens isolates were recovered from oral and extraoral samples obtained from subjects in two geographic locations from 1985 to 1995. The clonality of the β-lactamase-positive and β-lactamase-negative isolates and the clustering of the genotypes were studied by arbitrarily primed-PCR fingerprinting. β-Lactamase production was detected in 29% of P. intermedia isolates, 29% of P. nigrescens isolates, and 57% of P. pallens isolates. No difference in the frequencies of β-lactamase production by P. intermedia and P. nigrescens between isolates from oral and extraoral sites, between isolates obtained at different time periods, or between P. intermedia isolates from different geographic locations was observed. However, the P. nigrescens isolates from the United States were significantly more frequently (P = 0.015) β-lactamase positive than those from Finland. No association between the genotypes and β-lactamase production or between the genotypes and the sources of the isolates was found. The penicillin G MICs at which 90% of the isolates were inhibited were 8 μg/ml for P. intermedia, 8 μg/ml for P. nigrescens, and 16 μg/ml for P. pallens. For the β-lactamase-negative isolates, the corresponding values were 0.031, 0.031, and 0.125 μg/ml, and for the β-lactamase-positive isolates, the corresponding values were 16, 8, and 32 μg/ml. All isolates were susceptible to amoxicillin-clavulanate, cefoxitin, metronidazole, azithromycin, and trovafloxacin. The MICs of amoxicillin-clavulanate and cefoxitin were relatively higher for the β-lactamase-positive population than for the β-lactamase-negative population. PMID:10508011

  16. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    : Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. ELIGIBILITY CRITERIA FOR STUDY SELECTION: Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after...

  17. Seleção de genótipos de capim-elefante quanto à resistência à cigarrinha-das-pastagens Selection of elephant grass genotypes for resistance to spittlebug

    Directory of Open Access Journals (Sweden)

    Alexander Machado Auad

    2007-08-01

    assessed every 15 days, in plants kept at greenhouse, where adults of M. spectabilis were periodically released, in a completely randomized design, with three repetitions per genotype in two sampling periods. Cameroon de Piracicaba, Pioneiro, Cuba 169, Santa Rita, Mineiro Ipeaco, Mercker Comum de Pinda and CNPGL 96-27-3 genotypes were selected for resistance, by antibiosis mechanism. In the study of the nonpreference mechanism, the number and average size of the nymphs varied significantly as a function of the elephant grass genotype. Roxo de Botucatu and Pioneiro genotypes are, respectively, susceptible and resistant check candidates by the antibiosis mechanism, and Cameroon and Cameroon Piracicaba genotypes are promising by the nonpreference mechanism.

  18. Misidentification of recombinant hepatitis C virus leading to treatment failure with direct acting antivirals.

    Science.gov (United States)

    Mourez, Thomas; Decroos, Amandine; Goria, Odile; Montialoux, Hélène; De Oliveira, Fabienne; Larrat, Sylvie; Plantier, Jean-Christophe; Riachi, Ghassan

    2018-05-01

    The use of new Direct Acting Antivirals, specific of HCV, has greatly improved the HCV treatment. Most of the DAA are specific of HCV genotypes. Genotyping methods may target different regions of the HCV genome, though only the whole genome sequencing could confirm the correct genotype. The present study describes the virological investigation of a treatment failure due to the false identification of an unusual 2k/1b recombinant HCV form. It describes the sequencing methods, and the similarity analysis of the sequences to different genotype query sequences, to identify the recombination breakpoint. © 2018 Wiley Periodicals, Inc.

  19. Large-scale analysis of differential gene expression in coffee genotypes resistant and susceptible to leaf miner–toward the identification of candidate genes for marker assisted-selection

    Science.gov (United States)

    2014-01-01

    Background A successful development of herbivorous insects into plant tissues depends on coordination of metabolic processes. Plants have evolved complex mechanisms to recognize such attacks, and to trigger a defense response. To understand the transcriptional basis of this response, we compare gene expression profiles of two coffee genotypes, susceptible and resistant to leaf miner (Leucoptera coffella). A total of 22000 EST sequences from the Coffee Genome Database were selected for a microarray analysis. Fluorescence probes were synthesized using mRNA from the infested and non-infested coffee plants. Array hybridization, scanning and data normalization were performed using Nimble Scan® e ArrayStar® platforms. Genes with foldchange values +/-2 were considered differentially expressed. A validation of 18 differentially expressed genes was performed in infected plants using qRT-PCR approach. Results The microarray analysis indicated that resistant plants differ in gene expression profile. We identified relevant transcriptional changes in defense strategies before insect attack. Expression changes (>2.00-fold) were found in resistant plants for 2137 genes (1266 up-regulated and 873 down-regulated). Up-regulated genes include those responsible for defense mechanisms, hypersensitive response and genes involved with cellular function and maintenance. Also, our analyses indicated that differential expression profiles between resistant and susceptible genotypes are observed in the absence of leaf-miner, indicating that defense is already build up in resistant plants, as a priming mechanism. Validation of selected genes pointed to four selected genes as suitable candidates for markers in assisted-selection of novel cultivars. Conclusions Our results show evidences that coffee defense responses against leaf-miner attack are balanced with other cellular functions. Also analyses suggest a major metabolic reconfiguration that highlights the complexity of this response. PMID

  20. Recombinant protein production technology

    Science.gov (United States)

    Recombinant protein production is an important technology for antibody production, biochemical activity study, and structural determination during the post-genomic era. Limiting factors in recombinant protein production include low-level protein expression, protein precipitation, and loss of protein...

  1. Genetic diversity, recombination, and divergence in animal associated Penicillium dipodomyis.

    Directory of Open Access Journals (Sweden)

    Daniel A Henk

    Full Text Available Penicillium dipodomyis is thought to be an exclusively asexual fungus associated with Kangaroo Rats, Dipodomys species, and is unique among Penicillium species in growing at 37°C but producing no known toxins. Lack of recombination within P. dipodomyis would result in limited adaptive flexibility but possibly enhance local adaptation and host selection via maintenance of favourable genotypes. Here, analysis of DNA sequence data from five protein-coding genes shows that recombination occurs within P. dipodomyis on a small spatial scale. Furthermore, detection of mating-type alleles supports outcrossing and a sexual cycle in P. dipodomyis. P. dipodomyis was a weaker competitor in in vitro assays with other Penicillium species found in association with Kanagaroo rats. Bayesian species level analysis suggests that the P. dipodomyis lineage diverged from closely related species also found in cheek pouches of Kangaroo Rats and their stored seeds about 11 million years ago, a similar divergence time as Dipodomys from its sister rodent taxa.

  2. Development of JFH1-based cell culture systems for hepatitis C virus genotype 4a and evidence for cross-genotype neutralization

    DEFF Research Database (Denmark)

    Scheel, Troels Kasper Høyer; Gottwein, Judith Margarete; Jensen, Tina Birk

    2008-01-01

    as well as drug and vaccine research on an increasingly important genotype in the Middle East, Africa, and Europe. We also developed genotype 1a intergenotypic recombinants from H77C with vital mutations in NS3. Using H77C/JFH1 and ED43/JFH1 viruses, we demonstrated high homologous neutralizing antibody...

  3. Effect of Genotypes and Seed Production Environments on Seed ...

    African Journals Online (AJOL)

    Fourteen genetically diverse sesame (Sesamum indicum L.) genotypes were grown under three diverse .... genetic line. GenotypiC differences in the quality of seed provide an opportunity for employing. genotypiC selection as a method of improving seed quality (Adebisi,. 2004). ...... Sugar beet (Beta vulgaris L.) seed vigour ...

  4. Evidence of recombination in intrapatient populations of hepatitis C virus.

    Science.gov (United States)

    Sentandreu, Vicente; Jiménez-Hernández, Nuria; Torres-Puente, Manuela; Bracho, María Alma; Valero, Ana; Gosalbes, María José; Ortega, Enrique; Moya, Andrés; González-Candelas, Fernando

    2008-09-18

    Hepatitis C virus (HCV) is a major cause of liver disease worldwide and a potential cause of substantial morbidity and mortality in the future. HCV is characterized by a high level of genetic heterogeneity. Although homologous recombination has been demonstrated in many members of the family Flaviviridae, to which HCV belongs, there are only a few studies reporting recombination on natural populations of HCV, suggesting that these events are rare in vivo. Furthermore, these few studies have focused on recombination between different HCV genotypes/subtypes but there are no reports on the extent of intra-genotype or intra-subtype recombination between viral strains infecting the same patient. Given the important implications of recombination for RNA virus evolution, our aim in this study has been to assess the existence and eventually the frequency of intragenic recombination on HCV. For this, we retrospectively have analyzed two regions of the HCV genome (NS5A and E1-E2) in samples from two different groups: (i) patients infected only with HCV (either treated with interferon plus ribavirin or treatment naïve), and (ii) HCV-HIV co-infected patients (with and without treatment against HIV). The complete data set comprised 17712 sequences from 136 serum samples derived from 111 patients. Recombination analyses were performed using 6 different methods implemented in the program RDP3. Recombination events were considered when detected by at least 3 of the 6 methods used and were identified in 10.7% of the amplified samples, distributed throughout all the groups described and the two genomic regions studied. The resulting recombination events were further verified by detailed phylogenetic analyses. The complete experimental procedure was applied to an artificial mixture of relatively closely viral populations and the ensuing analyses failed to reveal artifactual recombination. From these results we conclude that recombination should be considered as a potentially

  5. Investigations of the fate of radiation-induced mutations in dependence of selection and recombination with recessive gene marks in experimental populations of Drosophila melanogaster

    International Nuclear Information System (INIS)

    Pfriem, P.

    1978-01-01

    Three dichromosomal experimental populations of Drosophila melanogaster were started with heterozygons dp b/+ +- animals with identical dp b- and + +- II-chromosomes for all three populations. The male ++/++- parents had been exposed to 9000 r prior to the experiments. In 7 random samples of the first 15 generations of the experiment, the incidence of the mutant alleles dp and b, the exchange inequilibrium between the alleles of the two labelled loci, and the letthal factor frequency were investigatet. It was found that - The b allele had an equilibrium frequency of about 57% in all populations, while the frequency of the dp allele decreased to about 10% within the first 15 generations. - The association values a as measures of an exchange inequilibrium showed a fast development towards exchange inequilibrium within these 15 generations for the three populations. - The incidence of lethal factors remained constant throughout the generations for the tested type ++ and + b chromosomes, in irradiated ++- chromosomes, it was higher on an average than in the + b- chromosomes. The total lethal factor incidence was about 30%. - The alleling rate of lethal factors and the viability values of several distinguishable genotypes indicated individualities of the three populations in spite of their identical behaviour. In two of the three populations, the near-constant incidence of lethal factors was supposed to be due to a small number of lethal which accurred with high frequency. (orig.) [de

  6. Effects of citalopram and escitalopram on fMRI response to affective stimuli in healthy volunteers selected by serotonin transporter genotype.

    Science.gov (United States)

    Henry, Michael E; Lauriat, Tara L; Lowen, Steven B; Churchill, Jeffrey H; Hodgkinson, Colin A; Goldman, David; Renshaw, Perry F

    2013-09-30

    This study was designed to assess whether functional magnetic resonance imaging (fMRI) following antidepressant administration (pharmaco-fMRI) is sufficiently sensitive to detect differences in patterns of activation between enantiomers of the same compound. Healthy adult males (n=11) participated in a randomized, double-blind, cross-over trial with three medication periods during which they received citalopram (racemic mixture), escitalopram (S-citalopram alone), or placebo for 2 weeks. All participants had high expression serotonin transporter genotypes. An fMRI scan that included passive viewing of overt and covert affective faces and affective words was performed after each medication period. Activation in response to overt faces was greater following escitalopram than following citalopram in the right insula, thalamus, and putamen when the faces were compared with a fixation stimulus. For the rapid covert presentation, a greater response was observed in the left middle temporal gyrus in the happy versus fearful contrast following escitalopram than following citalopram. Thus, the combination of genomics and fMRI was successful in discriminating between two very similar drugs. However, the pattern of activation observed suggests that further studies are indicated to understand how to optimally combine the two techniques. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  7. Propriedades e classificação da madeira aplicadas à seleção de genótipos de Eucalyptus Properties and classification of wood for selecting Eucalyptus genotypes

    Directory of Open Access Journals (Sweden)

    Ronaldo Pereira Caixeta

    2003-02-01

    Full Text Available Os objetivos do presente estudo foram classificar e selecionar genótipos superiores de eucalipto por meio das propriedades de sua madeira, utilizando como ferramenta a análise de agrupamento, método de otimização de Tocher, com o intuito de obter múltiplos produtos. Foram utilizados 44 genótipos de eucaliptos, adaptados para as condições ambientais do noroeste de Minas Gerais. Para classificação dos materiais foram utilizadas características físicas, de resistência mecânica e químicas da madeira. Os resultados da análise de agrupamento classificaram os 44 genótipos em 11 grupos distintos, com alta variabilidade ou divergência entre si. De acordo com os valores médios das características apresentadas pelos grupos formados, foi possível definir novos clones de potencial, que certamente forneceram madeira de qualidade superior para atender a diversos usos. Os genótipos pertencentes aos grupos V, VI e VIII apresentam potencial favorável à produção de madeira serrada. Eles possibilitarão, também, a geração de híbridos artificiais a serem usados em futuros programas de melhoramento genético de Eucalyptus.The objective of this study was to classify and select superior genotypes of eucalypt based on the properties of its wood, utilizing cluster analysis, the Tocher's optimization method aiming to obtain various products. Forty-four genotypes adapted to the environmental conditions of northwestern Minas Gerais were used. Physical, mechanical resistance and chemical wood characteristics were used for the classification of the materials. Cluster analysis classified the genotypes in 11 different groups with high variability or divergence among them. According to the average values of the characteristics presented by the formed groups, it was possible to define new potential clones, which will certainly provide wood of superior quality. The genotypes from groups V, VI and VIII show potential for the production of sawed wood

  8. Antixenosis of bean genotypes to Chrysodeixis includens (Lepidoptera: Noctuidae)

    OpenAIRE

    Morando, Rafaela [UNESP; Lopes Baldin, Edson Luiz [UNESP; Cruz, Patricia Leite [UNESP; Lourencao, Andre Luiz; Chiorato, Alisson Fernando

    2015-01-01

    The objective of this work was to evaluate bean genotypes for resistance to soybean looper (Chrysodeixis includens). Initially, free-choice tests were carried out with 59 genotypes, divided into three groups according to leaf color intensity (dark green, light green, and medium green), in order to evaluate oviposition preference. Subsequently, 12 genotypes with high potential for resistance were selected, as well as two susceptible commercial standards. With these genotypes, new tests were pe...

  9. Effect of acute swim stress on plasma corticosterone and brain monoamine levels in bidirectionally selected DxH recombinant inbred mouse strains differing in fear recall and extinction.

    Science.gov (United States)

    Browne, Caroline A; Hanke, Joachim; Rose, Claudia; Walsh, Irene; Foley, Tara; Clarke, Gerard; Schwegler, Herbert; Cryan, John F; Yilmazer-Hanke, Deniz

    2014-12-01

    Stress-induced changes in plasma corticosterone and central monoamine levels were examined in mouse strains that differ in fear-related behaviors. Two DxH recombinant inbred mouse strains with a DBA/2J background, which were originally bred for a high (H-FSS) and low fear-sensitized acoustic startle reflex (L-FSS), were used. Levels of noradrenaline, dopamine, and serotonin and their metabolites 3,4-dihydroxyphenyacetic acid (DOPAC), homovanillic acid (HVA), and 5-hydroxyindoleacetic acid (5-HIAA) were studied in the amygdala, hippocampus, medial prefrontal cortex, striatum, hypothalamus and brainstem. H-FSS mice exhibited increased fear levels and a deficit in fear extinction (within-session) in the auditory fear-conditioning test, and depressive-like behavior in the acute forced swim stress test. They had higher tissue noradrenaline and serotonin levels and lower dopamine and serotonin turnover under basal conditions, although they were largely insensitive to stress-induced changes in neurotransmitter metabolism. In contrast, acute swim stress increased monoamine levels but decreased turnover in the less fearful L-FSS mice. L-FSS mice also showed a trend toward higher basal and stress-induced corticosterone levels and an increase in noradrenaline and serotonin in the hypothalamus and brainstem 30 min after stress compared to H-FSS mice. Moreover, the dopaminergic system was activated differentially in the medial prefrontal cortex and striatum of the two strains by acute stress. Thus, H-FSS mice showed increased basal noradrenaline tissue levels compatible with a fear phenotype or chronic stressed condition. Low corticosterone levels and the poor monoamine response to stress in H-FSS mice may point to mechanisms similar to those found in principal fear disorders or post-traumatic stress disorder.

  10. Electron-ion recombination at low energy

    International Nuclear Information System (INIS)

    Andersen, L.H.

    1993-01-01

    The work is based on results obtained with a merged-beams experiment. A beam of electronics with a well characterized density and energy distribution was merged with a fast, monoenergetic ion beam. Results have been obtained for radiative recombination and dielectronic recombination at low relative energies (0 to ∼70eV). The obtained energy resolution was improved by about a factor of 30. High vacuum technology was used to suppress interactions with electrons from the environments. The velocity distribution of the electron beam was determined. State-selective dielectronic-recombination measurements were performable. Recombination processes were studied. The theoretical background for radiative recombination and Kramers' theory are reviewed. The quantum mechanical result and its relation to the semiclassical theory is discussed. Radiative recombination was also measured with several different non-bare ions, and the applicability of the semiclassical theory to non-bare ions was investigated. The use of an effective charge is discussed. For dielectronic recombination, the standard theoretical approach in the isolated resonance and independent-processes approximation is debated. The applicability of this method was tested. The theory was able to reproduce most of the experimental data except when the recombination process was sensitive to couplings between different electronic configurations. The influence of external perturbing electrostatic fields is discussed. (AB) (31 refs.)

  11. Evolution of molecular phenotypes under stabilizing selection

    Science.gov (United States)

    Nourmohammad, Armita; Schiffels, Stephan; Lässig, Michael

    2013-01-01

    Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype’s genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes.

  12. Evolution of molecular phenotypes under stabilizing selection

    International Nuclear Information System (INIS)

    Nourmohammad, Armita; Schiffels, Stephan; Lässig, Michael

    2013-01-01

    Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype’s genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes. (paper)

  13. Seleção de genótipos de pessegueiro F1 com baixa necessidade de frio hibernal Selection of F1 peach genotypes with low chilling requirements

    Directory of Open Access Journals (Sweden)

    Américo Wagner Júnior

    2009-12-01

    Full Text Available A baixa necessidade de frio é característica fundamental para que se possa cultivar economicamente o pessegueiro em condições de clima subtropical, devendo ser este, portanto, o principal objetivo dos programas de melhoramento nestas regiões. o objetivo deste trabalho foi avaliar e selecionar progênies de pessegueiro com baixa necessidade de frio hibernal por meio do método de ramos destacados e indicar o melhor genitor para utilização em programas de melhoramento, visando a esta característica. Foram avaliados 180 genótipos pertencentes a 25 populações de pessegueiro, sendo que o número de genótipos em cada população variou de três a dezenove. os ramos foram submetidos a 50; 100; 150; 200 e 400 unidades de frio, e, ao término de cada tratamento, os ramos foram transferidos para o interior da casa de vegetação. Após 21 dias, foram avaliados quanto às porcentagens de floração e brotação,e com os resultados obtidos, 5 populações e 29 genótipos de pessegueiro com baixa necessidade de frio hibernal foram selecionados. A cultivar Real mostrou-se eficiente na obtenção de pessegueiros com baixa necessidade de frio hibernal, quando utilizada como genitor feminino.Low chilling requirement is the main characteristic for the economic cultivation of peaches under subtropical climate conditions, therefore it should be the most important objective in breeding programs for these regions. The aim of this work was to evaluate and to select peach progenies with low chilling requirement through detached twigs methodology, to indicate a good genitor for using in the breeding program with this characteristic. A total of 180 genotypes, from 25 peach populations, were observed. The genotypes of each population varied from three to nineteen plants. The twigs were submitted to 50, 100, 150, 200 and 400 chilly units. once the treatments were concluded, the twigs were transferred to a greenhouse and after twenty one days the budbreak and

  14. Production of recombinant Ig molecules from antigen-selected single B cells and restricted usage of Ig-gene segments by anti-D antibodies

    NARCIS (Netherlands)

    Dohmen, Serge E.; Mulder, Arend; Verhagen, Onno J. H. M.; Eijsink, Chantal; Franke-van Dijk, Marry E. I.; van der Schoot, C. Ellen

    2005-01-01

    The Ig-genes of the heavy chains in anti-D-specific hybridomas and Fab/scFv-fragments selected from phage-display libraries are restricted to a group of closely related genes (IGHV3s genes). We analyzed the Ig-gene repertoire in anti-D-specific B cells of two hyperimmunized donors using a completely

  15. Evaluation of genome-enabled selection for bacterial cold water disease resistance using progeny performance data in Rainbow Trout: Insights on genotyping methods and genomic prediction models

    Science.gov (United States)

    Bacterial cold water disease (BCWD) causes significant economic losses in salmonid aquaculture, and traditional family-based breeding programs aimed at improving BCWD resistance have been limited to exploiting only between-family variation. We used genomic selection (GS) models to predict genomic br...

  16. Efficient cell culture system for hepatitis C virus genotype 6A

    DEFF Research Database (Denmark)

    2013-01-01

    The present inventors developed hepatitis C virus 6a/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and the complete NS2 were replaced by the corresponding genes of the genotype 6a reference strain HK6a. Sequence analysis of recovered 6a/2a recombinants from...

  17. Efficient cell culture system for hepatitis C virus genotype 2B

    DEFF Research Database (Denmark)

    2014-01-01

    The present inventors developed hepatitis C virus 2b/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and the complete NS2 were replaced by the corresponding genes of the genotype 2b reference strain J8. Sequence analysis of recovered 2b/2a recombinants from 2...

  18. Estimating and testing the effect of allelic recombination on the ...

    African Journals Online (AJOL)

    Jane

    2011-01-21

    Jan 21, 2011 ... The significance of the correlation coefficient as well as the fitted regression model was obtained using. Analysis of Variance method. Key words: Allele, genotype, regression, correlation, F-ratio, analysis of variance. INTRODUCTION. Genetic recombination is an effective means of combining one individual ...

  19. Efficient cell culture system for hepatitis C virus genotype 1a and 1b

    DEFF Research Database (Denmark)

    2013-01-01

    The present inventors developed hepatitis C virus 1a/2a and 1b/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and NS2 were replaced by the corresponding genes of the genotype Ia reference strain H77C or TN or the corresponding genes of the genotype Ib...

  20. Efficient cell culture system for hepatitis C virus genotype 7a

    DEFF Research Database (Denmark)

    2013-01-01

    Genotype 7a has been identified recently, thus not much is known about the biology of this new, major HCV genotype. The present inventors developed hepatitis C virus 7a/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and the complete NS2 were replaced...

  1. Resolving ambiguity in the phylogenetic relationship of genotypes A, B, and C of hepatitis B virus

    Science.gov (United States)

    2013-01-01

    Background Hepatitis B virus (HBV) is an important infectious agent that causes widespread concern because billions of people are infected by at least 8 different HBV genotypes worldwide. However, reconstruction of the phylogenetic relationship between HBV genotypes is difficult. Specifically, the phylogenetic relationships among genotypes A, B, and C are not clear from previous studies because of the confounding effects of genotype recombination. In order to clarify the evolutionary relationships, a rigorous approach is required that can effectively explore genetic sequences with recombination. Result In the present study, phylogenetic relationship of the HBV genotypes was reconstructed using a consensus phylogeny of phylogenetic trees of HBV genome segments. Reliability of the reconstructed phylogeny was extensively evaluated in agreements of local phylogenies of genome segments. The reconstructed phylogenetic tree revealed that HBV genotypes B and C had a closer phylogenetic relationship than genotypes A and B or A and C. Evaluations showed the consensus method was capable to reconstruct reliable phylogenetic relationship in the presence of recombinants. Conclusion The consensus method implemented in this study provides an alternative approach for reconstructing reliable phylogenetic relationships for viruses with possible genetic recombination. Our approach revealed the phylogenetic relationships of genotypes A, B, and C of HBV. PMID:23758960

  2. Genotypic Characterization of Azotobacteria Isolated from Argentinean Soils and Plant-Growth-Promoting Traits of Selected Strains with Prospects for Biofertilizer Production

    Directory of Open Access Journals (Sweden)

    Esteban Julián Rubio

    2013-01-01

    Full Text Available The genetic diversity among 31 putative Azotobacter isolates obtained from agricultural and non-agricultural soils was assessed using rep-PCR genomic fingerprinting and identified to species level by ARDRA and partial 16S rRNA gene sequence analysis. High diversity was found among the isolates, identified as A. chroococcum, A. salinestris, and A. armeniacus. Selected isolates were characterized on the basis of phytohormone biosynthesis, nitrogenase activity, siderophore production, and phosphate solubilization. Indole-3 acetic-acid (IAA, gibberellin (GA3 and zeatin (Z biosynthesis, nitrogenase activity, and siderophore production were found in all evaluated strains, with variation among them, but no phosphate solubilization was detected. Phytohormones excreted to the culture medium ranged in the following concentrations: 2.2–18.2 μg IAA mL−1, 0.3–0.7 μg GA3 mL−1, and 0.5–1.2 μg Z mL−1. Seed inoculations with further selected Azotobacter strains and treatments with their cell-free cultures increased the number of seminal roots and root hairs in wheat seedlings. This latter effect was mimicked by treatments with IAA-pure solutions, but it was not related to bacterial root colonization. Our survey constitutes a first approach to the knowledge of Azotobacter species inhabiting Argentinean soils in three contrasting geographical regions. Moreover, this phenotypic characterization constitutes an important contribution to the selection of Azotobacter strains for biofertilizer formulations.

  3. Genotypic characterization of Azotobacteria isolated from Argentinean soils and plant-growth-promoting traits of selected strains with prospects for biofertilizer production.

    Science.gov (United States)

    Rubio, Esteban Julián; Montecchia, Marcela Susana; Tosi, Micaela; Cassán, Fabricio Darío; Perticari, Alejandro; Correa, Olga Susana

    2013-01-01

    The genetic diversity among 31 putative Azotobacter isolates obtained from agricultural and non-agricultural soils was assessed using rep-PCR genomic fingerprinting and identified to species level by ARDRA and partial 16S rRNA gene sequence analysis. High diversity was found among the isolates, identified as A. chroococcum, A. salinestris, and A. armeniacus. Selected isolates were characterized on the basis of phytohormone biosynthesis, nitrogenase activity, siderophore production, and phosphate solubilization. Indole-3 acetic-acid (IAA), gibberellin (GA3) and zeatin (Z) biosynthesis, nitrogenase activity, and siderophore production were found in all evaluated strains, with variation among them, but no phosphate solubilization was detected. Phytohormones excreted to the culture medium ranged in the following concentrations: 2.2-18.2 μ g IAA mL(-1), 0.3-0.7 μ g GA3 mL(-1), and 0.5-1.2 μ g Z mL(-1). Seed inoculations with further selected Azotobacter strains and treatments with their cell-free cultures increased the number of seminal roots and root hairs in wheat seedlings. This latter effect was mimicked by treatments with IAA-pure solutions, but it was not related to bacterial root colonization. Our survey constitutes a first approach to the knowledge of Azotobacter species inhabiting Argentinean soils in three contrasting geographical regions. Moreover, this phenotypic characterization constitutes an important contribution to the selection of Azotobacter strains for biofertilizer formulations.

  4. Recombinant clotting factors.

    Science.gov (United States)

    Pipe, Steven W

    2008-05-01

    The recombinant era for haemophilia began in the early 1980s with the cloning and subsequent expression of functional proteins for both factors VIII and IX. Efficient production of recombinant clotting factors in mammalian cell culture systems required overcoming significant challenges due to the complex post-translational modifications that were integral to their pro-coagulant function. The quick development and commercialization of recombinant clotting factors was, in part, facilitated by the catastrophic impact of viral contamination of plasma-derived clotting factor concentrates at the time. Since their transition into the clinic, the recombinant versions of both factor VIII and IX have proven to be remarkable facsimiles of their plasma-derived counterparts. The broad adoption of recombinant therapy throughout the developed world has significantly increased the supply of clotting factor concentrates and helped advance aggressive therapeutic interventions such as prophylaxis. The development of recombinant VIIa was a further advance bringing a recombinant option to haemophilia patients with inhibitors. Recombinant DNA technology remains the platform to address ongoing challenges in haemophilia care such as reducing the costs of therapy, increasing the availability to the developing world, and improving the functional properties of these proteins. In turn, the ongoing development of new recombinant clotting factor concentrates is providing alternatives for patients with other inherited bleeding disorders.

  5. Seleção preliminar de genótipos de pinheira em Bom Jesus-PI Preliminary selection of sugar apple genotypes in Bom Jesus county, Piauí state, Brazil

    Directory of Open Access Journals (Sweden)

    Ítalo Herbert Lucena Cavalcante

    2011-01-01

    Full Text Available A pinheira (Annona squamosa L. ocorre espontaneamente no Nordeste Brasileiro, onde é explorada de forma extrativista, caracterizando-se pela falta de manejo adequado e material genético selecionado. Nesse sentido, foi realizado um experimento com objetivo de avaliar a produtividade, as características físicas e químicas de frutos de dez genótipos de pinheira no município de Bom Jesus, PI. Adotou-se delineamento inteiramente casualizado, com tratamentos representados por dez genótipos de pinheira e três repetições. Foram avaliadas as seguintes variáveis: vitamina C, acidez titulável, sólidos solúveis, relação SS/AT "ratio", diâmetros longitudinal e transversal, relação DL/DT, número se sementes por fruto, massa dos frutos e produção por planta. Os genótipos apresentam diferenças quanto às características químicas, físicas e produtivas dos frutos. Os genótipos foram agrupados em sete grupos, com destaque para o grupo III (Gen-02 e grupo IV (Gen-05, fato que explicitou as diferenças entre os genótipos de pinheira quanto às características produtivas e químicas e físicas dos frutos. Genótipos Gen-01 e Gen-02 apresentam potencial para instalação em plantios comerciais, pela produtividade, formato do fruto ou por caracterizarem fontes naturais de vitamina C.The sugar apple (Annona squamosa L. is native to tropical America, occurring spontaneously in Northeastern Brazil, where it is exploited mainly as subsistence without adequate management and without genetic material selection. An experiment was developed aiming to evaluate yield, physical and chemical characteristics of the fruits of ten sugar apple genotypes in Bom Jesus, Piauí State, Brazil. A completely randomized design with treatments represented by ten genotypes and three replications was adopted. The following variables were evaluated: vitamin C, titratable acidity, soluble solids, SS/TA ratio, longitudinal diameter and transverse, LD/TD, number of

  6. Random population model to explain the recombination dynamics in single InAs/GaAs quantum dots under selective optical pumping

    Energy Technology Data Exchange (ETDEWEB)

    Gomis-Bresco, Jordi; Munoz-Matutano, Guillermo; Martinez-Pastor, Juan [Institut de Ciencies dels Materials de la Universitat de Valencia, Universitat de Valencia, Valencia (Spain); Alen, Benito [IMM, Instituto de Microelectronica de Madrid (CNM, CSIC), Isaac Newton 8, 28760 Tres Cantos, Madrid (Spain); Seravalli, Luca; Frigeri, Paola; Trevisi, Giovanna; Franchi, Secondo, E-mail: jrdi.gomis@icn.cat [CNR-IMEM Institute, Parco delle Scienze 37a, I-43100 Parma (Italy)

    2011-02-15

    We model the time-resolved and time-integrated photoluminescence of a single InAs/GaAs quantum dot (QD) using a random population description. We reproduce the joint power dependence of the single QD exciton complexes (neutral exciton, neutral biexciton and charged trions). We use the model to investigate the selective optical pumping phenomenon, a predominance of the negative trion observed when the optical excitation is resonant to a non-intentional impurity level. Our experiments and simulations determine that the negative charge confined in the QD after exciting resonance to the impurity level escapes in 10 ns.

  7. Genotype to phenotype

    National Research Council Canada - National Science Library

    Malcolm, Sue; Goodship, Timothy H. J

    2001-01-01

    ... Disorders Molecular Genetics of Hypertension Human Gene EvolutionAnalysis of Multifactorial Disease Transcription Factors Molecular Genetics of Cancer, Second edition Genotype to Phenotype, second e...

  8. The potential of transgenic green microalgae; a robust photobioreactor to produce recombinant therapeutic proteins.

    Science.gov (United States)

    Akbari, Fariba; Eskandani, Morteza; Khosroushahi, Ahmad Yari

    2014-11-01

    Microalgae have been used in food, cosmetic, and biofuel industries as a natural source of lipids, vitamins, pigments and antioxidants for a long time. Green microalgae, as potent photobioreactors, can be considered as an economical expression system to produce recombinant therapeutical proteins at large-scale due to low cost of production and scaling-up capitalization owning to the inexpensive medium requirement, fast growth rate, and the ease of manipulation. These microalgae possess all benefit eukaryotic expression systems including the ability of post-translational modifications required for proper folding and stability of active proteins. Among the many items regarded as recombinant protein production, this review compares the different expression systems with green microalgae like Dunaliella by viewing the nuclear/chloroplast transformation challenges/benefits, related selection markers/reporter genes, and crucial factors/strategies affecting the increase of foreign protein expression in microalgae transformants. Some important factors were discussed regarding the increase of protein yielding in microalgae transformants including: transformation-associated genotypic modifications, endogenous regulatory factors, promoters, codon optimization, enhancer elements, and milking of recombinant protein.

  9. Evaluation of sequencing of HCV core/E1, NS5A and NS5B as a genotype predictive tool in comparison with commercial assays targeting 5'UTR.

    Science.gov (United States)

    McCormick, Adele L; Macartney, Malcolm J; Abdi-Abshir, Ikran; Labbett, Wendy; Smith, Colette; Irish, Dianne; Webster, Daniel P; Haque, Tanzina

    2015-05-01

    Hepatitis C virus (HCV) genotyping is required for tailoring the dose and duration of antiviral therapy, predicting virological response rates, and selecting future treatment options. To establish whether baseline genotypes, performed by INNO-LiPA Version 1.0 (v1.0), before 2008, were valid for making treatment decisions now or whether genotypic determination should be repeated. Furthermore, to evaluate concordance between Abbott RealTime genotype II assay (RT) and genotyping by sequencing HCV C/E1, NS5A, NS5B. Genotyping by RT and sequencing was performed on paired historic and current specimens from 50 patients previously baseline genotyped using INNO-LiPA. Of 100 samples from 50 patients, ≥ 2 of HCV genomic target regions yielded a sequence that was suitable for genotyping, with 100% concordance, providing no evidence of recombination events. Genotype and subtype prediction based on RT and sequencing agreed in 62.8% historic and 72.7% current specimens, with a kappa coefficient score of 0.48 and 0.76, respectively. LiPA could not subtype 46% of HCV gt1 infections, and LiPA subgenotype was only in agreement with RT and sequencing in 28.6% cases, where matched baseline and historic specimens were available. Three patients were indeterminate by RT, and five patients with HCV gt1 infections could not be subtyped by RT. However, RT revealed mixed infections in five patients where sequencing detected only single HCV infection at 20% threshold. Genotyping by sequencing, exhibited excellent concordance, with moderate to good agreement with RT, and could resolve RT indeterminates and subtype HCV-gt1 infections not possible by LiPA. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Recombinant gene expression protocols

    National Research Council Canada - National Science Library

    Tuan, Rocky S

    1997-01-01

    .... A fundamental requirement for successful recombinant gene expression is the design of the cloning vector and the choice of the host organism for expression. Recombinant Gene Expression Protocols grows out of the need for a laboratory manual that provides the reader the background and rationale, as well as the practical protocols for the preparation of...

  11. Evaluation of ( Sesamum indicum L) genotypes for yield stability and ...

    African Journals Online (AJOL)

    After years of preliminary and advanced yield trials, seven advanced beniseed genotypes were selected for on-station evaluation at NCRI, Badeggi in 1996 and 1997. Four genotypes identified as promising lines were selected with the farmers' variety (Yandev-55) for multi-locational on-farm evaluation in six states.

  12. Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus

    Directory of Open Access Journals (Sweden)

    Mark W. Jackwood

    2011-09-01

    Full Text Available Recombination in the family Coronaviridae has been well documented and is thought to be a contributing factor in the emergence and evolution of different coronaviral genotypes as well as different species of coronavirus. However, there are limited data available on the frequency and extent of recombination in coronaviruses in nature and particularly for the avian gamma-coronaviruses where only recently the emergence of a turkey coronavirus has been attributed solely to recombination. In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. Evidence of recombination was found in every sequence analyzed and was distributed throughout the entire genome. Areas that have the highest occurrence of recombination are located in regions of the genome that code for nonstructural proteins 2, 3 and 16, and the structural spike glycoprotein. The extent of the recombination observed, suggests that this may be one of the principal mechanisms for generating genetic and antigenic diversity within IBV. These data indicate that reticulate evolutionary change due to recombination in IBV, likely plays a major role in the origin and adaptation of the virus leading to new genetic types and strains of the virus.

  13. Mechanisms and factors that influence high frequency retroviral recombination

    DEFF Research Database (Denmark)

    Delviks-Frankenberry, Krista; Galli, Andrea; Nikolaitchik, Olga

    2011-01-01

    With constantly changing environmental selection pressures, retroviruses rely upon recombination to reassort polymorphisms in their genomes and increase genetic diversity, which improves the chances for the survival of their population. Recombination occurs during DNA synthesis, whereby reverse...... transcriptase undergoes template switching events between the two copackaged RNAs, resulting in a viral recombinant with portions of the genetic information from each parental RNA. This review summarizes our current understanding of the factors and mechanisms influencing retroviral recombination, fidelity...... of the recombination process, and evaluates the subsequent viral diversity and fitness of the progeny recombinant. Specifically, the high mutation rates and high recombination frequencies of HIV-1 will be analyzed for their roles in influencing HIV-1 global diversity, as well as HIV-1 diagnosis, drug treatment...

  14. [Genomic characteristics and recombination of enterovirus 71 strains isolated in Henan Province between 2008 and 2010].

    Science.gov (United States)

    Wei, Hai-Yan; Xu, Yu-Ling; Huang, Xue-Yong; Ma, Hong; Chen, Hao-Min; Xu, Bian-Li

    2011-09-01

    To reveal the genetic features and recombination of enterovirus 71 isolates between 2008 and 2010. A total of 5 enterovirus 71 isolates were sequenced completely and phylogenetic analysis and recombination were performed. Phylogenetic analysis based on VP1 regions revealed that the Henan enterovirus 71 between 2008 and 2010 belonged to C4a in subgenotype C4. Bootscan analyses and phylogenetic analysis based on the 5'UTR, P1, P2, P3 genomic regions revealed the recombinations between EV71 genotypes B and C at the 2A-2B junction, and between EV71 genotype B and CA16 strain G-10 at the 3B-3C junction. Henan enterovirus 71 isolates between 2008 and 2010 belonged to C4a in subgenotype C4 which was the predominant virus genotype circulating in mainland China since 2004, a combination of intratypic and intertypic recombination were found in EV71 subgenotype C4.

  15. Efficient cell culture system for hepatitis C virus genotype 2B

    DEFF Research Database (Denmark)

    2014-01-01

    The present inventors developed hepatitis C virus 2b/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and the complete NS2 were replaced by the corresponding genes of the genotype 2b reference strain J8. Sequence analysis of recovered 2b/2a recombinants from...... transfection experiments revealed that 2b/2a was genetically stable. Conclusion: The developed 2b/2a viruses provide a robust in vitro tool for research in HCV genotype 2b, including vaccine studies and functional analysis.......The present inventors developed hepatitis C virus 2b/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and the complete NS2 were replaced by the corresponding genes of the genotype 2b reference strain J8. Sequence analysis of recovered 2b/2a recombinants from 2...

  16. Adaptability and genotypic stability of Coffea arabica genotypes based on REML/BLUP analysis in Rio de Janeiro State, Brazil.

    Science.gov (United States)

    Rodrigues, W P; Vieira, H D; Barbosa, D H S G; Souza Filho, G R; Candido, L S

    2013-07-15

    Biannuality in coffee culture causes temporal variability in plant productivity. Consequently, it is essential to evaluate genotypes during various crop years to ensure selection of productive and stable genotypes. We evaluated the effectiveness of simultaneous selection of coffee genotypes along harvests, based on productivity, stability, and adaptability, via mixed models, for indication of varieties suitable for Rio de Janeiro State. We evaluated 25 genotypes during 4 crop seasons (2009-2012), in a randomized block design with 5 replications. The ranking of genotypes was obtained on the basis of the adaptability and temporal stability methods (harmonic average of genetic values, relative performance of genetic values, and harmonic mean of the relative performance of the genetic values), obtained via restricted maximum likelihood/best linear unbiased procedure analysis. The selection accuracy (0.8717), associated with the high magnitude of mean heritability, indicate good reliability and prospects for success in the indication of agronomically superior genotypes. There was little variation in the ordering of genotypes among the environments, indicating low influence of harvests in the performance of the genotypes. Five of the 25 genotypes were superior and could be recommended for planting in the northwestern region of Rio de Janeiro State, due to high predicted productivity and stability. We recommend that these methodologies for evaluation of productivity, stability, and adaptability be included in the selection criteria for recommendation of genotypes for commercial plantings.

  17. Utilização do inseticida Methomyl na seleção de genótipos de aveia resistentes à helmintosporiose User of Methomyl insecticide for the selection of spot blotch resistant oat genotypes

    Directory of Open Access Journals (Sweden)

    Cristine Luise Handel

    1999-06-01

    Full Text Available A helmintosporiose é uma moléstia que afeta a cultura da aveia, reduzindo seu rendimento e qualidade de grão. A seleção de genótipos resistentes com utilização de filtrados tóxicos do fungo Helminthosporium sativum é eficaz, pois delimita a variabilidade do patógeno e reduz a interferência do ambiente na expressão do genótipo. Contudo, a obtenção dos filtrados tóxicos deste fungo é um processo lento e delicado. Dessa forma, a possibilidade do uso de substâncias sintéticas que simulem seu efeito, inibindo o transporte de elétrons da cadeia respiratória, é de grande interesse. O inseticida Methomyl é eficaz para simular o efeito da toxina do fungo que causa a helmintosporiose em milho, tendo o presente trabalho visado testar sua eficiência na cultura da aveia. Para isso, foi avaliado o crescimento de calos e raízes de aveia expostas ao Methomyl, quando crescimentos maiores indicaram maior resistência ao produto, e possível resistência à moléstia. Os resultados indicam que o Methomyl afeta o crescimento de raízes e calos de aveia e pode ser utilizado para separar os grupos de genótipos com e sem resistência à helmintosporiose. Assim, UFRGS 14, com maior sensibilidade aos filtrados tóxicos de H. sativum em outros estudos, também apresentou crescimento mais afetado pelo Methomyl em todos os experimentos aqui conduzidos.Spot Blotch is a plant disease which causes yield losses in oat and other cereals. Selection for resistant genotypes using Helminthosporium sativum toxic filtrates is an efficient technique, which reduces the pathogen variability and the influence of the environment over the genotype expression. The filtrates extraction is time consuming and a difficult process, and the possibility of using a synthetic product to simulate its action of inhibiting the cell electron transport chain would be useful. The Methomyl insecticide is an efficient product to simulate the effects of the fungus that causes spot

  18. (Cyamopsis tetragonoloba) genotypes

    Indian Academy of Sciences (India)

    Molecular assessment of genetic diversity in cluster bean. (Cyamopsis tetragonoloba) genotypes. Rakesh Pathak, S. K. Singh, Manjit Singh and A. Henry. J. Genet. 89, 243–246. Figure 1. RAPD profile of 1–16 Cyamopsis tetragonoloba genotypes amplified with arbitrary primer OPA-16. Figure 2. RAPD profile of 17–32 ...

  19. (Prunus armeniaca L.) genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... Table 2. Leaf stomatal frequency, stomata size and stomatal conductance of apricot genotypes. Stomatal conductance (mmol m-2 s-1). Apricot genotype. Stomata frequency. (number/mm2). Stomata size. (μm). 2006. 2007. Orange Red. 349.0 a. 71.6 abc. 192 a-d. 176 bc. Palstein. 311.7 ab. 76.6 abc.

  20. ACTN3 Genotype in Professional Sport Climbers.

    Science.gov (United States)

    Ginszt, Michał; Michalak-Wojnowska, Małgorzata; Gawda, Piotr; Wojcierowska-Litwin, Magdalena; Korszeń-Pilecka, Iwona; Kusztelak, Małgorzata; Muda, Rafał; Filip, Agata A; Majcher, Piotr

    2018-02-01

    The functional RR genotype of the alpha-actinin-3 (ACTN3) gene has been reported to be associated with elite sprint/power athlete status. Although large and rapidly increasing number of studies have investigated the associations between the ACTN3 genotypes and athletic performance in various sport disciplines, there is a lack of studies on the genetic predisposition in Sport Climbing, which was selected to be part of the next Summer Olympic Games in Tokyo 2020 with three subdisciplines ('Lead Climbing', 'Speed Climbing' and 'Bouldering'). The aim of the study is to determine the frequency distribution of ACTN3 genotypes and alleles in professional lead climbers and boulderers.100 professional sport climbers from Poland, Russia and Austria, divided into two equal groups: professional boulderers and professional lead climbers were involved in the study. ACTN3 allele frequencies and genotypes were compared with 100 sedentary controls. Genotypes were determined using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism method. The percent distribution of RR genotype in the boulderers was significantly higher than in lead climbers and controls (62% vs. 26%; 33%, respectively; χ2=17.230, p=0.0017). The frequencies of ACTN3 R allele in boulderers differed significantly from lead climbers and controls (77% vs. 51%; 58%, respectively; χ2=15.721, p=0.0004). The proportion of the ACTN3 RR genotype is significantly higher in boulderers than in lead climbers and may be related to the specific type of predisposition to this subdiscipline.

  1. Relationship of some upland rice genotype after gamma irradiation

    Science.gov (United States)

    Suliartini, N. W. S.; Wijayanto, T.; Madiki, A.; Boer, D.; Muhidin; Juniawan

    2018-02-01

    The objective of the research was to group local upland rice genotypes after being treated with gamma irradiation. The research materials were upland rice genotypes resulted from mutation of the second generation and two parents: Pae Loilo (K3D0) and Pae Pongasi (K2D0) Cultivars. The research was conducted at the Indonesian Sweetener and Fiber Crops Research Institute, Malang Regency, and used the augmented design method. Research data were analyzed with R Program. Eight hundred and seventy one genotypes were selected with the selection criteria were based on yields on the average parents added 1.5 standard deviation. Based on the selection, eighty genotypes were analyzed with cluster analyses. Nine observation variables were used to develop cluster dendrogram using average linked method. Genetic distance was measured by euclidean distance. The results of cluster dendrogram showed that tested genotypes were divided into eight groups. Group 1, 2, 7, and 8 each had one genotype, group 3 and 6 each had two genotypes, group 4 had 25 genotypes, and group 5 had 51 genotypes. Check genotypes formed a separate group. Group 6 had the highest yield per plant of 126.11 gram, followed by groups 5 and 4 of 97.63 and 94.08 gram, respectively.

  2. The estimation of recombination rates from population genetic data

    OpenAIRE

    2007-01-01

    Genetic recombination is an important process that generates new combinations of genes on which natural selection can operate. As such, an understanding of recombination in the human genome will provide insight into the evolutionary processes that have shaped our genetic history. The aim of this thesis is to use samples of population genetic data to explore the patterns of variation in the rate of recombination in the human genome. To do this I introduce a novel means of estimating recombinat...

  3. Genomic evaluations with many more genotypes

    Directory of Open Access Journals (Sweden)

    Wiggans George R

    2011-03-01

    Full Text Available Abstract Background Genomic evaluations in Holstein dairy cattle have quickly become more reliable over the last two years in many countries as more animals have been genotyped for 50,000 markers. Evaluations can also include animals genotyped with more or fewer markers using new tools such as the 777,000 or 2,900 marker chips recently introduced for cattle. Gains from more markers can be predicted using simulation, whereas strategies to use fewer markers have been compared using subsets of actual genotypes. The overall cost of selection is reduced by genotyping most animals at less than the highest density and imputing their missing genotypes using haplotypes. Algorithms to combine different densities need to be efficient because numbers of genotyped animals and markers may continue to grow quickly. Methods Genotypes for 500,000 markers were simulated for the 33,414 Holsteins that had 50,000 marker genotypes in the North American database. Another 86,465 non-genotyped ancestors were included in the pedigree file, and linkage disequilibrium was generated directly in the base population. Mixed density datasets were created by keeping 50,000 (every tenth of the markers for most animals. Missing genotypes were imputed using a combination of population haplotyping and pedigree haplotyping. Reliabilities of genomic evaluations using linear and nonlinear methods were compared. Results Differing marker sets for a large population were combined with just a few hours of computation. About 95% of paternal alleles were determined correctly, and > 95% of missing genotypes were called correctly. Reliability of breeding values was already high (84.4% with 50,000 simulated markers. The gain in reliability from increasing the number of markers to 500,000 was only 1.6%, but more than half of that gain resulted from genotyping just 1,406 young bulls at higher density. Linear genomic evaluations had reliabilities 1.5% lower than the nonlinear evaluations with 50

  4. Seleção para resistência de genótipos de cenoura aos nematóides-das-galhas Selection for carrot genotypes resistance to root-knot nematodes in field and greenhouse

    Directory of Open Access Journals (Sweden)

    Giovani O da Silva

    2011-09-01

    identify for which ones it is possible to differentiate among genotypes and to verify the possibility of evaluation only in one environment or the elimination of characters with high correlation. Thirty eight and thirty one families from the carrot populations '0812518' and '0812519', and the cultivars Brasília and Kuronan as tolerant and susceptible standards, respectively, were evaluated. In a field whose soil was naturally infected by a mix of Meloidogyne incognita race 1 and Meloidogyne javanica, the selection to resistance to root-knot nematode was based on lower percentage of infection in the root, of the major genotypes of carrot production in t/ha and reproduction factor; and in greenhouse, to each one of the same nematode species and too for a mix of both, was evaluated the index of gall and index of egg mass. There is no possibility of selection in only one condition or the elimination of some characters, indicating that, to obtain more yielding and more tolerant cultivars, the combined selection in the various characters and environments are necessary. In the field experiment, it was only possible to differentiate the genotypes for root yield. In the greenhouse, it was possible to identify superior genotypes for all characters tested. However, the average population was not better than the 'Brasilia' standard that originated these populations. This result confirms the necessity to search for more efficient methods of selection.

  5. Evolution at 'Sutures' and 'Centers': Recombination Can Aid Adaptation of Spatially Structured Populations on Rugged Fitness Landscapes.

    Directory of Open Access Journals (Sweden)

    Jacob D Cooper

    2016-12-01

    Full Text Available Epistatic interactions among genes can give rise to rugged fitness landscapes, in which multiple "peaks" of high-fitness allele combinations are separated by "valleys" of low-fitness genotypes. How populations traverse rugged fitness landscapes is a long-standing question in evolutionary biology. Sexual reproduction may affect how a population moves within a rugged fitness landscape. Sex may generate new high-fitness genotypes by recombination, but it may also destroy high-fitness genotypes by shuffling the genes of a fit parent with a genetically distinct mate, creating low-fitness offspring. Either of these opposing aspects of sex require genotypic diversity in the population. Spatially structured populations may harbor more diversity than well-mixed populations, potentially amplifying both positive and negative effects of sex. On the other hand, spatial structure leads to clumping in which mating is more likely to occur between like types, diminishing the effects of recombination. In this study, we use computer simulations to investigate the combined effects of recombination and spatial structure on adaptation in rugged fitness landscapes. We find that spatially restricted mating and offspring dispersal may allow multiple genotypes inhabiting suboptimal peaks to coexist, and recombination at the "sutures" between the clusters of these genotypes can create genetically novel offspring. Sometimes such an offspring genotype inhabits a new peak on the fitness landscape. In such a case, spatially restricted mating allows this fledgling subpopulation to avoid recombination with distinct genotypes, as mates are more likely to be the same genotype. Such population "centers" can allow nascent peaks to establish despite recombination. Spatial structure may therefore allow an evolving population to enjoy the creative side of sexual recombination while avoiding its destructive side.

  6. Hadron correlations from recombination

    Energy Technology Data Exchange (ETDEWEB)

    Fries, Rainer J [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)

    2005-01-01

    Quark recombination is a successful model to describe the hadronization of a deconfined quark gluon plasma. Jet-like dihadron correlations measured at RHIC provide a challenge for this picture. We discuss how correlations between hadrons can arise from correlations between partons before hadronization. An enhancement of correlations through the recombination process, similar to the enhancement of elliptic flow is found. Hot spots from completely or partially quenched jets are a likely source of such parton correlations.

  7. Mobility dependent recombination models for organic solar cells

    Science.gov (United States)

    Wagenpfahl, Alexander

    2017-09-01

    Modern solar cell technologies are driven by the effort to enhance power conversion efficiencies. A main mechanism limiting power conversion efficiencies is charge carrier recombination which is a direct function of the encounter probability of both recombination partners. In inorganic solar cells with rather high charge carrier mobilities, charge carrier recombination is often dominated by energetic states which subsequently trap both recombination partners for recombination. Free charge carriers move fast enough for Coulomb attraction to be irrelevant for the encounter probability. Thus, charge carrier recombination is independent of charge carrier mobilities. In organic semiconductors charge carrier mobilities are much lower. Therefore, electrons and holes have more time react to mutual Coulomb-forces. This results in the strong charge carrier mobility dependencies of the observed charge carrier recombination rates. In 1903 Paul Langevin published a fundamental model to describe the recombination of ions in gas-phase or aqueous solutions, known today as Langevin recombination. During the last decades this model was used to interpret and model recombination in organic semiconductors. However, certain experiments especially with bulk-heterojunction solar cells reveal much lower recombination rates than predicted by Langevin. In search of an explanation, many material and device properties such as morphology and energetic properties have been examined in order to extend the validity of the Langevin model. A key argument for most of these extended models is, that electron and hole must find each other at a mutual spatial location. This encounter may be limited for instance by trapping of charges in trap states, by selective electrodes separating electrons and holes, or simply by the morphology of the involved semiconductors, making it impossible for electrons and holes to recombine at high rates. In this review, we discuss the development of mobility limited

  8. Selection via simulated individual BLUP based on family genotypic effects in sugarcane Seleção via BLUP individual simulado baseado nos efeitos genotípicos de famílias em cana-de-açúcar

    Directory of Open Access Journals (Sweden)

    Marcos Deon Vilela de Resende

    2006-03-01

    Full Text Available The objective of this work was to propose a new selection strategy for the initial stages of sugarcane improvement, based on the methodology 'simulated individual BLUP (BLUPIS', which promotes a dynamic allocation of individuals selected in each full-sib family, using BLUP as a base for both the genotypic effects of the referred families and plot effects. The method proposed applies to single full-sib families or those obtained from unbalanced or balanced diallel crosses, half-sib families and self-pollinated families. BLUPIS indicates the number of individuals to be selected within each family, the total number of clones to be advanced, and the number of families to contribute with selected individuals. Correlation between BLUPIS and true BLUP was 0.96, by method validation. Additionally, BLUPIS allows the identification of which replication contains the best individuals of each family.O objetivo deste trabalho foi propor uma nova estratégia de seleção nos estádios iniciais do desenvolvimento da cana-de-açúcar, utilizando-se a metodologia BLUP individual simulado (BLUPIS que promove a distribuição dinâmica dos indivíduos selecionados em cada família de irmãos-completos, usando BLUP como base para os efeitos genotípicos da família e para os efeitos de parcela. O método proposto se aplica a famílias de irmãos-completos simples ou obtidas de cruzamentos dialélicos desbalanceados ou balanceados, famílias de meios-irmãos e famílias de autofecundação. Por meio do BLUPIS, indica-se o número de indivíduos a ser selecionado por família, o número total de clones a ser avançado e o número de famílias a contribuir com indivíduos selecionados. A validação do método propiciou uma correlação de 0,96 entre o BLUPIS e o BLUP verdadeiro. Além disso, o BLUPIS permite identificar em qual repetição encontram-se os melhores indivíduos de cada família.

  9. Dielectronic recombination measurements using the Electron Beam Ion Trap

    International Nuclear Information System (INIS)

    Knapp, D.A.

    1991-01-01

    We have used the Electron Beam Ion Trap at LLNL to study dielectronic recombination in highly charged ions. Our technique is unique because we observe the x-rays from dielectronic recombination at the same time we see x-rays from all other electron-ion interactions. We have recently taken high-resolution, state-selective data that resolves individual resonances

  10. Resistance Potential of Bread Wheat Genotypes Against Yellow Rust Disease Under Egyptian Climate.

    Science.gov (United States)

    Mahmoud, Amer F; Hassan, Mohamed I; Amein, Karam A

    2015-12-01

    Yellow rust (stripe rust), caused by Puccinia striiformis f. sp. tritici, is one of the most destructive foliar diseases of wheat in Egypt and worldwide. In order to identify wheat genotypes resistant to yellow rust and develop molecular markers associated with the resistance, fifty F8 recombinant inbred lines (RILs) derived from a cross between resistant and susceptible bread wheat landraces were obtained. Artificial infection of Puccinia striiformis was performed under greenhouse conditions during two growing seasons and relative resistance index (RRI) was calculated. Two Egyptian bread wheat cultivars i.e. Giza-168 (resistant) and Sakha-69 (susceptible) were also evaluated. RRI values of two-year trial showed that 10 RILs responded with RRI value >6 2 rust. However, further molecular analyses would be performed to confirm markers associated with the resistance and suitable for marker-assisted selection. Resistant RILs identified in the study could be efficiently used to improve the resistance to yellow rust in wheat.

  11. APOE Genotyping, Cardiovascular Disease

    Science.gov (United States)

    ... it ordered? As a test to evaluate lipid metabolism or cardiovascular risk, APOE genotyping is ordered when someone has: Significantly elevated cholesterol and triglyceride levels that do not respond to dietary and ...

  12. Molecular and phylogenetic analyses suggest an additional hepatitis B virus genotype "I".

    Directory of Open Access Journals (Sweden)

    Hai Yu

    Full Text Available A novel hepatitis B virus (HBV strain (W29 was isolated from serum samples in the northwest of China. Phylogenetic and distance analyses indicate that this strain is grouped with a series of distinct strains discovered in Vietnam and Laos that have been proposed to be a new genotype I. TreeOrderScan and GroupScan methods were used to study the intergenotype recombination of this special group. Recombination plots and tree maps of W29 and these putative genotype I strains exhibit distinct characteristics that are unexpected in typical genotype C strains of HBV. The amino acids of P gene, S gene, X gene, and C gene of all genotypes (including subtypes were compared, and eight unique sites were found in genotype I. In vitro and in vivo experiments were also conducted to determine phenotypic characteristics between W29 and other representative strains of different genotypes obtained from China. Secretion of HBsAg in Huh7 cells is uniformly abundant among genotypes A, B, C, and I (W29, but not genotype D. HBeAg secretion is low in genotype I (W29, whose level is close to genotype A and much lower than genotypes B, C, and D. Results from the acute hydrodynamic injection mouse model also exhibit a similar pattern. From an overview of the results, the viral markers of W29 (I1 in Huh7 cells and mice had a more similar level to genotype A than genotype C, although the latter was closer to W29 in distance analysis. All evidence suggests that W29, together with other related strains found in Vietnam and Laos, should be classified into a new genotype.

  13. Affinity purification of recombinant human plasminogen activator ...

    African Journals Online (AJOL)

    Purpose: To develop processes for effective isolation and purification of recombinant human plasminogen activator (rhPA) from transgenic rabbit milk. Methods: Immunoaffinity chromatography was selected and improved by a special polyol-responsive monoclonal antibody (PR-mAb). Alteplase was used as immunogen ...

  14. Selection of Gossypium hirsutum genotypes for interspecific ...

    African Journals Online (AJOL)

    FORRESTER

    ARS), Crop Genetics Research Unit in. Stoneville, Mississippi ... Key words: Cotton, germplasm, immature embryo, tissue culture, wide-hybridization. INTRODUCTION. Tetraploid upland cotton, Gossypium hirsutum L., is comprised of over 90% ...

  15. Selection of Gossypium hirsutum genotypes for interspecific ...

    African Journals Online (AJOL)

    Ovule culture is one of the techniques currently used to introgress desirable traits from Gossypium arboreum germplasm into G. hirsutum cultivars. Twenty-six (26) G. hirsutum breeding lines were used as female parents in crosses with five G. arboreum accessions to determine if the G. hirsutum parent influenced the ...

  16. Heteroduplex formation, mismatch resolution, and genetic sectoring during homologous recombination in the hyperthermophilic archaeon Sulfolobus acidocaldarius

    Directory of Open Access Journals (Sweden)

    Dennis W. Grogan

    2012-06-01

    Full Text Available Hyperthermophilic archaea exhibit certain molecular-genetic features not seen in bacteria or eukaryotes, and their systems of homologous recombination (HR remain largely unexplored in vivo. We transformed a Sulfolobus acidocaldarius pyrE mutant with short DNAs that contained multiple non-selected genetic markers within the pyrE gene. From 20 to 40% of the resulting colonies were found to contain two Pyr+ clones with distinct sets of the non-selected markers. The dual-genotype colonies could not be attributed to multiple DNAs entering the cells or conjugation between transformed and non-transformed cells. These colonies thus appear to represent genetic sectoring in which stretches of heteroduplex DNA formed during HR and segregated without complete resolution of inter-strand differences. Surprisingly, sectoring was also frequent in transformation with single-stranded DNAs. Oligonucleotides, for example, produced somewhat more sectored transformants when electroporated as single strands than as a duplex, although all forms (positive-strand, negative-strand, and duplex produced a diversity of genotypes from the limited number of markers. The marker patterns in the recombinants indicate that S. acidocaldarius resolves individual mismatches through un-coordinated short-patch excision followed by re-filling of the resulting gap. These gene-conversion events exhibit little strand bias, and can occur in pre-formed heteroduplex. These properties suggest that this process does not play a central role in the fidelity of genome replication, but may generate 3’ single-strand tails, and thereby initiate the incorporation of duplex DNA into the recipient chromosome. Regardless of the molecular details of its mechanism, HR between the S. acidocaldarius chromosome and a multiply-marked DNA produces a strikingly high level of genetic diversity in a very short chromosomal interval, and suggests that HR in Sulfolobus has significant mutagenic potential if not

  17. SIMULTANEOUS SELECTION FOR GENOTYPIC PRODUCTION, ADAPTABILITY, AND STABILITY IN CASHEW CLONES BY MIXED MODELS SELEÇÃO SIMULTÂNEA PARA PRODUÇÃO, ADAPTABILIDADE E ESTABILIDADE GENOTÍPICAS EM CLONES DE CAJUEIRO, VIA MODELOS MISTOS

    Directory of Open Access Journals (Sweden)

    José Jaime Vasconcelos Cavalcanti

    2009-01-01

    genotypic adaptability and stability. The experiments were set up employing a complete block design, with eleven treatments, three repetitions and five plants per plot. The results showed an alteration in the clone order, in the different environments, as reflected from the genotypic correlation of average magnitude (0.58. The heritability of clones presented moderate to high magnitude for the different traits, indicating excellent possibilities for selection, allowing selective accuracy of 83%. The methods MHVG, PRVG, and MHPRVG can be part of selective criteria in the cashew breeding program.

     

    KEY-WORDS: Anacardium occidentale; genotype x environment interaction; BLUP/REML.

  1. Clusters of incompatible genotypes evolve with limited dispersal

    Science.gov (United States)

    Erin L. Landguth; Norman A. Johnson; Samuel A. Cushman

    2015-01-01

    Theoretical and empirical studies have shown heterogeneous selection to be the primary driver for the evolution of reproductively isolated genotypes in the absence of geographic barriers. Here, we ask whether limited dispersal alone can lead to the evolution of reproductively isolated genotypes despite the absence of any geographic barriers or heterogeneous...

  2. Genotype x row spacing and environment interaction of cowpea in ...

    African Journals Online (AJOL)

    Because of significant genotype x environment and WRS interaction effects, this effectiveness would require stable genotypes to be tested for more than a year. Also preliminary testing of large populations in high-productivity environment only, would not maximise gain from selection in low-productivity zones. But the most ...

  3. Screening ten genotypes of natural rubber seedlings ( Hevea ...

    African Journals Online (AJOL)

    A field study was conducted in 2012 and 2013 cropping season at the Research Farm of National Root Crops Research Institute, (NRCRI) Umudike, in Abia State, to screen 10 rubber genotypes collected from Rubber Research Institute of Nigeria for tolerant to drought conditions. The aim was to select tolerant genotypes for ...

  4. genotype by environment interaction and grain yield stability

    African Journals Online (AJOL)

    Preferred Customer

    ABSTRACT: Genotypes by environment (GXE) interactions are almost unanimously considered to be among the major factors limiting response to selection and, in general, the efficiency of breeding programs. Cognizant of this fact, 15 advanced triticale genotypes and one standard check, Dilfikir, were evaluated at Arjo ...

  5. Gateway Recombinational Cloning.

    Science.gov (United States)

    Reece-Hoyes, John S; Walhout, Albertha J M

    2018-01-02

    The Gateway recombinatorial cloning system was developed for cloning multiple DNA fragments in parallel (e.g., in 96-well formats) in a standardized manner using the same enzymes. Gateway cloning is based on the highly specific integration and excision reactions of bacteriophage λ into and out of the Escherichia coli genome. Because the sites of recombination (" att " sites) are much longer (25-242 bp) than restriction sites, they are extremely unlikely to occur by chance in DNA fragments. Therefore, the same recombination enzyme can be used to robustly clone many different fragments of variable size in parallel reactions. © 2018 Cold Spring Harbor Laboratory Press.

  6. Genetic characterization of EV71 isolates from 2004 to 2010 reveals predominance and persistent circulation of the newly proposed genotype D and recent emergence of a distinct lineage of subgenotype C2 in Hong Kong.

    Science.gov (United States)

    Yip, Cyril C Y; Lau, Susanna K P; Lo, Janice Y C; Chan, Kwok-Hung; Woo, Patrick C Y; Yuen, Kwok-Yung

    2013-07-04

    Enterovirus 71 (EV71) is a common etiological agent of hand, foot and mouth disease (HFMD) in children. EV71 epidemics have been reported in Hong Kong in recent years, and yet the genetic information of EV71 strains circulating in our locality is limited. The objective of this study was to investigate the genetic evolution of these EV71 isolates in Hong Kong over a 7-year period. Twenty-two EV71 isolates from Hong Kong during 2004-2010 were included for phylogenetic analysis using partial VP2-VP3, 2C and 3D regions. Eight EV71 strains were selected for complete genome sequencing and recombination analysis. Among the 22 EV71 isolates, 20 belonged to subgenotype C4 and 2 belonged to subgenotype C2 based on the phylogenetic analysis of partial VP2-VP3, 2C and 3D gene regions. Phylogenetic, similarity plot and bootscan analyses using complete genome sequences of seven EV71 isolates of subgenotype C4 supported that the "double-recombinant" strains of subgenotype C4 persistently circulating in Hong Kong should belong to a newly proposed genotype D. Further analysis revealed two clusters, subgenotypes C4b and C4a (proposed genotypes D1a and D1b respectively), with "genotype D1b" strains being predominant in recent years in Hong Kong. A distinct lineage of EV71 subgenotype C2 has emerged in Hong Kong in 2008. The evolutionary rate of EV71 was 3.1 × 10-3 nucleotide substitutions per site per year similar to that of other enterovirus, such as EV68, but was relatively lower than those of echovirus 30 and poliovirus. Molecular clock analysis using VP1 gene dated the time to the most recent common ancestor of all EV71 genotypes to 1900s, while the EV71 "double-recombinant" strains of "genotype D" were detected as early as 1998. This study provides the molecular basis for proposing a new "genotype D" of EV71 and assigning a discrete lineage of subgenotype C2. EV71 strains of "genotype D" have been circulating in Hong Kong for over 7 years, with "genotype D1b" being predominant.

  7. Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamanders.

    Science.gov (United States)

    Johnson, Jarrett R; Fitzpatrick, Benjamin M; Shaffer, H Bradley

    2010-05-18

    Introductions of non-native tiger salamanders into the range of California tiger salamanders have provided a rare opportunity to study the early stages of secondary contact and hybridization. We produced first- and second-generation hybrid salamanders in the lab and measured viability among these early-generation hybrid crosses to determine the strength of the initial barrier to gene exchange. We also created contemporary-generation hybrids in the lab and evaluated the extent to which selection has affected fitness over approximately 20 generations of admixture. Additionally, we examined the inheritance of quantitative phenotypic variation to better understand how evolution has progressed since secondary contact. We found significant variation in the fitness of hybrids, with non-native backcrosses experiencing the highest survival and F2 hybrids the lowest. Contemporary-generation hybrids had similar survival to that of F2 families, contrary to our expectation that 20 generations of selection in the wild would eliminate unfit genotypes and increase survival. Hybrid survival clearly exhibited effects of epistasis, whereas size and growth showed mostly additive genetic variance, and time to metamorphosis showed substantial dominance. Based on first- and second- generation cross types, our results suggest that the initial barrier to gene flow between these two species was relatively weak, and subsequent evolution has been generally slow. The persistence of low-viability recombinant hybrid genotypes in some contemporary populations illustrates that while hybridization can provide a potent source of genetic variation upon which natural selection can act, the sorting of fit from unfit gene combinations might be inefficient in highly admixed populations. Spatio-temporal fluctuation in selection or complex genetics has perhaps stalled adaptive evolution in this system despite selection for admixed genotypes within generations.

  8. Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamanders

    Directory of Open Access Journals (Sweden)

    Shaffer H Bradley

    2010-05-01

    Full Text Available Abstract Background Introductions of non-native tiger salamanders into the range of California tiger salamanders have provided a rare opportunity to study the early stages of secondary contact and hybridization. We produced first- and second-generation hybrid salamanders in the lab and measured viability among these early-generation hybrid crosses to determine the strength of the initial barrier to gene exchange. We also created contemporary-generation hybrids in the lab and evaluated the extent to which selection has affected fitness over approximately 20 generations of admixture. Additionally, we examined the inheritance of quantitative phenotypic variation to better understand how evolution has progressed since secondary contact. Results We found significant variation in the fitness of hybrids, with non-native backcrosses experiencing the highest survival and F2 hybrids the lowest. Contemporary-generation hybrids had similar survival to that of F2 families, contrary to our expectation that 20 generations of selection in the wild would eliminate unfit genotypes and increase survival. Hybrid survival clearly exhibited effects of epistasis, whereas size and growth showed mostly additive genetic variance, and time to metamorphosis showed substantial dominance. Conclusions Based on first- and second- generation cross types, our results suggest that the initial barrier to gene flow between these two species was relatively weak, and subsequent evolution has been generally slow. The persistence of low-viability recombinant hybrid genotypes in some contemporary populations illustrates that while hybridization can provide a potent source of genetic variation upon which natural selection can act, the sorting of fit from unfit gene combinations might be inefficient in highly admixed populations. Spatio-temporal fluctuation in selection or complex genetics has perhaps stalled adaptive evolution in this system despite selection for admixed genotypes within

  9. Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar).

    Science.gov (United States)

    Houston, Ross D; Taggart, John B; Cézard, Timothé; Bekaert, Michaël; Lowe, Natalie R; Downing, Alison; Talbot, Richard; Bishop, Stephen C; Archibald, Alan L; Bron, James E; Penman, David J; Davassi, Alessandro; Brew, Fiona; Tinch, Alan E; Gharbi, Karim; Hamilton, Alastair

    2014-02-06

    Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture

  10. A New Metazoan Recombination Rate Record and Consistently High Recombination Rates in the Honey Bee Genus Apis Accompanied by Frequent Inversions but Not Translocations

    Science.gov (United States)

    Kuster, Ryan; Miller, Katelyn; Fouks, Bertrand; Rubio Correa, Sara; Collazo, Juan; Phaincharoen, Mananya; Tingek, Salim; Koeniger, Nikolaus

    2016-01-01

    Abstract Western honey bees (Apis mellifera) far exceed the commonly observed 1–2 meiotic recombination events per chromosome and exhibit the highest Metazoan recombination rate (20 cM/Mb) described thus far. However, the reasons for this exceptional rate of recombination are not sufficiently understood. In a comparative study, we report on the newly constructed genomic linkage maps of Apis florea and Apis dorsata that represent the two honey bee lineages without recombination rate estimates so far. Each linkage map was generated de novo, based on SNP genotypes of haploid male offspring of a single female. The A. florea map spans 4,782 cM with 1,279 markers in 16 linkage groups. The A. dorsata map is 5,762 cM long and contains 1,189 markers in 16 linkage groups. Respectively, these map sizes result in average recombination rate estimates of 20.8 and 25.1 cM/Mb. Synteny analyses indicate that frequent intra-chromosomal rearrangements but no translocations among chromosomes accompany the high rates of recombination during the independent evolution of the three major honey bee lineages. Our results imply a common cause for the evolution of very high recombination rates in Apis. Our findings also suggest that frequent homologous recombination during meiosis might increase ectopic recombination and rearrangements within but not between chromosomes. It remains to be investigated whether the resulting inversions may have been important in the evolutionary differentiation between honey bee species. PMID:28173114

  11. Axiom turkey genotyping array

    Science.gov (United States)

    The Axiom®Turkey Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turk...

  12. (Phaseolus vulgaris L) Genotypes

    African Journals Online (AJOL)

    Bruening 2001; Ho 1988). At whole plant level, the differences in drought resistance among drought-resistant and susceptible genotypes are related to the ability to accumulate biomass, remobilization of stored biomass to reproductive organs and the subsequent capacity to establish new reproductive sinks (Koç et al. 2003 ...

  13. Applications of blood group genotyping

    Directory of Open Access Journals (Sweden)

    Mariza A. Mota

    2006-03-01

    Full Text Available Introduction: The determination of blood group polymorphism atthe genomic level facilitates the resolution of clinical problemsthat cannot be addressed by hemagglutination. They are useful to(a determine antigen types for which currently available antibodiesare weakly reactive; (b type patients who have been recentlytransfused; (c identify fetuses at risk for hemolytic disease of thenewborn; and (d to increase the reliability of repositories of antigennegative RBCs for transfusion. Objectives: This review assessedthe current applications of blood group genotyping in transfusionmedicine and hemolytic disease of the newborn. Search strategy:Blood group genotyping studies and reviews were searched ingeneral database (MEDLINE and references were reviewed.Selection criteria: All published data and reviews were eligible forinclusion provided they reported results for molecular basis ofblood group antigens, DNA analysis for blood group polymorphisms,determination of fetal group status and applications of blood groupgenotyping in blood transfusion. Data collection: All data werecollected based on studies and reviews of blood grouppolymorphisms and their clinical applications.

  14. p53 gene targeting by homologous recombination in fish ES cells.

    Directory of Open Access Journals (Sweden)

    Yan Yan

    Full Text Available BACKGROUND: Gene targeting (GT provides a powerful tool for the generation of precise genetic alterations in embryonic stem (ES cells to elucidate gene function and create animal models for human diseases. This technology has, however, been limited to mouse and rat. We have previously established ES cell lines and procedures for gene transfer and selection for homologous recombination (HR events in the fish medaka (Oryzias latipes. METHODOLOGY AND PRINCIPAL FINDINGS: Here we report HR-mediated GT in this organism. We designed a GT vector to disrupt the tumor suppressor gene p53 (also known as tp53. We show that all the three medaka ES cell lines, MES1∼MES3, are highly proficient for HR, as they produced detectable HR without drug selection. Furthermore, the positive-negative selection (PNS procedure enhanced HR by ∼12 folds. Out of 39 PNS-resistant colonies analyzed, 19 (48.7% were positive for GT by PCR genotyping. When 11 of the PCR-positive colonies were further analyzed, 6 (54.5% were found to be bona fide homologous recombinants by Southern blot analysis, sequencing and fluorescent in situ hybridization. This produces a high efficiency of up to 26.6% for p53 GT under PNS conditions. We show that p53 disruption and long-term propagation under drug selection conditions do not compromise the pluripotency, as p53-targeted ES cells retained stable growth, undifferentiated phenotype, pluripotency gene expression profile and differentiation potential in vitro and in vivo. CONCLUSIONS: Our results demonstrate that medaka ES cells are proficient for HR-mediated GT, offering a first model organism of lower vertebrates towards the development of full ES cell-based GT technology.

  15. Genotyping with CRISPR-Cas-derived RNA-guided endonucleases.

    Science.gov (United States)

    Kim, Jong Min; Kim, Daesik; Kim, Seokjoong; Kim, Jin-Soo

    2014-01-01

    Restriction fragment length polymorphism (RFLP) analysis is one of the oldest, most convenient and least expensive methods of genotyping, but is limited by the availability of restriction endonuclease sites. Here we present a novel method of employing CRISPR/Cas-derived RNA-guided engineered nucleases (RGENs) in RFLP analysis. We prepare RGENs by complexing recombinant Cas9 protein derived from Streptococcus pyogenes with in vitro transcribed guide RNAs that are complementary to the DNA sequences of interest. Then, we genotype recurrent mutations found in cancer and small insertions or deletions (indels) induced in cultured cells and animals by RGENs and other engineered nucleases such as transcription activator-like effector nucleases (TALENs). Unlike T7 endonuclease I or Surveyor assays that are widely used for genotyping engineered nuclease-induced mutations, RGEN-mediated RFLP analysis can detect homozygous mutant clones that contain identical biallelic indel sequences and is not limited by sequence polymorphisms near the nuclease target sites.

  16. [Whole-sequence Analyses for 12 HBV C/D Recombinants from a Population in Tibet (China)].

    Science.gov (United States)

    Liu, Tiezhu; Shen, Liping; Yin, Wenjiao; Wang, Feng; Wang, Fuzhen; Zhang, Guomin; Zheng, Hui; Dunzhu, Duoji; Bi, Shengli; Cui, Fuqiang

    2016-03-01

    We wished to undertake molecular genetic typing and evaluate recombinants of the hepatitis-B virus (HBV) in Tibet (China). Multistage random sampling was used to collect HBsAg-positive samples. Nested polymerase chain reactions were used to amplify the whole sequence of the HBV. DNAstar, MEGA6 and SimPlot were used to assemble sequences, create phylogenetic trees, and undertake recombination analyses. Twelve whole sequences of the HBV of a Tibetan population were collected using these methods. Results showed that all 12 strains were C/D recombinants. Nine of the recombinations were at nt750, and the other three at nt1526. Therefore, the 12 strains could be divided into two types of recombinants: C/Da and C/Db. Analyses of the sequence of the whole genome revealed that the 12 strains belonged to genotype C, and that the nucleotide distance was > 4% between the 12 strains and sub-genotypes C1 to C15 in Genbank. The most likely sub-genotype was C1. Individuals with C/Da were from central and northern Tibet (e.g., Lasa, Linzhi, Ali) and those with C/Db recombinants were from Shannan in southern Tibet. These data suggest that the two types of recombinants had a good distribution in Tibet. Also, they can provide important information for studies on HBV recombination, gene features, virus evolution, as well as the control and prevention of HBV infection in Tibet.

  17. Construction of chromosomal recombination maps of three genomes of lilies (Lilium) based on GISH analysis.

    Science.gov (United States)

    Khan, Nadeem; Barba-Gonzalez, Rodrigo; Ramanna, M S; Visser, Richard G F; Van Tuyl, Jaap M

    2009-03-01

    Chromosomal recombination maps were constructed for three genomes of lily (Lilium) using GISH analyses. For this purpose, the backcross (BC) progenies of two diploid (2n = 2x = 24) interspecific hybrids of lily, viz. Longiflorum x Asiatic (LA) and Oriental x Asiatic (OA), were used. Mostly the BC progenies of LA hybrids consisted of both triploid (2n = 3x = 36) and diploid (2n = 2x = 24) with some aneuploid genotypes and those of OA hybrids consisted of triploid (2n = 3x = 36) and some aneuploid genotypes. In all cases, it was possible to identify the homoeologous recombinant chromosomes as well as accurately count the number of crossover points, which are called "recombination sites". Recombination sites were estimated in the BC progeny of 71 LA and 41 OA genotypes. In the case of BC progenies of LA hybrids, 248 recombination sites were cytologically localized on 12 different chromosomes of each genome (i.e., L and A). Similarly, 116 recombinant sites were localized on the 12 chromosomes each from the BC progenies of OA hybrids (O and A genomes). Cytological maps were constructed on the basis of the percentages of distances (micrometres) of the recombination sites from the centromeres. Since an Asiatic parent was involved in both hybrids, viz. LA and OA, two maps were constructed for the A genome that were indicated as Asiatic (L) and Asiatic (O). The other two maps were Longiflorum (A) and Oriental (A). Remarkably, the recombination sites were highly unevenly distributed among the different chromosomes of all four maps. Because the recombination sites can be unequivocally identified through GISH, they serve as reliable landmarks and pave the way for assigning molecular markers or desirable genes to chromosomes of Lilium and also monitor introgression of alien segments.

  18. Irrigated rice genotype performance under excess iron stress in hydroponic culture

    Directory of Open Access Journals (Sweden)

    Maraisa Crestani

    2009-01-01

    Full Text Available Iron stress is a major stress factor in irrigated rice. The complete mechanism underlying iron metabolism andtransport is still unknown. Irrigated rice (Oryza sativa L. cultivars were exposed to Fe2+ stress in hydroponic conditions,aiming to assess genotype performance under stress as well as to develop a protocol for genotype selection. The experimentaldesign was completely randomized, using a triple factorial scheme 2 x 5 x 6 (time x dose x genotype. The trait shoot length andnine days under stress were favorable for genotype discrimination under iron stress. The genotypes BR IRGA 409 and BRSAGRISUL were, respectively, the most sensitive and tolerant genotypes to iron stress. According to the genotype performance,hydroponics can be recommended as an efficient cultivation technique for the selection of iron stress-tolerant rice genotypes.

  19. Site directed recombination

    Science.gov (United States)

    Jurka, Jerzy W.

    1997-01-01

    Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

  20. Looking for the optimal rate of recombination for evolutionary dynamics

    Science.gov (United States)

    Saakian, David B.

    2018-01-01

    We consider many-site mutation-recombination models of evolution with selection. We are looking for situations where the recombination increases the mean fitness of the population, and there is an optimal recombination rate. We found two fitness landscapes supporting such nonmonotonic behavior of the mean fitness versus the recombination rate. The first case is related to the evolution near the error threshold on a neutral-network-like fitness landscape, for moderate genome lengths and large population. The more realistic case is the second one, in which we consider the evolutionary dynamics of a finite population on a rugged fitness landscape (the smooth fitness landscape plus some random contributions to the fitness). We also give the solution to the horizontal gene transfer model in the case of asymmetric mutations. To obtain nonmonotonic behavior for both mutation and recombination, we need a specially designed (ideal) fitness landscape.

  1. Nonradiative recombination in semiconductors

    CERN Document Server

    Abakumov, VN; Yassievich, IN

    1991-01-01

    In recent years, great progress has been made in the understandingof recombination processes controlling the number of excessfree carriers in semiconductors under nonequilibrium conditions. As a result, it is now possible to give a comprehensivetheoretical description of these processes. The authors haveselected a number of experimental results which elucidate theunderlying physical problems and enable a test of theoreticalmodels. The following topics are dealt with: phenomenological theory ofrecombination, theoretical models of shallow and deep localizedstates, cascade model of carrier captu

  2. Response to angiotensin-converting enzyme inhibition is selectively blunted by high sodium in angiotensin-converting enzyme DD genotype : Evidence for gene-environment interaction in healthy volunteers

    NARCIS (Netherlands)

    Lely, A. Titia; Lambers Heerspink, Hiddo J.; Zuurman, Mike; Visser, Folkert W.; Kocks, Menno J. A.; Boomsma, Frans; Navis, Gerjan

    2010-01-01

    Background Renin-angiotensin-aldosterone system blockade is a cornerstone in cardiovascular protection. Angiotensin-converting enzyme (ACE)-DD genotype has been associated with resistance to angiotensin-converting enzyme inhibition (ACEi), but data are conflicting. As sodium intake modifies the

  3. Performance of Bemisia tabaci Biotype B on Soybean Genotypes.

    Science.gov (United States)

    Cruz, P L; Baldin, E L L

    2017-04-01

    Bemisia tabaci (Genn.) (Hemiptera: Aleyrodidae) has been recognized as an important pest of many agricultural systems including soybean [Glycine max (L.) Merrill] crops. As an alternative to chemical control, the use of resistant genotypes represents an important tool for integrated pest management (IPM). This study aimed to evaluate the biological development of Bemisia tabaci biotype B confined on 13 soybean genotypes under greenhouse conditions. Initially, the nymphal period, complete development period (egg-adult), and the viability of the silverleaf whitefly nymphs were evaluated in all genotypes. Then, four genotypes promising for resistance ('Jackson,' UX-2569-159, 'P98Y11,' and 'TMG132 RR') and a susceptible genotype (PI-227687) were selected for further assays, where two insect populations were compared: a first population from the initial rearing (cabbage plants) and another corresponding to insects previously reared out on the selected genotypes. In addition to the parameters evaluated in preliminary tests, we also determined the viability and incubation period of eggs. Moderate levels of resistance (antibiosis/antixenosis) to B. tabaci biotype B were found in three genotypes. 'P98Y11' and 'TMG132 RR' were less suitable for insect development, extending the development cycle, and UX-2569-159 caused high nymphal mortality. We did not observe a significant increase in the level of plant resistance by the use of previously stressed insects. This suggests that the evaluation of a single whitefly generation may be sufficient to make correct decisions on promising soybean genotypes.

  4. Agronomic evaluation of some rice genotypes in Nsukka | Agbo ...

    African Journals Online (AJOL)

    The highly significant differences in the agronomic characters and biotic stresses measured gives room for further selection. Thus, genotypes that showed higher resistance to the stresses and had higher yields will be favoured in selection. Keywords: Biotic stresses, G x Y interaction, Selection Agro-Science Vol. 4 (2) 2005: ...

  5. Genotypes selection of Dendrobium (Orchidaceae in vitro propagation phase/ Seleção de genótipos de Dendrobium (Orchidaceae na fase de propagação in vitro

    Directory of Open Access Journals (Sweden)

    Lúcia Sadayo Assari Takahashi

    2004-05-01

    Full Text Available The process of artificial hibridization in orchids is used to obtain new varieties. The objective of the present paper was to select genotypes of Dendrobium favourable for in vitro propagation for commercial utilization through crossings and self polinization of selected matrice plants. Fifteen different plants with contrasting colors, flower sizes and plant heighs were used; the flowers were artificially polinated and the seeds germinated in vitro on MS medium, with half concentration of nutrients. The following crossings were made D9 x D7; D11 x Df22; D6 x D15; D9 x D2; D16 x D15; D5 x D9; D14 x D7; D7 x D14; D4 x D9; D6 x D9; D3 x D8; and the self polinizations: Df22; D7; D5; D21; D2; D15; D8; D23; D3 and D6. The obtained plants were avaluated for: plant heigh, number of roots, fresh and dry matter weight. The best results was observed in the following crosses D9 x D7; D11 x Df22; D6 x D15; D16 x D15 and D14 x D7 and for self polinizations Df22 and D7.O processo de hibridação artificial em orquídeas é utilizado para obtenção de novas variedades. O trabalho teve como objetivo a seleção de genótipos de Dendrobium favoráveis à propagação in vitro em escala comercial através de cruzamentos e autofecundações de plantas matrizes selecionadas. Foram utilizadas 15 plantas com características contrastantes de coloração, tamanho das flores e altura da planta; as flores polinizadas artificialmente e as sementes germinadas in vitro em meio MS, com metade da concentração dos macronutrientes. Foram realizados os cruzamentos: D9 x D7; D11 x Df22; D6 x D15; D9 x D2; D16 x D15; D5 x D9; D14 x D7; D7 x D14; D4 x D9; D6 x D9; D3 x D8; e as autofecundações: Df22; D7; D5; D21; D2; D15; D8; D23; D3 e D6. As plantas resultantes do cultivo foram avaliadas para as características: altura da planta, número de raízes, peso das massas fresca e seca total. Os melhores resultados para as características analisadas foram observados nos

  6. megasat: automated inference of microsatellite genotypes from sequence data.

    Science.gov (United States)

    Zhan, Luyao; Paterson, Ian G; Fraser, Bonnie A; Watson, Beth; Bradbury, Ian R; Nadukkalam Ravindran, Praveen; Reznick, David; Beiko, Robert G; Bentzen, Paul

    2017-03-01

    megasat is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important feature of megasat is the generation of histograms of the length-frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. megasat is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demonstrate megasat using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0-1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs. © 2016 John Wiley & Sons Ltd.

  7. Cultivating Insect Cells To Produce Recombinant Proteins

    Science.gov (United States)

    Spaulding, Glenn; Goodwin, Thomas; Prewett, Tacey; Andrews, Angela; Francis, Karen; O'Connor, Kim

    1996-01-01

    Method of producing recombinant proteins involves growth of insect cells in nutrient solution in cylindrical bioreactor rotating about cylindrical axis, oriented horizontally and infecting cells with viruses into which genes of selected type cloned. Genes in question those encoding production of desired proteins. Horizontal rotating bioreactor preferred for use in method, denoted by acronym "HARV", described in "High-Aspect-Ratio Rotating Cell-Culture Vessel" (MSC-21662).

  8. Detection, Validation, and Application of Genotyping-by-Sequencing Based Single Nucleotide Polymorphisms in Upland Cotton

    Directory of Open Access Journals (Sweden)

    M. Sariful Islam

    2015-03-01

    Full Text Available The presence of two closely related subgenomes in the allotetraploid Upland cotton, combined with a narrow genetic base of the cultivated varieties, has hindered the identification of polymorphic genetic markers and their use in improving this important crop. Genotyping-by-sequencing (GBS is a rapid way to identify single nucleotide polymorphism (SNP markers; however, these SNPs may be specific to the sequenced cotton lines. Our objective was to obtain a large set of polymorphic SNPs with broad applicability to the cultivated cotton germplasm. We selected 11 diverse cultivars and their random-mated recombinant inbred progeny for SNP marker development via GBS. Two different GBS methodologies were used by Data2Bio (D2B and the Institute for Genome Diversity (IGD to identify 4441 and 1176 polymorphic SNPs with minor allele frequency of ≥0.1, respectively. We further filtered the SNPs and aligned their sequences to the diploid reference genome. We were able to use homeologous SNPs to assign 1071 SNP loci to the At subgenome and 1223 to the Dt subgenome. These filtered SNPs were located in genic regions about twice as frequently as expected by chance. We tested 111 of the SNPs in 154 diverse Upland cotton lines, which confirmed the utility of the SNP markers developed in such approach. Not only were the SNPs identified in the 11 cultivars present in the 154 cotton lines, no two cultivars had identical SNP genotypes. We conclude that GBS can be easily used to discover SNPs in Upland cotton, which can be converted to functional genotypic assays for use in breeding and genetic studies.

  9. An experimental genetic system using Berberis vulgaris confirms sexual recombination in Puccinia striiformis

    DEFF Research Database (Denmark)

    Rodriguez Algaba, Julian; Walter, Stephanie; Sørensen, Chris Khadgi

    , the use of B. vulgaris plants originating from nature reserves in Sweden and Denmark proved to be successful for infection and selfing a European Pst isolate in the Danish laboratory in 2013. The progeny isolates in the S1 generation were genotyped with microsatellite markers to confirm parental origin...... and to study genotypic diversity. The markers confirmed the parental origin and markers that were heterozygous in the parent generally segregated in the S1 progenies. A largest number of multilocus genotypes observed among the progeny isolates confirmed successful sexual recombination. Segregation...

  10. Vaccine-induced cross-genotype reactive neutralizing antibodies against hepatitis C virus

    DEFF Research Database (Denmark)

    Meunier, Jean-Christophe; Gottwein, Judith M; Houghton, Michael

    2011-01-01

    We detected cross-reactive neutralizing antibodies (NtAb) against hepatitis C virus (HCV) in chimpanzees vaccinated with HCV-1 (genotype 1a) recombinant E1/E2 envelope glycoproteins. Five vaccinated chimpanzees, protected following HCV-1 challenge, were initially studied using the heterologous H77...... (genotype 1a) HCVpp assay. All animals had developed NtAb after the second vaccination; 4 animals had reciprocal titers of =200 at the time of challenge. Using genotypes 1a-6a HCV pseudoparticles (HCVpp) and cell culture-derived HCV (HCVcc) assays, cross-reactive NtAb were detected against 1a, 4a, 5a, and 6...

  11. Comparative analysis of expressed sequence tags (ESTs between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress

    Directory of Open Access Journals (Sweden)

    Raju N L

    2011-04-01

    Full Text Available Abstract Background Chickpea (Cicer arietinum L. is an important grain-legume crop that is mainly grown in rainfed areas, where terminal drought is a major constraint to its productivity. We generated expressed sequence tags (ESTs by suppression subtraction hybridization (SSH to identify differentially expressed genes in drought-tolerant and -susceptible genotypes in chickpea. Results EST libraries were generated by SSH from root and shoot tissues of IC4958 (drought tolerant and ICC 1882 (drought resistant exposed to terminal drought conditions by the dry down method. SSH libraries were also constructed by using 2 sets of bulks prepared from the RNA of root tissues from selected recombinant inbred lines (RILs (10 each for the extreme high and low root biomass phenotype. A total of 3062 unigenes (638 contigs and 2424 singletons, 51.4% of which were novel in chickpea, were derived by cluster assembly and sequence alignment of 5949 ESTs. Only 2185 (71% unigenes showed significant BLASTX similarity ( Conclusion Our study compares not only genes that are up- and down-regulated in a drought-tolerant genotype under terminal drought stress and a drought susceptible genotype but also between the bulks of the selected RILs exhibiting extreme phenotypes. More than 50% of the genes identified have been shown to be associated with drought stress in chickpea for the first time. This study not only serves as resource for marker discovery, but can provide a better insight into the selection of candidate genes (both up- and downregulated associated with drought tolerance. These results can be used to identify suitable targets for manipulating the drought-tolerance trait in chickpea.

  12. Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus.

    Directory of Open Access Journals (Sweden)

    Etienne Simon-Loriere

    2009-05-01

    Full Text Available The ability of pathogens to escape the host's immune response is crucial for the establishment of persistent infections and can influence virulence. Recombination has been observed to contribute to this process by generating novel genetic variants. Although distinctive recombination patterns have been described in many viral pathogens, little is known about the influence of biases in the recombination process itself relative to selective forces acting on newly formed recombinants. Understanding these influences is important for determining how recombination contributes to pathogen genome and proteome evolution. Most previous research on recombination-driven protein evolution has focused on relatively simple proteins, usually in the context of directed evolution experiments. Here, we study recombination in the envelope gene of HIV-1 between primary isolates belonging to subtypes that recombine naturally in the HIV/AIDS pandemic. By characterizing the early steps in the generation of recombinants, we provide novel insights into the evolutionary forces that shape recombination patterns within viral populations. Specifically, we show that the combined effects of mechanistic processes that determine the locations of recombination breakpoints across the HIV-1 envelope gene, and purifying selection acting against dysfunctional recombinants, can explain almost the entire distribution of breakpoints found within this gene in nature. These constraints account for the surprising paucity of recombination breakpoints found in infected individuals within this highly variable gene. Thus, the apparent randomness of HIV evolution via recombination may in fact be relatively more predictable than anticipated. In addition, the dominance of purifying selection in localized areas of the HIV genome defines regions where functional constraints on recombinants appear particularly strong, pointing to vulnerable aspects of HIV biology.

  13. Genetic variability and selection criteria in rice mutant lines as revealed by quantitative traits.

    Science.gov (United States)

    Oladosu, Yusuff; Rafii, M Y; Abdullah, Norhani; Abdul Malek, Mohammad; Rahim, H A; Hussin, Ghazali; Abdul Latif, Mohammad; Kareem, Isiaka

    2014-01-01

    Genetic based knowledge of different vegetative and yield traits play a major role in varietal improvement of rice. Genetic variation gives room for recombinants which are essential for the development of a new variety in any crop. Based on this background, this work was carried out to evaluate genetic diversity of derived mutant lines and establish relationships between their yield and yield components using multivariate analysis. To achieve this objective, two field trials were carried out on 45 mutant rice genotypes to evaluate their growth and yield traits. Data were taken on vegetative traits and yield and its components, while genotypic and phenotypic coefficients, variance components, expected genetic advance, and heritability were calculated. All the genotypes showed variations for vegetative traits and yield and its components. Also, there was positive relationship between the quantitative traits and the final yield with the exception of number of tillers. Finally, the evaluated genotypes were grouped into five major clusters based on the assessed traits with the aid of UPGMA dendrogram. So hybridization of group I with group V or group VI could be used to attain higher heterosis or vigour among the genotypes. Also, this evaluation could be useful in developing reliable selection indices for important agronomic traits in rice.

  14. A simple and robust statistical test for detecting the presence of recombination.

    Science.gov (United States)

    Bruen, Trevor C; Philippe, Hervé; Bryant, David

    2006-04-01

    Recombination is a powerful evolutionary force that merges historically distinct genotypes. But the extent of recombination within many organisms is unknown, and even determining its presence within a set of homologous sequences is a difficult question. Here we develop a new statistic, phi(w), that can be used to test for recombination. We show through simulation that our test can discriminate effectively between the presence and absence of recombination, even in diverse situations such as exponential growth (star-like topologies) and patterns of substitution rate correlation. A number of other tests, Max chi2, NSS, a coalescent-based likelihood permutation test (from LDHat), and correlation of linkage disequilibrium (both r2 and /D'/) with distance, all tend to underestimate the presence of recombination under strong population growth. Moreover, both Max chi2 and NSS falsely infer the presence of recombination under a simple model of mutation rate correlation. Results on empirical data show that our test can be used to detect recombination between closely as well as distantly related samples, regardless of the suspected rate of recombination. The results suggest that phi(w) is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances.

  15. Identification of zoonotic genotypes of Giardia duodenalis.

    Directory of Open Access Journals (Sweden)

    Hein Sprong

    Full Text Available Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset. The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the

  16. Recombinant Collagenlike Proteins

    Science.gov (United States)

    Fertala, Andzej

    2007-01-01

    A group of collagenlike recombinant proteins containing high densities of biologically active sites has been invented. The method used to express these proteins is similar to a method of expressing recombinant procollagens and collagens described in U. S. Patent 5,593,859, "Synthesis of human procollagens and collagens in recombinant DNA systems." Customized collagenous proteins are needed for biomedical applications. In particular, fibrillar collagens are attractive for production of matrices needed for tissue engineering and drug delivery. Prior to this invention, there was no way of producing customized collagenous proteins for these and other applications. Heretofore, collagenous proteins have been produced by use of such biological systems as yeasts, bacteria, and transgenic animals and plants. These products are normal collagens that can also be extracted from such sources as tendons, bones, and hides. These products cannot be made to consist only of biologically active, specific amino acid sequences that may be needed for specific applications. Prior to this invention, it had been established that fibrillar collagens consist of domains that are responsible for such processes as interaction with cells, binding of growth factors, and interaction with a number of structural proteins present in the extracellular matrix. A normal collagen consists of a sequence of domains that can be represented by a corresponding sequence of labels, e.g., D1D2D3D4. A collagenlike protein of the present invention contains regions of collagen II that contain multiples of a single domain (e.g., D1D1D1D1 or D4D4D4D4) chosen for its specific biological activity. By virtue of the multiplicity of the chosen domain, the density of sites having that specific biological activity is greater than it is in a normal collagen. A collagenlike protein according to this invention can thus be made to have properties that are necessary for tissue engineering.

  17. Rapid generation of markerless recombinant MVA vaccines by en passant recombineering of a self-excising bacterial artificial chromosome.

    Science.gov (United States)

    Cottingham, Matthew G; Gilbert, Sarah C

    2010-09-01

    The non-replicating poxviral vector modified vaccinia virus Ankara (MVA) is currently a leading candidate for development of novel recombinant vaccines against globally important diseases. The 1980s technology for making recombinant MVA (and other poxviruses) is powerful and robust, but relies on rare recombination events in poxviral-infected cells. In the 21st century, it has become possible to apply bacterial artificial chromosome (BAC) technology to poxviruses, as first demonstrated by B. Moss' lab in 2002 for vaccinia virus. A similar BAC clone of MVA was subsequently derived, but while recombination-mediated genetic engineering for rapid production was used of deletion mutants, an alternative method was required for efficient insertion of transgenes. Furthermore "markerless" viruses, which carry no trace of the selectable marker used for their isolation, are increasingly required for clinical trials, and the viruses derived via the new method contained the BAC sequence in their genomic DNA. Two methods are adapted to MVA-BAC to provide more rapid generation of markerless recombinants in weeks rather than months. "En passant" recombineering is applied to the insertion of a transgene expression cassette and the removal of the selectable marker in bacteria; and a self-excising variant of MVA-BAC is constructed, in which the BAC cassette region is rapidly and efficiently lost from the viral genome following rescue of the BAC into infectious virus. These methods greatly facilitate and accelerate production of recombinant MVA, including markerless constructs. Copyright 2010 Elsevier B.V. All rights reserved.

  18. Recombinant Protein Production and Insect Cell Culture and Process

    Science.gov (United States)

    Spaulding, Glenn F. (Inventor); Goodwin, Thomas J. (Inventor); OConnor, Kim C. (Inventor); Francis, Karen M. (Inventor); Andrews, Angela D. (Inventor); Prewett, Tracey L. (Inventor)

    1997-01-01

    A process has been developed for recombinant production of selected polypeptides using transformed insect cells cultured in a horizontally rotating culture vessel modulated to create low shear conditions. A metabolically transformed insect cell line is produced using the culture procedure regardless of genetic transformation. The recombinant polypeptide can be produced by an alternative process using virtually infected or stably transformed insect cells containing a gene encoding the described polypeptide. The insect cells can also be a host for viral production.

  19. Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis.

    Science.gov (United States)

    Stevison, Laurie S; Noor, Mohamed A F

    2010-12-01

    Recombination is fundamental to meiosis in many species and generates variation on which natural selection can act, yet fine-scale linkage maps are cumbersome to construct. We generated a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, we report significant fine-scale heterogeneity of local recombination rates. However, we also observed "recombinational neighborhoods," where adjacent intervals had similar recombination rates after excluding regions near the centromere and telomere. We further found significant positive associations of fine-scale recombination rate with repetitive element abundance and a 13-bp sequence motif known to associate with human recombination rates. We noted strong crossover interference extending 5-7 Mb from the initial crossover event. Further, we observed that fine-scale recombination rates in D. persimilis are strongly correlated with those obtained from a comparable study of its sister species, D. pseudoobscura. We documented a significant relationship between recombination rates and intron nucleotide sequence diversity within species, but no relationship between recombination rate and intron divergence between species. These results are consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining the relationship of recombination with nucleotide diversity within species. Finally, we found significant correlations between recombination rate and GC content, supporting both GC-biased gene conversion (BGC) models and selection-driven codon bias models. Overall, this genome-enabled map of fine-scale recombination rates allowed us to confirm findings of broader-scale studies and identify multiple novel features that merit further investigation.

  20. Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference.

    Science.gov (United States)

    Segura, Joana; Ferretti, Luca; Ramos-Onsins, Sebastián; Capilla, Laia; Farré, Marta; Reis, Fernanda; Oliver-Bonet, Maria; Fernández-Bellón, Hugo; Garcia, Francisca; Garcia-Caldés, Montserrat; Robinson, Terence J; Ruiz-Herrera, Aurora

    2013-11-22

    Recombination allows faithful chromosomal segregation during meiosis and contributes to the production of new heritable allelic variants that are essential for the maintenance of genetic diversity. Therefore, an appreciation of how this variation is created and maintained is of critical importance to our understanding of biodiversity and evolutionary change. Here, we analysed the recombination features from species representing the major eutherian taxonomic groups Afrotheria, Rodentia, Primates and Carnivora to better understand the dynamics of mammalian recombination. Our results suggest a phylogenetic component in recombination rates (RRs), which appears to be directional, strongly punctuated and subject to selection. Species that diversified earlier in the evolutionary tree have lower RRs than those from more derived phylogenetic branches. Furthermore, chromosome-specific recombination maps in distantly related taxa show that crossover interference is especially weak in the species with highest RRs detected thus far, the tiger. This is the first example of a mammalian species exhibiting such low levels of crossover interference, highlighting the uniqueness of this species and its relevance for the study of the mechanisms controlling crossover formation, distribution and resolution.

  1. Combined use of phenotypic and genotypic information in sampling animalsfor genotyping in detection of quantitative trait loci

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P

    2008-01-01

    Conventional selective genotyping which is using the extreme phenotypes (EP) was compared with alternative criteria to find the most informative animals for genotyping with respects to mapping quantitative trait loci (QTL). Alternative sampling strategies were based on minimizing the sampling error...... of the estimated QTL effect (MinERR) and maximizing likelihood ratio test (MaxLRT) using both phenotypic and genotypic information. In comparison, animals were randomly genotyped either within or across families. One hundred data sets were simulated each with 30 half-sib families and 120 daughters per family....... The strategies were compared in these datasets with respect to estimated effect and position of a QTL within a previously defined genomic region at genotyping 10, 20 or 30% of the animals. Combined linkage disequilibrium linkage analysis (LDLA) was applied in a variance component approach. Power to detect QTL...

  2. Efficient cell culture system for hepatitis C virus genotype 5A

    DEFF Research Database (Denmark)

    2013-01-01

    The present inventors developed 5a/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and all of or part of NS2 were replaced by the corresponding genes of the genotype 5a reference strain SA13. Compared to the J6/JFH control virus, after transfection of in vi...

  3. Seleção de genótipos de arroz tolerantes à salinidade durante a fase vegetativa Selection of genotypes of salinity tolerance rice during the vegetative phase

    Directory of Open Access Journals (Sweden)

    Palmira Cabral Sales de Melo

    2006-02-01

    Full Text Available O objetivo deste trabalho foi avaliar o grau de tolerância e sensibilidade à salinidade de genótipos de arroz durante a fase vegetativa da planta. O experimento foi conduzido sob condições de telado, nas dependências da Empresa Pernambucana de Pesquisa Agropecuária-IPA (Recife-PE, em 1996. Foram avaliados doze genótipos de arroz, sendo dez tolerantes e dois sensíveis à salinidade no estádio de desenvolvimento vegetativo. O delineamento experimental foi em blocos ao acaso com arranjo fatorial (doze genótipos x quatro níveis de NaCl, em três repetições. Os resultados constataram existência de variabilidade entre os genótipos de arroz na população estudada para tolerância e sensibilidade à salinidade. As linhagens PR492, PR504, CNA8250, CNA8262 e CNA8267 são tolerantes e a CNA8270, CNA8258, CNA8269, PR475 e PR477 são sensíveis à salinidade dos solos durante a fase vegetativa.The objective of this work was to evaluate the degree of tolerance and sensibility to the salinity of genoty,pes of rice (Oryza sativa L. during the vegetative phase of the plant. The experiment was lead under greenhouse conditions at IPA (Empresa Pernambucana de Pesquisa Agropecuária, in 1996. Twelve genotypes of rice had been evaluated, being ten tolerant and two sensible ones to salinity in the vegetative development stadium. The randomized blocks design were performed into three repetitions of factorials arrangements (twelve genotypes x four levels of NaCl. Results had evidenced variability existence among the genotypes of rice, in the specific population, for tolerance and sensitivity to the salinity. Samples PR492, PR504, CNA8250, CNA8262 and CNA8267 can be considered tolerant to salinity, while the genotypes CNA8270, CNA8258, CNA8269, PR475 and PR477 are sensible to salinity of soil during the vegetative phase.

  4. Cell biology of mitotic recombination

    DEFF Research Database (Denmark)

    Lisby, Michael; Rothstein, Rodney

    2015-01-01

    Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules...... as well as the cellular organization of the process of homologous recombination. Herein we review the cell biological aspects of mitotic homologous recombination with a focus on Saccharomyces cerevisiae and mammalian cells, but will also draw on findings from other experimental systems. Key topics...

  5. Chlorophyll a fluorescence to phenotype wheat genotypes for heat tolerance

    DEFF Research Database (Denmark)

    Sharma, Dew Kumari; Andersen, Sven Bode; Ottosen, Carl-Otto

    parameter, maximum quantum yield efficiency of PSII (Fv/Fm) is used as a physiological marker for early stress detection in PSII in plants. We established a reproducible protocol to measure response of wheat genotypes to high temperature based on Fv/Fm. The heat treatment of 40°C in 300 µmol m-2s-1 PAR...... for 72h was appropriate to induce genotype dependent variation in Fv/Fm. This standardized protocol was used to phenotype wheat genotypes until the variation in the genotypes was consistently high with increased heritability for the trait, Fv/Fm. Mass screening of 1273 wheat genotypes in a milder stress...... of 38oC for 2h showed a heritability of 7%. However, a stronger stress at 40oC for 72h in repeated experiments on 138 extreme performing selected genotypes resulted in an increased genetic component of 15% which was further increased to 29% in the third selection cycle with 41 genotypes. Our protocol...

  6. Among-year variation in selection during early life stages and the genetic basis of fitness in Arabidopsis thaliana.

    Science.gov (United States)

    Postma, Froukje M; Ågren, Jon

    2018-04-19

    Incomplete information regarding both selection regimes and the genetic basis of fitness limits our understanding of adaptive evolution. Among-year variation in the genetic basis of fitness is rarely quantified, and estimates of selection are typically based on single components of fitness, thus potentially missing conflicting selection acting during other life-history stages. Here, we examined among-year variation in selection on a key life-history trait and the genetic basis of fitness covering the whole life cycle in the annual plant Arabidopsis thaliana. We planted freshly-matured seeds of >200 recombinant inbred lines (RILs) derived from a cross between two locally-adapted populations (Italy and Sweden), and both parental genotypes at the native site of the Swedish population in three consecutive years. We quantified selection against the nonlocal Italian genotype, mapped quantitative trait loci (QTL) for fitness and its components, and quantified selection on timing of germination during different life stages. In all three years, the local Swedish genotype outperformed the non-local Italian genotype. However, both the contribution of early life stages to relative fitness, and the effects of fitness QTL varied among years. Timing of germination was under conflicting selection through seedling establishment vs. adult survival and fecundity, and both the direction and magnitude of net selection varied among years. Our results demonstrate that selection during early life stages and the genetic basis of fitness can vary markedly among years, emphasizing the need for multi-year studies considering the whole life cycle for a full understanding of natural selection and mechanisms maintaining local adaptation. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  7. The potential of shifting recombination hotspots to increase genetic gain in livestock breeding.

    Science.gov (United States)

    Gonen, Serap; Battagin, Mara; Johnston, Susan E; Gorjanc, Gregor; Hickey, John M

    2017-07-04

    This study uses simulation to explore and quantify the potential effect of shifting recombination hotspots on genetic gain in livestock breeding programs. We simulated three scenarios that differed in the locations of quantitative trait nucleotides (QTN) and recombination hotspots in the genome. In scenario 1, QTN were randomly distributed along the chromosomes and recombination was restricted to occur within specific genomic regions (i.e. recombination hotspots). In the other two scenarios, both QTN and recombination hotspots were located in specific regions, but differed in whether the QTN occurred outside of (scenario 2) or inside (scenario 3) recombination hotspots. We split each chromosome into 250, 500 or 1000 regions per chromosome of which 10% were recombination hotspots and/or contained QTN. The breeding program was run for 21 generations of selection, after which recombination hotspot regions were kept the same or were shifted to adjacent regions for a further 80 generations of selection. We evaluated the effect of shifting recombination hotspots on genetic gain, genetic variance and genic variance. Our results show that shifting recombination hotspots reduced the decline of genetic and genic variance by releasing standing allelic variation in the form of new allele combinations. This in turn resulted in larger increases in genetic gain. However, the benefit of shifting recombination hotspots for increased genetic gain was only observed when QTN were initially outside recombination hotspots. If QTN were initially inside recombination hotspots then shifting them decreased genetic gain. Shifting recombination hotspots to regions of the genome where recombination had not occurred for 21 generations of selection (i.e. recombination deserts) released more of the standing allelic variation available in each generation and thus increased genetic gain. However, whether and how much increase in genetic gain was achieved by shifting recombination hotspots depended

  8. Experimental study of para- and ortho-H3+ recombination

    International Nuclear Information System (INIS)

    Plasil, R; Varju, J; Hejduk, M; Dohnal, P; KotrIk, T; Glosik, J

    2011-01-01

    Recombination of H 3 + with electrons is a key process for many plasmatic environments. Recent experiments on storage ring devices used ion sources producing H 3 + with enhanced populations of H 3 + ions in the para nuclear spin configuration to shed light on the theoretically predicted faster recombination of para states. Although increased recombination rates were observed, no in situ characterization of recombining ions was performed. We present a state selective recombination study of para- and ortho-H 3 + ions with electrons at 77 K in afterglow plasma in a He/Ar/H 2 gas-mixture. Both spin configurations of H 3 + have been observed in situ with a near infrared cavity ring down spectrometer (NIR-CRDS) using the two lowest energy levels of H 3 + . Using hydrogen with an enhanced population of H 2 molecules in para states allowed us to influence the [para-H 3 + ]/[ortho-H 3 + ] ratio in the discharge and in the afterglow. We observed an increase in the measured effective recombination rate coefficients with the increase of the fraction of para-H 3 + . Measurements with different fractions of para-H 3 + at otherwise identical conditions allowed us to determine the binary recombination rate coefficients for pure para-H 3 + p α bin (77 K) = (2.0±0.4)x10 -7 cm 3 s -1 and pure ortho-H 3 + o α bin (77 K) = (4±3)x10 -8 cm 3 s -1 .

  9. Hadron Correlations and Parton Recombination

    Energy Technology Data Exchange (ETDEWEB)

    Fries, R.J. [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)]. E-mail: rjfries@comp.tamu.edu

    2007-02-15

    Parton recombination has been found to be an extremely useful model to understand hadron production at the Relativistic Heavy Ion Collider. It is particularly important to explore its connections with hard processes. This article reviews some of the aspects of the quark recombination model and places particular emphasis on hadron correlations.

  10. Genotype-by-temperature interactions may help to maintain clonal diversity in Asterionella formosa (Bacillariophyceae)

    NARCIS (Netherlands)

    Gsell, A.S.; De Senerpont Domis, L.N.; Przytulska-Bartosiewicz, A.; Mooij, W.M.; Van Donk, E.; Ibelings, B.W.

    2012-01-01

    Marine and freshwater phytoplankton populations often show large clonal diversity, which is in disagreement with clonal selection of the most vigorous genotype(s). Temporal fluctuation in selection pressures in variable environments is a leading explanation for maintenance of such genetic diversity.

  11. Genotype-by-temperature interactions may help to maintain clonal diversity in asterionella formosa (Bacillariophyceae)

    NARCIS (Netherlands)

    Gsell, A.S.; Domis, L.N.D.; Przytulska-Bartosiewicz, A.; Mooij, W.M.; Donk, van E.; Ibelings, B.W.

    2012-01-01

    Marine and freshwater phytoplankton populations often show large clonal diversity, which is in disagreement with clonal selection of the most vigorous genotype(s). Temporal fluctuation in selection pressures in variable environments is a leading explanation for maintenance of such genetic diversity.

  12. Common genotypes of hepatitis B virus

    International Nuclear Information System (INIS)

    Idrees, M.; Khan, S.; Riazuddin, S.

    2004-01-01

    Objective: To find out the frequency of common genotypes of hepatitis-B virus (HBV). Subjects and Methods: HBV genotypes were determined in 112 HBV DNA positive sera by a simple and precise molecular genotyping system base on PCR using type-specific primers for the determination of genotypes of HBV A through H. Results: Four genotypes (A,B,C and D) out of total eight reported genotypes so far were identified. Genotypes A, B and C were predominant. HBV genotype C was the most predominant in this collection, appearing in 46 samples (41.7%). However, the genotypes of a total of 5 (4.46%) samples could not be determined with the present genotyping system. Mixed genotypes were seen in 8(7.14% HBV) isolates. Five of these were infected with genotypes A/D whereas two were with genotypes C/D. One patient was infected with 4 genotypes (A/B/C/D). Genotype A (68%) was predominant in Sindh genotype C was most predominant in North West Frontier Province (NWFP) (68.96) whereas genotype C and B were dominant in Punjab (39.65% and 25.86% respectively). Conclusion: All the four common genotypes of HBV found worldwide (A,B,C and D) were isolated. Genotype C is the predominant Genotypes B and C are predominant in Punjab and N.W.F.P. whereas genotype A is predominant in Sindh. (author)

  13. Molecular characterization of varicella-zoster virus clinical isolates from 2006 to 2008 in a tertiary care hospital, Dublin, Ireland, using different genotyping methods.

    LENUS (Irish Health Repository)

    Roycroft, Emma

    2012-10-01

    Varicella-zoster virus (VZV), a herpesvirus, is a ubiquitous organism that causes considerable morbidity worldwide and can cause severe complications on reactivation. Phylogenetic analysis was performed on 19 clinical VZV isolates (16 zoster and 3 varicella) found in Ireland, between December 2006 and November 2008, in order to determine whether previously reported viral heterogeneity was still present and whether viral recombination was evident. Open reading-frames (ORFs) from genes 1, 21, 50, and 54, were sequenced. Clades 1, 2, 3, and 5 were identified. Four putative recombinant isolates were detected (three clade 3\\/1 and one clade 5\\/3\\/1). Further sequencing and examination of ORF 22 and 21\\/50, did not elucidate the putative recombinant genotypes further. These two previously published genotyping schemes were examined in light of the new consensus genotyping scheme proposed in 2010. Remarkable VZV heterogeneity remains prevalent in Ireland. This is the first evidence of putative VZV recombination found in Ireland.

  14. Analysis of intermolecular RNA-RNA recombination by rubella virus

    International Nuclear Information System (INIS)

    Adams, Sandra D.; Tzeng, W.-P.; Chen, M.-H.; Frey, Teryl K.

    2003-01-01

    To investigate whether rubella virus (RUB) undergoes intermolecular RNA-RNA recombination, cells were cotransfected with pairs of in vitro transcripts from genomic cDNA plasmid vectors engineered to contain nonoverlapping deletions: the replicative transcript maintained the 5'-proximal nonstructural (NS) ORF (which contained the replicase, making it RNA replication competent), had a deletion in the 3'-proximal structural protein (SP) ORF, and maintained the 3' end of the genome, including the putative 3' cis-acting elements (CSE), while the nonreplicative transcript consisted of the 3' half of the genome including the SP-ORF and 3' CSE. Cotransfection yielded plaque-forming virus that synthesized the standard genomic and subgenomic RNAs and thus was generated by RNA-RNA recombination. Using transcripts tagged with a 3'-terminal deletion, it was found that recombinants contained the 3' end derived from the replicative strand, indicating a cis-preference for initiation of negative-strand synthesis. In cotransfections in which the replicative transcript lacked the 3' CSE, recombination occurred, albeit at lower efficiency, indicating that initiation in trans from the NS-ORF can occur. The 3' CSE was sufficient as a nonreplicative transcript, showing that it can serve as a promoter for negative-strand RNA synthesis. While deletion mutagenesis showed that the presence of the junction untranslated region (J-UTR) between the ORFs appeared to be necessary on both transcripts for recombination in this region of the genome, analysis with transcripts tagged with restriction sites showed that the J-UTR was not a hot spot for recombination compared to neighboring regions in both ORFs. Sequence analysis of recombinants revealed that both precise (homologous) and imprecise recombination (aberrant, homologous resulting in duplications) occurred; however, imprecise recombination only involved the J-UTR or the 3' end of the NS-ORF and the J-UTR (maintaining the NS-ORF), indicating

  15. Functional bottlenecks for generation of HIV-1 intersubtype Env recombinants.

    Science.gov (United States)

    Bagaya, Bernard S; Vega, José F; Tian, Meijuan; Nickel, Gabrielle C; Li, Yuejin; Krebs, Kendall C; Arts, Eric J; Gao, Yong

    2015-05-23

    Intersubtype recombination is a powerful driving force for HIV evolution, impacting both HIV-1 diversity within an infected individual and within the global epidemic. This study examines if viral protein function/fitness is the major constraint shaping selection of recombination hotspots in replication-competent HIV-1 progeny. A better understanding of the interplay between viral protein structure-function and recombination may provide insights into both vaccine design and drug development. In vitro HIV-1 dual infections were used to recombine subtypes A and D isolates and examine breakpoints in the Env glycoproteins. The entire env genes of 21 A/D recombinants with breakpoints in gp120 were non-functional when cloned into the laboratory strain, NL4-3. Likewise, cloning of A/D gp120 coding regions also produced dead viruses with non-functional Envs. 4/9 replication-competent viruses with functional Env's were obtained when just the V1-V5 regions of these same A/D recombinants (i.e. same A/D breakpoints as above) were cloned into NL4-3. These findings on functional A/D Env recombinants combined with structural models of Env suggest a conserved interplay between the C1 domain with C5 domain of gp120 and extracellular domain of gp41. Models also reveal a co-evolution within C1, C5, and ecto-gp41 domains which might explain the paucity of intersubtype recombination in the gp120 V1-V5 regions, despite their hypervariability. At least HIV-1 A/D intersubtype recombination in gp120 may result in a C1 from one subtype incompatible with a C5/gp41 from another subtype.

  16. The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms.

    Science.gov (United States)

    Tiley, George P; Burleigh, J Gordon; Burleigh, Gordon

    2015-09-16

    Although homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC biased gene conversion, contribute to complex histories of gene duplication and loss through tandem duplication, and enhance purifying selection on genes. Therefore, variation in recombination rate across species may explain some of the variation in genomic architecture as well as rates of molecular evolution. We used phylogenetic comparative methods to investigate the evolution of global meiotic recombination rate in angiosperms and its effects on genome architecture and selection at the molecular level using genetic maps and genome sequences from thirty angiosperm species. Recombination rate is negatively correlated with genome size, which is likely caused by the removal of LTR retrotransposons. After correcting recombination rates for euchromatin content, we also found an association between global recombination rate and average gene family size. This suggests a role for recombination in the preservation of duplicate genes or expansion of gene families. An analysis of the correlation between the ratio of nonsynonymous to synonymous substitution rates (dN/dS) and recombination rate in 3748 genes indicates that higher recombination rates are associated with an increased efficacy of purifying selection, suggesting that global recombination rates affect variation in rates of molecular evolution across distantly related angiosperm species, not just between populations. We also identified shifts in dN/dS for recombination proteins that are associated with shifts in global recombination rate across our sample of angiosperms. Although our analyses only reveal correlations, not mechanisms, and do not include potential covariates of recombination rate, like effective

  17. Punctuated Distribution of Recombination Hotspots and Demarcation of Pericentromeric Regions in Phaseolus vulgaris L.

    Science.gov (United States)

    Bhakta, Mehul S.; Jones, Valerie A.; Vallejos, C. Eduardo

    2015-01-01

    High density genetic maps are a reliable tool for genetic dissection of complex plant traits. Mapping resolution is often hampered by the variable crossover and non-crossover events occurring across the genome, with pericentromeric regions (pCENR) showing highly suppressed recombination rates. The efficiency of linkage mapping can further be improved by characterizing and understanding the distribution of recombinational activity along individual chromosomes. In order to evaluate the genome wide recombination rate in common beans (Phaseolus vulgaris L.) we developed a SNP-based linkage map using the genotype-by-sequencing approach with a 188 recombinant inbred line family generated from an inter gene pool cross (Andean x Mesoamerican). We identified 1,112 SNPs that were subsequently used to construct a robust linkage map with 11 groups, comprising 513 recombinationally unique marker loci spanning 943 cM (LOD 3.0). Comparative analysis showed that the linkage map spanned >95% of the physical map, indicating that the map is almost saturated. Evaluation of genome-wide recombination rate indicated that at least 45% of the genome is highly recombinationally suppressed, and allowed us to estimate locations of pCENRs. We observed an average recombination rate of 0.25 cM/Mb in pCENRs as compared to the rest of genome that showed 3.72 cM/Mb. However, several hot spots of recombination were also detected with recombination rates reaching as high as 34 cM/Mb. Hotspots were mostly found towards the end of chromosomes, which also happened to be gene-rich regions. Analyzing relationships between linkage and physical map indicated a punctuated distribution of recombinational hot spots across the genome. PMID:25629314

  18. Selective and genetic constraints on pneumococcal serotype switching.

    Directory of Open Access Journals (Sweden)

    Nicholas J Croucher

    2015-03-01

    Full Text Available Streptococcus pneumoniae isolates typically express one of over 90 immunologically distinguishable polysaccharide capsules (serotypes, which can be classified into "serogroups" based on cross-reactivity with certain antibodies. Pneumococci can alter their serotype through recombinations affecting the capsule polysaccharide synthesis (cps locus. Twenty such "serotype switching" events were fully characterised using a collection of 616 whole genome sequences from systematic surveys of pneumococcal carriage. Eleven of these were within-serogroup switches, representing a highly significant (p < 0.0001 enrichment based on the observed serotype distribution. Whereas the recombinations resulting in between-serogroup switches all spanned the entire cps locus, some of those that caused within-serogroup switches did not. However, higher rates of within-serogroup switching could not be fully explained by either more frequent, shorter recombinations, nor by genetic linkage to genes involved in β-lactam resistance. This suggested the observed pattern was a consequence of selection for preserving serogroup. Phenotyping of strains constructed to express different serotypes in common genetic backgrounds was used to test whether genotypes were physiologically adapted to particular serogroups. These data were consistent with epistatic interactions between the cps locus and the rest of the genome that were specific to serotype, but not serogroup, meaning they were unlikely to account for the observed distribution of capsule types. Exclusion of these genetic and physiological hypotheses suggested future work should focus on alternative mechanisms, such as host immunity spanning multiple serotypes within the same serogroup, which might explain the observed pattern.

  19. Antixenosis of bean genotypes to Chrysodeixis includens (Lepidoptera: Noctuidae

    Directory of Open Access Journals (Sweden)

    Rafaela Morando

    2015-06-01

    Full Text Available The objective of this work was to evaluate bean genotypes for resistance to soybean looper (Chrysodeixis includens. Initially, free-choice tests were carried out with 59 genotypes, divided into three groups according to leaf color intensity (dark green, light green, and medium green, in order to evaluate oviposition preference. Subsequently, 12 genotypes with high potential for resistance were selected, as well as two susceptible commercial standards. With these genotypes, new tests were performed for oviposition in a greenhouse, besides tests for attractiveness and consumption under laboratory conditions (26±2ºC, 65±10% RH, and 14 h light: 10 h dark photophase. In the no-choice test with adults, in the greenhouse, the 'IAC Jabola', Arcelina 1, 'IAC Boreal', 'Flor de Mayo', and 'IAC Formoso' genotypes were the least oviposited, showing antixenosis-type resistance for oviposition. In the free-choice test with larvae, Arcelina 4, 'BRS Horizonte', 'Pérola', H96A102-1-1-1-52, 'IAC Boreal', 'IAC Harmonia', and 'IAC Formoso' were the less consumed genotypes, which indicates antixenosis to feeding. In the no-choice test, all genotypes (except for 'IAPAR 57' expressed moderate levels of antixenosis to feeding against C. includens larvae.

  20. The occurrence of fungi on roots and stem bases of Triticum aestivum ssp. spelta L. Thell. grown under two levels of chemical protection and harmfulness of Fusarium graminearum Schwabe to seedlings of selected genotypes

    Directory of Open Access Journals (Sweden)

    Małgorzata Cegiełko

    2016-09-01

    Full Text Available Investigations were carried out in 2007–2009 on the plots of the Felin Experimental Station belonging to the University of Life Sciences in Lublin, Poland. The studies comprised two breeding lines of spelt wheat (Triticum aestivum ssp. spelta L. Thell. – STH 3 and STH 715. Two levels of chemical protection were applied in the cultivation with minimal and complex protection. Infection of winter spelt wheat roots and stem bases was recorded in each growing season at hard dough stage (87 in Zadok’s scale. After 3 years of the study, the mean values of disease indexes for the analyzed spelt wheat lines in the experimental treatment with minimal protection were 28.53 and 40.30 respectively for STH 3 and STH 715. In the experimental combination with complex protection, after 3 years of the study the mean values of disease indexes ranged from 25.96 (STH 3 to 26.90 (STH 715. The mycological analysis showed that Fusarium spp., especially F. culmorum, caused root rot and necrosis of stem bases of spelt wheat in the experimental combination with minimal and complex protection. Moreover, Fusarium avenaceum and Bipolaris sorokiniana caused root rot and necrosis of stem bases of spelt wheat. Investigation carried out in a growth chamber on susceptibility of seedlings of three lines of spelt wheat (LO 2/09/n/2, LO 5/09/13/3, LO 5/09/5/4 to infection with Fusarium graminearum No. 8 and F. graminearum No. 45 showed that the genotypes did not differ in their susceptibility. All of them were susceptible, as indicated by high values of the disease indexes. No interaction was found between genotypes and strains of the fungus. This indicates the differential pathogenicity of Fusarium graminearum species.

  1. Analyzing genotype-by-environment interaction using curvilinear regression

    Directory of Open Access Journals (Sweden)

    Dulce Gamito Santinhos Pereira

    2012-12-01

    Full Text Available In the context of multi-environment trials, where a series of experiments is conducted across different environmental conditions, the analysis of the structure of genotype-by-environment interaction is an important topic. This paper presents a generalization of the joint regression analysis for the cases where the response (e.g. yield is not linear across environments and can be written as a second (or higher order polynomial or another non-linear function. After identifying the common form regression function for all genotypes, we propose a selection procedure based on the adaptation of two tests: (i a test for parallelism of regression curves; and (ii a test of coincidence for those regressions. When the hypothesis of parallelism is rejected, subgroups of genotypes where the responses are parallel (or coincident should be identified. The use of the Scheffé multiple comparison method for regression coefficients in second-order polynomials allows to group the genotypes in two types of groups: one with upward-facing concavity (i.e. potential yield growth, and the other with downward-facing concavity (i.e. the yield approaches saturation. Theoretical results for genotype comparison and genotype selection are illustrated with an example of yield from a non-orthogonal series of experiments with winter rye (Secalecereale L.. We have deleted 10 % of that data at random to show that our meteorology is fully applicable to incomplete data sets, often observed in multi-environment trials.

  2. Estudio de parámetros hídricos foliares en trigo (Triticum aestivum L. y su uso en selección de genotipos resistentes a sequía Leaf water parameters of wheat (Triticum aestivum L. and their use in the selection of drought resistant genotypes

    Directory of Open Access Journals (Sweden)

    MAURICIO ORTIZ

    2003-06-01

    , CRA y AO, y otra que consideró la pendiente y el promedio de psish y CRA. Luego se correlacionó el orden de los genotipos de ambas selecciones con los ordenes establecidos para los métodos de calculo de AO y se estableció que el orden que considera la pendiente y el promedio de ysh, CRA y AO se correlaciona con los ordenes establecidos por los tres métodos de cálculo de AO. Los parámetros hídricos foliares CRA, psish y AO no estuvieron correlacionados con el rendimiento bajo estrés hídrico. La pendiente de psish se correlacionó negativamente con el rendimiento, lo que indica que el AO permite a la planta sobrevivir al estrés pero no tener mayor rendimiento. Se concluye que con la metodología utilizada es posible seleccionar genotipos resistentes a sequía en base a la pendiente y el promedio de los parámetros psish, CRA y AO obtenidos en campo, removiendo parte del ruido ambientalThe leaf water parameters ys (solute potential, RWC (relative water content and OA (osmotic adjustment characterize the response of plants to water stress and presumably allow the identification of better adapted genotypes. These parameters, however, are highly influenced by the environment what makes their analysis difficult. In this work we hypothesize that it is possible to characterize and select drought resistant wheat genotypes based on the field value of the leaf water parameters using the appropriate analytical techniques. Thirty one wheat (Triticum aestivum L. genotypes were grown in two field trials, one irrigated and one non-irrigated that received 218.3 mm of winter rain. The statistical design was a randomized complete block with two replicates. Between 77 and 121 days after emergence (DC 41 to DC 77, five samplings of relative water content (RWC and solute potential of hydrated flag leaves (psish were made in each replication of each trial (10 observations per trial. The replicates were sampled in alternate days with a 24-h interval between 12:00 and 14:00 h

  3. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

    Science.gov (United States)

    Yabe, Shiori; Yamasaki, Masanori; Ebana, Kaworu; Hayashi, Takeshi; Iwata, Hiroyoshi

    2016-01-01

    Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS), which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the potential of genomic

  4. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

    Directory of Open Access Journals (Sweden)

    Shiori Yabe

    Full Text Available Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS, which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the

  5. Neutralizing antibodies in patients with chronic hepatitis C, genotype 1, against a panel of genotype 1 culture viruses

    DEFF Research Database (Denmark)

    Pedersen, Jannie; Jensen, Tanja B; Carlsen, Thomas H R

    2013-01-01

    , infection treated with pegylated interferon-α and ribavirin. Thirty-nine patients with chronic hepatitis C, genotype 1a or 1b, with either sustained virologic response (n = 23) or non-sustained virologic response (n = 16) were enrolled. Samples taken prior to treatment were tested for their ability...... to neutralize 6 different HCV genotype 1 cell culture recombinants (1a: H77/JFH1, TN/JFH1, DH6/JFH1; 1b: J4/JFH1, DH1/JFH1, DH5/JFH1). The results were expressed as the highest dilution yielding 50% neutralization (NAb50-titer). We observed no genotype or subtype specific differences in NAb50-titers between......The correlation of neutralizing antibodies to treatment outcome in patients with chronic hepatitis C virus (HCV) infection has not been established. The aim of this study was to determine whether neutralizing antibodies could be used as an outcome predictor in patients with chronic HCV, genotype 1...

  6. Seleção de genótipos de amendoim forrageiro para cobertura do solo e produção de biomassa aérea no período de estabelecimento utilizando-se metodologia de modelos mistos Selection of forage peanut genotypes for ground cover and aerial biomass production during establishment period using mixed model methodology

    Directory of Open Access Journals (Sweden)

    Giselle Mariano Lessa de Assis

    2008-11-01

    Full Text Available Objetivou-se estimar parâmetros genéticos e selecionar genótipos de amendoim forrageiro para maior cobertura do solo e produção de biomassa aérea durante o período de estabelecimento nas condições ambientais do Acre. A área experimental foi estabelecida em dezembro de 2005. O experimento foi realizado em delineamento de blocos ao acaso com quatro repetições utilizando-se 21 genótipos de amendoim forrageiro, incluindo três cultivares (Amarillo, Alqueire 1 e Belmonte. A seleção dos genótipos foi realizada considerando a cobertura do solo e a produção de matéria seca. As avaliações de cobertura do solo foram realizadas entre janeiro e outubro de 2006, em intervalos de quatro semanas. A produção de matéria seca foi mensurada 304 dias após o plantio. Os componentes de variância foram estimados pelo Método da Máxima Verossimilhança Restrita (REML e os valores genotípicos foram preditos pelo método da Melhor Predição Linear Não-Viesada (BLUP, conforme metodologia dos modelos mistos. Verificou-se a presença de variabilidade genética para ambas as características. As herdabilidades individuais foram de magnitude mediana, com valores de 0,36 a 0,58 para as características cobertura do solo e produção de matéria seca, respectivamente. A maior variabilidade entre os genótipos para cobertura do solo ocorreu entre a 12ª e a 16ª semana após o plantio, indicando que esse intervalo é o mais adequado para a seleção de genótipos de cobertura mais rápida do solo. Os valores genotípicos para produção de matéria seca variaram de 1.609 a 4.132 kg/ha para os genótipos BRA 015083 e BRA 040550, respectivamente. Os genótipos selecionados para maior cobertura do solo e produção de biomassa aérea durante o período de estabelecimento foram Belmonte, Amarillo, BRA 040550, BRA 039187, Alqueire 1, BRA 039799 e BRA 035033.This study aimed to estimate genetic parameters and to select genotypes of forage peanut with

  7. Genotypic diversity and spatial-temporal distribution of Symbiodinium clones in an abundant reef coral.

    Science.gov (United States)

    Pettay, Daniel T; Wham, Drew C; Pinzón, Jorge H; LaJeunesse, Todd C

    2011-12-01

    Genetic data are rapidly advancing our understanding of various biological systems including the ecology and evolution of coral-algal symbioses. The fine-scale interactions between individual genotypes of host and symbiont remain largely unstudied and constitute a major gap in knowledge. By applying microsatellite markers developed for both host and symbiont, we investigated the intracolony diversity, prevalence and stability of Symbiodinium glynni (type D1) multilocus genotypes in association with dense populations of Pocillopora at two sites in the Gulf of California. The genetic diversity and allelic frequencies in reef populations of S. glynni remained stable over 3 years. Common clone genotypes persisted over this period, and no temporal population subdivision (Φ(PT) = 0.021 and -0.003) was detected. Collections from circular plots showed no statistical correlation between related Pocillopora individuals and their associations with particular S. glynni genotypes, with no spatial structuring or clonal aggregation across a reef for the symbiont. From permanent linear transects, samples were analysed from multiple locations within a colony and some were resampled approximately 1 year later. Many of these multisampled colonies (approximately 53%) were dominated by a single S. glynni genotype and tended to associate with the same symbiont genotype(s) over time, while colony ramets often possessed unrelated symbiont genotypes. In contrast to the species level, associations between genotypes of Pocillopora and S. glynni are apparently more flexible over space and time. The abundance of sexually recombinant genotypes of S. glynni combined with greater flexibility might provide adaptive mechanisms for these symbioses to evolve rapidly to changes in environmental conditions and allow particular symbiont genotypes to spread through a host population. © 2011 Blackwell Publishing Ltd.

  8. Genetic diversity for grain Zn concentration in finger millet genotypes: Potential for improving human Zn nutrition

    Directory of Open Access Journals (Sweden)

    Ramegowda Yamunarani

    2016-06-01

    Full Text Available Nearly half of the world population suffers from micronutrient malnutrition, particularly Zn deficiency. It is important to understand genetic variation for uptake and translocation behaviors of Zn in relevant crop species to increase Zn concentration in edible parts. In the present study, genetic variation in grain Zn concentration of 319 finger millet genotypes was assessed. Large genetic variation was found among the genotypes, with concentrations ranging from 10 to 86 μg g− 1 grain. Uptake and translocation studies with Zn/65Zn application in 12 selected low-Zn genotypes showed wide variation in root uptake and shoot translocation, with genotypes GEC331 and GEC164 showing greater uptake and translocation. Genotypes GEC164 and GEC543 showed increased grain Zn concentration. Genotypes GEC331 and GEC164 also showed improved yield under Zn treatment. Appreciable variation in grain Zn concentration among finger millet genotypes found in this study offers opportunities to improve Zn nutrition through breeding.

  9. Evidence of intratypic recombination in natural populations of hepatitis C virus

    International Nuclear Information System (INIS)

    Colina, R.; Garcia-Aguirre, L.; Cristina, J.; Casane, D.; Vasquez, S.; Khan, Baldip

    2004-01-01

    Hepatitis C virus (HCV) has high genomic variability and, since its discovery, at least six different types and an increasing number of subtypes have been reported. Genotype 1 is the most prevalent genotype found in South America. In the present study, three different genomic regions (5 UTR, core and NS5B) of four HCV strains isolated from Peruvian patients were sequenced in order to investigate the congruence of HCV genotyping for these three genomic regions. Phylogenetic analysis using 5 UTR-core sequences found strain PE22 to be related to subtype 1a. To test the possibility of genetic recombination, phylogenetic studies were carried out, revealing that a crossover event had taken place in the NS5B protein. We discuss the consequences of this observation on HCV genotype classification, laboratory diagnosis and treatment of HCV infection

  10. Controlled Release from Recombinant Polymers

    Science.gov (United States)

    Price, Robert; Poursaid, Azadeh; Ghandehari, Hamidreza

    2014-01-01

    Recombinant polymers provide a high degree of molecular definition for correlating structure with function in controlled release. The wide array of amino acids available as building blocks for these materials lend many advantages including biorecognition, biodegradability, potential biocompatibility, and control over mechanical properties among other attributes. Genetic engineering and DNA manipulation techniques enable the optimization of structure for precise control over spatial and temporal release. Unlike the majority of chemical synthetic strategies used, recombinant DNA technology has allowed for the production of monodisperse polymers with specifically defined sequences. Several classes of recombinant polymers have been used for controlled drug delivery. These include, but are not limited to, elastin-like, silk-like, and silk-elastinlike proteins, as well as emerging cationic polymers for gene delivery. In this article, progress and prospects of recombinant polymers used in controlled release will be reviewed. PMID:24956486

  11. Hydrogen recombiner development at AECL

    International Nuclear Information System (INIS)

    Dewit, W.A.; Koroll, G.W.; Loesel Sitar, J.; Graham, W.R.C.

    1997-01-01

    Catalytic recombiners have been developed at AECL for the purpose of hydrogen removal in post-accident nuclear containment buildings. The recombiners are based on a particular catalyst designed by AECL which has extraordinary resistance to fouling from water and water vapour and a large thermodynamic range of operation. The catalysts were developed, originally, for the purpose of heavy water manufacturing by way of a catalytic exchange process. Application of these catalyst materials in recombiners for containment applications began in the late 1980's. The first application was a passive recombiner, qualified for use in control of radiolytic hydrogen in the headspace of a pool-type experimental reactor of AECL design in 1988. The passive, or natural convection recombiner concept has continued development to commercial stage for application in power reactor containments. This paper reviews the AECL recombiner development, describes the current model and shows results from tests of full-scale recombiners in the Large Scale Vented Combustion Test Facility at AECL-WL. The AECL recombiner is designed for compactness and ease of engineering into containment. The design is a simple, open-ended rectangular enclosure with catalyst elements arranged inside to promote optimum convective flow driven by heat of recombination at the catalyst surface. Self start, as evidenced by catalyst heating and initiation of flow, is achieved in less than 1% hydrogen, with available oxygen, at room temperature and 100% relative humidity. This low temperature start-up in condensing atmospheres is viewed as the most challenging condition for wet-proofing effectiveness. Cold start-up is a vital performance requirement in containments, such as CANDU, where engineered air-cooling systems are operating and where long-term hydrogen control is required, after containment atmospheres have cooled. Once started, the removal capacity scales linearly with the inlet cross-section area and the partial

  12. Echinococcus granulosus genotypes in Iran

    Science.gov (United States)

    Sharafi, Seyedeh Maryam; Rostami-Nejad, Mohammad; Moazeni, Mohammad; Yousefi, Morteza; Saneie, Behnam; Hosseini-Safa, Ahmad

    2014-01-01

    Hydatidosis, caused by Echinococcus granulosus is one of the most important zoonotic diseases, throughout most parts of the world. Hydatidosis is endemic in Iran and responsible for approximately 1% of admission to surgical wards. There are extensive genetic variations within E. granulosus and 10 different genotypes (G1–G10) within this parasite have been reported. Identification of strains is important for improvement of control and prevention of the disease. No new review article presented the situation of Echinococcus granulosus genotypes in Iran in the recent years; therefore in this paper we reviewed the different studies regarding Echinococcus granulosus genotypes in Iran. PMID:24834298

  13. Review of Parton Recombination Models

    International Nuclear Information System (INIS)

    Bass, Steffen A

    2006-01-01

    Parton recombination models have been very successful in explaining data taken at RHIC on hadron spectra and emission patterns in Au+Au collisions at transverse momenta above 2 GeV/c, which have exhibited features which could not be understood in the framework of basic perturbative QCD. In this article I will review the current status on recombination models and outline which future challenges need to be addressed by this class of models

  14. Recombinant snake venom prothrombin activators

    OpenAIRE

    L?vgren, Ann

    2012-01-01

    Three prothrombin activators; ecarin, which was originally isolated from the venom of the saw-scaled viper Echis carinatus, trocarin from the rough-scaled snake Tropidechis carinatus, and oscutarin from the Taipan snake Oxyuranus scutellatus, were expressed in mammalian cells with the purpose to obtain recombinant prothrombin activators that could be used to convert prothrombin to thrombin. We have previously reported that recombinant ecarin can efficiently generate thrombin without the need ...

  15. Designed construction of recombinant DNA at the ura3Δ0 locus in the yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Fukunaga, Tomoaki; Cha-Aim, Kamonchai; Hirakawa, Yuki; Sakai, Ryota; Kitagawa, Takao; Nakamura, Mikiko; Nonklang, Sanom; Hoshida, Hisashi; Akada, Rinji

    2013-06-01

    Recombinant DNAs are traditionally constructed using Escherichia coli plasmids. In the yeast Saccharomyces cerevisiae, chromosomal gene targeting is a common technique, implying that the yeast homologous recombination system could be applied for recombinant DNA construction. In an attempt to use a S. cerevisiae chromosome for recombinant DNA construction, we selected the single ura3Δ0 locus as a gene targeting site. By selecting this single locus, repeated recombination using the surrounding URA3 sequences can be performed. The recombination system described here has several advantages over the conventional plasmid system, as it provides a method to confirm the selection of correct recombinants because transformation of the same locus replaces the pre-existing selection marker, resulting in the loss of the marker in successful recombinations. In addition, the constructed strains can serve as both PCR templates and hosts for preparing subsequent recombinant strains. Using this method, several yeast strains that contained selection markers, promoters, terminators and target genes at the ura3Δ0 locus were successfully generated. The system described here can potentially be applied for the construction of any recombinant DNA without the requirement for manipulations in E. coli. Interestingly, we unexpectedly found that several G/C-rich sequences used for fusion PCR lowered gene expression when located adjacent to the start codon. Copyright © 2013 John Wiley & Sons, Ltd.

  16. Measurements of experimental precision for trials with cowpea (Vigna unguiculata L. Walp.) genotypes.

    Science.gov (United States)

    Teodoro, P E; Torres, F E; Santos, A D; Corrêa, A M; Nascimento, M; Barroso, L M A; Ceccon, G

    2016-05-09

    The aim of this study was to evaluate the suitability of statistics as experimental precision degree measures for trials with cowpea (Vigna unguiculata L. Walp.) genotypes. Cowpea genotype yields were evaluated in 29 trials conducted in Brazil between 2005 and 2012. The genotypes were evaluated with a randomized block design with four replications. Ten statistics that were estimated for each trial were compared using descriptive statistics, Pearson correlations, and path analysis. According to the class limits established, selective accuracy and F-test values for genotype, heritability, and the coefficient of determination adequately estimated the degree of experimental precision. Using these statistics, 86.21% of the trials had adequate experimental precision. Selective accuracy and the F-test values for genotype, heritability, and the coefficient of determination were directly related to each other, and were more suitable than the coefficient of variation and the least significant difference (by the Tukey test) to evaluate experimental precision in trials with cowpea genotypes.

  17. 7 CFR 331.3 - PPQ select agents and toxins.

    Science.gov (United States)

    2010-01-01

    ...) Select agents and toxins listed in paragraph (b) of this section that have been genetically modified. (d... variegated chlorosis strain). (c) Genetic elements, recombinant nucleic acids, and recombinant organisms: (1...

  18. Seleção de genótipos de milho mais promissores para o consumo in natura Selection of corn on the cob genotypes more appropriate to the in natura consumption

    Directory of Open Access Journals (Sweden)

    Luiz Fernando Ganassali Oliveira Jr.

    2006-03-01

    Full Text Available Seis genótipos pertencentes ao programa de melhoramento de milho da UENF: H43IN, P43, C43, 43IN, HDC e Uenf506-8 foram avaliados, objetivando-se identificar aqueles com melhores características agronômicas e preferidos para o consumo de milho verde. O trabalho foi desenvolvido entre setembro de 2003 e janeiro de 2004, seguindo delineamento experimental de blocos inteiramente casualizados e plantio em dois locais distintos. Estudaram-se as seguintes características agronômicas: produtividade com palha (PrCP, produtividade sem palha (PrSP, porcentagem de espigas comerciais (EC comprimento de espigas sem palha (CESP, diâmetro de espigas sem palha (DE e rendimento de espiga (R, além de ter sido avaliada a preferência do consumidor para os produtos em relação ao sabor, doçura e maciez. Considerando apenas os resultados agronômicos, o milho mais indicado para ser consumido na forma de milho verde foi o híbrido comum Uenf506-8. Porém, observando os resultados do teste de preferência realizado com consumidores do produto, verificou-se que o referido milho não alcançou adequada aceitação pelos participantes, em função da maciez e da doçura inadequadas, sendo mais indicado o H43IN e HDC.Six genotypes belonging to the UENF sweet corn improvement program: H43IN, P43, C43, 43IN, HDC and Uenf506-8 were evaluated aiming at identifying those with better agronomic characteristics and preferred for the consumption of corn on the cob. This investigation was conducted from September 2003 to January 2004, following a randomized complete block design, with four replications and two locations. The following agronomic traits were evaluated: yield with straw (PrCP, productivity without straw (PrSP, percentage of commercial ears (EC, length of ears without straw (CESP, diameter of ears without straw (OF and ears yielding (R. Besides, the consumer preference for the products in relation to the flavor, sweetness, and softness was investigated. The

  19. Frequent intra-subtype recombination among HIV-1 circulating in Tanzania.

    Science.gov (United States)

    Kiwelu, Ireen E; Novitsky, Vladimir; Margolin, Lauren; Baca, Jeannie; Manongi, Rachel; Sam, Noel; Shao, John; McLane, Mary F; Kapiga, Saidi H; Essex, M

    2013-01-01

    The study estimated the prevalence of HIV-1 intra-subtype recombinant variants among female bar and hotel workers in Tanzania. While intra-subtype recombination occurs in HIV-1, it is generally underestimated. HIV-1 env gp120 V1-C5 quasispecies from 45 subjects were generated by single-genome amplification and sequencing (median (IQR) of 38 (28-50) sequences per subject). Recombination analysis was performed using seven methods implemented within the recombination detection program version 3, RDP3. HIV-1 sequences were considered recombinant if recombination signals were detected by at least three methods with p-values of ≤0.05 after Bonferroni correction for multiple comparisons. HIV-1 in 38 (84%) subjects showed evidence for intra-subtype recombination including 22 with HIV-1 subtype A1, 13 with HIV-1 subtype C, and 3 with HIV-1 subtype D. The distribution of intra-patient recombination breakpoints suggested ongoing recombination and showed selective enrichment of recombinant variants in 23 (60%) subjects. The number of subjects with evidence of intra-subtype recombination increased from 29 (69%) to 36 (82%) over one year of follow-up, although the increase did not reach statistical significance. Adjustment for intra-subtype recombination is important for the analysis of multiplicity of HIV infection. This is the first report of high prevalence of intra-subtype recombination in the HIV/AIDS epidemic in Tanzania, a region where multiple HIV-1 subtypes co-circulate. HIV-1 intra-subtype recombination increases viral diversity and presents additional challenges for HIV-1 vaccine design.

  20. Frequent intra-subtype recombination among HIV-1 circulating in Tanzania.

    Directory of Open Access Journals (Sweden)

    Ireen E Kiwelu

    Full Text Available The study estimated the prevalence of HIV-1 intra-subtype recombinant variants among female bar and hotel workers in Tanzania. While intra-subtype recombination occurs in HIV-1, it is generally underestimated. HIV-1 env gp120 V1-C5 quasispecies from 45 subjects were generated by single-genome amplification and sequencing (median (IQR of 38 (28-50 sequences per subject. Recombination analysis was performed using seven methods implemented within the recombination detection program version 3, RDP3. HIV-1 sequences were considered recombinant if recombination signals were detected by at least three methods with p-values of ≤0.05 after Bonferroni correction for multiple comparisons. HIV-1 in 38 (84% subjects showed evidence for intra-subtype recombination including 22 with HIV-1 subtype A1, 13 with HIV-1 subtype C, and 3 with HIV-1 subtype D. The distribution of intra-patient recombination breakpoints suggested ongoing recombination and showed selective enrichment of recombinant variants in 23 (60% subjects. The number of subjects with evidence of intra-subtype recombination increased from 29 (69% to 36 (82% over one year of follow-up, although the increase did not reach statistical significance. Adjustment for intra-subtype recombination is important for the analysis of multiplicity of HIV infection. This is the first report of high prevalence of intra-subtype recombination in the HIV/AIDS epidemic in Tanzania, a region where multiple HIV-1 subtypes co-circulate. HIV-1 intra-subtype recombination increases viral diversity and presents additional challenges for HIV-1 vaccine design.

  1. First identification of a recombinant form of hepatitis C virus in Austrian patients by full-genome next generation sequencing.

    Directory of Open Access Journals (Sweden)

    Evelyn Stelzl

    Full Text Available Hepatitis C virus (HCV intergenotypic recombinant forms have been reported for various HCV genotypes/subtypes in several countries worldwide. In a recent study, four patients living in Austria had been identified to be possibly infected with a recombinant HCV strain. To clarify results and determine the point of recombination, full-genome next-generation sequencing using the Illumina MiSeq v2 300 cycle kit (Illumina, San Diego, CA, USA was performed in the present study. Samples of all of the patients contained the recombinant HCV strain 2k/1b. The point of recombination was found to be within the HCV NS2 gene between nucleotide positions 3189-3200 based on H77 numbering. While three of four patients were male and had migration background from Chechnya (n = 2 and Azerbaijan (n = 1, the forth patient was a female born in Austria. Three of the four patients including the female had intravenous drug abuse as a risk factor for HCV transmission. While sequencing techniques are limited to a few specialized laboratories, a genotyping assay that uses both ends of the HCV genome should be employed to identify patients infected with a recombinant HCV strain. The correct identification of recombinant strains also has an impact considering the tailored choice of anti-HCV treatment.

  2. Nonhomologous recombination between defective poliovirus and coxsackievirus genomes suggests a new model of genetic plasticity for picornaviruses.

    Science.gov (United States)

    Holmblat, Barbara; Jégouic, Sophie; Muslin, Claire; Blondel, Bruno; Joffret, Marie-Line; Delpeyroux, Francis

    2014-08-05

    Most of the circulating vaccine-derived polioviruses (cVDPVs) implicated in poliomyelitis outbreaks in Madagascar have been shown to be recombinants between the type 2 poliovirus (PV) strain of the oral polio vaccine (Sabin 2) and another species C human enterovirus (HEV-C), such as type 17 coxsackie A virus (CA17) in particular. We studied intertypic genetic exchanges between PV and non-PV HEV-C by developing a recombination model, making it possible to rescue defective type 2 PV RNA genomes with a short deletion at the 3' end by the cotransfection of cells with defective or infectious CA17 RNAs. We isolated over 200 different PV/CA17 recombinants, using murine cells expressing the human PV receptor (PVR) and selecting viruses with PV capsids. We found some homologous (H) recombinants and, mostly, nonhomologous (NH) recombinants presenting duplications of parental sequences preferentially located in the regions encoding proteins 2A, 2B, and 3A. Short duplications appeared to be stable, whereas longer duplications were excised during passaging in cultured cells or after multiplication in PVR-transgenic mice, generating H recombinants with diverse sites of recombination. This suggests that NH recombination events may be a transient, intermediate step in the generation and selection of the fittest H recombinants. In addition to the classical copy-choice mechanism of recombination thought to generate mostly H recombinants, there may also be a modular mechanism of recombination, involving NH recombinant precursors, shaping the genomes of recombinant enteroviruses and other picornaviruses. Importance: The multiplication of circulating vaccine-derived polioviruses (cVDPVs) in poorly immunized human populations can render these viruses pathogenic, causing poliomyelitis outbreaks. Most cVDPVs are intertypic recombinants between a poliovirus (PV) strain and another human enterovirus, such as type 17 coxsackie A viruses (CA17). For further studies of the genetic exchanges

  3. Vaccine escape recombinants emerge after pneumococcal vaccination in the United States.

    Science.gov (United States)

    Brueggemann, Angela B; Pai, Rekha; Crook, Derrick W; Beall, Bernard

    2007-11-01

    The heptavalent pneumococcal conjugate vaccine (PCV7) was introduced in the United States (US) in 2000 and has significantly reduced invasive pneumococcal disease; however, the incidence of nonvaccine serotype invasive disease, particularly due to serotype 19A, has increased. The serotype 19A increase can be explained in part by expansion of a genotype that has been circulating in the US prior to vaccine implementation (and other countries since at least 1990), but also by the emergence of a novel "vaccine escape recombinant" pneumococcal strain. This strain has a genotype that previously was only associated with vaccine serotype 4, but now expresses a nonvaccine serotype 19A capsule. Based on prior evidence for capsular switching by recombination at the capsular locus, the genetic event that resulted in this novel serotype/genotype combination might be identifiable from the DNA sequence of individual pneumococcal strains. Therefore, the aim of this study was to characterise the putative recombinational event(s) at the capsular locus that resulted in the change from a vaccine to a nonvaccine capsular type. Sequencing the capsular locus flanking regions of 51 vaccine escape (progeny), recipient, and putative donor pneumococci revealed a 39 kb recombinational fragment, which included the capsular locus, flanking regions, and two adjacent penicillin-binding proteins, and thus resulted in a capsular switch and penicillin nonsusceptibility in a single genetic event. Since 2003, 37 such vaccine escape strains have been detected, some of which had evolved further. Furthermore, two new types of serotype 19A vaccine escape strains emerged in 2005. To our knowledge, this is the first time a single recombinational event has been documented in vivo that resulted in both a change of serotype and penicillin nonsusceptibility. Vaccine escape by genetic recombination at the capsular locus has the potential to reduce PCV7 effectiveness in the longer term.

  4. Vaccine escape recombinants emerge after pneumococcal vaccination in the United States.

    Directory of Open Access Journals (Sweden)

    Angela B Brueggemann

    2007-11-01

    Full Text Available The heptavalent pneumococcal conjugate vaccine (PCV7 was introduced in the United States (US in 2000 and has significantly reduced invasive pneumococcal disease; however, the incidence of nonvaccine serotype invasive disease, particularly due to serotype 19A, has increased. The serotype 19A increase can be explained in part by expansion of a genotype that has been circulating in the US prior to vaccine implementation (and other countries since at least 1990, but also by the emergence of a novel "vaccine escape recombinant" pneumococcal strain. This strain has a genotype that previously was only associated with vaccine serotype 4, but now expresses a nonvaccine serotype 19A capsule. Based on prior evidence for capsular switching by recombination at the capsular locus, the genetic event that resulted in this novel serotype/genotype combination might be identifiable from the DNA sequence of individual pneumococcal strains. Therefore, the aim of this study was to characterise the putative recombinational event(s at the capsular locus that resulted in the change from a vaccine to a nonvaccine capsular type. Sequencing the capsular locus flanking regions of 51 vaccine escape (progeny, recipient, and putative donor pneumococci revealed a 39 kb recombinational fragment, which included the capsular locus, flanking regions, and two adjacent penicillin-binding proteins, and thus resulted in a capsular switch and penicillin nonsusceptibility in a single genetic event. Since 2003, 37 such vaccine escape strains have been detected, some of which had evolved further. Furthermore, two new types of serotype 19A vaccine escape strains emerged in 2005. To our knowledge, this is the first time a single recombinational event has been documented in vivo that resulted in both a change of serotype and penicillin nonsusceptibility. Vaccine escape by genetic recombination at the capsular locus has the potential to reduce PCV7 effectiveness in the longer term.

  5. A robust, simple genotyping-by-sequencing (GBS approach for high diversity species.

    Directory of Open Access Journals (Sweden)

    Robert J Elshire

    Full Text Available Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs. This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM and barley (Oregon Wolfe Barley recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

  6. A new method for detecting the contribution of high Rydberg states to electron-ion recombination

    International Nuclear Information System (INIS)

    Orban, I; Boehm, S; Fogle, M; Paal, A; Schuch, R

    2007-01-01

    A position sensitive detector for measuring field ionized electrons in the fringe field of a dipole magnet is presented. The detector provides a means to study, in a state selective fashion, recombination into high Rydberg states and offers a new method to investigate recombination enhancement effects. Several experimental considerations and possibilities are discussed in the text

  7. Homologous recombination-mediated cloning and manipulation of genomic DNA regions using Gateway and recombineering systems.

    Science.gov (United States)

    Rozwadowski, Kevin; Yang, Wen; Kagale, Sateesh

    2008-11-17

    Employing genomic DNA clones to characterise gene attributes has several advantages over the use of cDNA clones, including the presence of native transcription and translation regulatory sequences as well as a representation of the complete repertoire of potential splice variants encoded by the gene. However, working with genomic DNA clones has traditionally been tedious due to their large size relative to cDNA clones and the presence, absence or position of particular restriction enzyme sites that may complicate conventional in vitro cloning procedures. To enable efficient cloning and manipulation of genomic DNA fragments for the purposes of gene expression and reporter-gene studies we have combined aspects of the Gateway system and a bacteriophage-based homologous recombination (i.e. recombineering) system. To apply the method for characterising plant genes we developed novel Gateway and plant transformation vectors that are of small size and incorporate selectable markers which enable efficient identification of recombinant clones. We demonstrate that the genomic coding region of a gene can be directly cloned into a Gateway Entry vector by recombineering enabling its subsequent transfer to Gateway Expression vectors. We also demonstrate how the coding and regulatory regions of a gene can be directly cloned into a plant transformation vector by recombineering. This construct was then rapidly converted into a novel Gateway Expression vector incorporating cognate 5' and 3' regulatory regions by using recombineering to replace the intervening coding region with the Gateway Destination cassette. Such expression vectors can be applied to characterise gene regulatory regions through development of reporter-gene fusions, using the Gateway Entry clones of GUS and GFP described here, or for ectopic expression of a coding region cloned into a Gateway Entry vector. We exemplify the utility of this approach with the Arabidopsis PAP85 gene and demonstrate that the expression

  8. Univariate Stability Analysis of Genotype×Environment Interaction of Oilseed Rape Seed Yield

    Directory of Open Access Journals (Sweden)

    Hassan Amiri Oghan

    2016-01-01

    Full Text Available Thirteen stability statistics were used to analyze genotype × environment (GE interaction of 36 canola genotypes. Combined analysis of variance indicated that GE interaction significantly influenced seed yield performance. According to Type I stability concept (environmental variance, coefficient of variation and stability variance genotypes G7, G9 and G13 were the most stable genotypes, while based on the Type II concept (coefficients of three linear regres­sion models, genotypes G33, G27 and G29 could be selected as the most favorable genotypes. Also, genotype G7 was the most favorable genotype according to Type III stability concept (deviation from linear regression method. Genotypes clustering based on stability properties and mean yield grouped them into three distinct classes. Coefficient of determination for the canola genotypes indicated that genotypes G27 and G33 were the most stable genotypes but the genotypes G1, G10 and G25 had the highest desirability index and were the most stable ones. The plot of principal component analysis was used for graphic display of the relationships among statistics and the first axis distinguished the Type II of stability concept from other types and mean yield groups near this stability type. However, based on most statistics and mean yield performance, genotypes G9 or Fanaei‑6 (2592.47 kg ha‑1, G11 or Fanaei‑14 (2592.47 kg ha−1, G12 Fanaei‑15 or (2592.47 kg ha‑1 and G19 or Dez‑7169 (2592.47 kg ha‑1 were the most stable and favorable genotypes and are recommended for national release Iran.

  9. Accuracy of a commercially available assay for HCV genotyping and subtyping in the clinical practice.

    Science.gov (United States)

    González, Victoria; Gomes-Fernandes, Meissiner; Bascuñana, Elisabet; Casanovas, Sònia; Saludes, Verónica; Jordana-Lluch, Elena; Matas, Lurdes; Ausina, Vicenç; Martró, Elisa

    2013-09-01

    Hepatitis C virus (HCV) genotyping is mandatory for tailoring dose and duration of pegylated interferon-α plus ribavirin treatment and for deciding on triple therapy eligibility. Additionally, subtyping may play a role in helping to select future treatment regimens that include directly-acting antivirals. However, commercial assays for HCV genotyping fail to identify the genotype/subtype in some cases. Our aims were (i) to determine the success rate of the commercial genotyping assay Abbott RealTime HCV Genotype II at identifying the genotype and the HCV-1 subtype; and (ii) to phylogenetically characterise the obtained indeterminate results. HCV genotyping results obtained between 2009 and 2012 in a Spanish reference hospital were reviewed. A total of 896 people were genotyped with the Abbott RealTime HCV Genotype II assay. Specimens with an indeterminate result were retrospectively genotyped using the reference method based on the phylogenetic analysis of HCV NS5B sequences. Using the commercially available assay, an indeterminate HCV genotype result was obtained in 20 of 896 patients (2.2%); these corresponded to genotypes 3a, 3k and 4d. Importantly, 8.6% of all cases where genotype 3 was detected were indeterminate. In addition, the HCV-1 subtype was not assigned in 29 of 533 cases (5.4%). The implementation in the clinical microbiology laboratory of the reference method for HCV genotyping allows indeterminate genotype/subtype results to be interpreted and may lead to the identification of previously uncharacterised subtypes. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Irrigated rice genotype performance under excess iron stress in hydroponic culture

    OpenAIRE

    Maraisa Crestani; José Antonio Gonzalez da Silva; Velci Queiróz de Souza; Irineu Hartwig; Henrique de Souza Luche; Rogério Oliveira de Sousa; Fernando Irajá Félix de Carvalho; Antonio Costa de Oliveira

    2009-01-01

    Iron stress is a major stress factor in irrigated rice. The complete mechanism underlying iron metabolism andtransport is still unknown. Irrigated rice (Oryza sativa L.) cultivars were exposed to Fe2+ stress in hydroponic conditions,aiming to assess genotype performance under stress as well as to develop a protocol for genotype selection. The experimentaldesign was completely randomized, using a triple factorial scheme 2 x 5 x 6 (time x dose x genotype). The trait shoot length andnine days un...

  11. Recombinant host cells and media for ethanol production

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Brent E; Ingram, Lonnie O; Yomano, Lorraine P; York, Sean W

    2014-02-18

    Disclosed are recombinant host cells suitable for degrading an oligosaccharide that have been optimized for growth and production of high yields of ethanol, and methods of making and using these cells. The invention further provides minimal media comprising urea-like compounds for economical production of ethanol by recombinant microorganisms. Recombinant host cells in accordance with the invention are modified by gene mutation to eliminate genes responsible for the production of unwanted products other than ethanol, thereby increasing the yield of ethanol produced from the oligosaccharides, relative to unmutated parent strains. The new and improved strains of recombinant bacteria are capable of superior ethanol productivity and yield when grown under conditions suitable for fermentation in minimal growth media containing inexpensive reagents. Systems optimized for ethanol production combine a selected optimized minimal medium with a recombinant host cell optimized for use in the selected medium. Preferred systems are suitable for efficient ethanol production by simultaneous saccharification and fermentation (SSF) using lignocellulose as an oligosaccharide source. The invention also provides novel isolated polynucleotide sequences, polypeptide sequences, vectors and antibodies.

  12. The potential of different lime tree (Tilia spp genotypes for phytoextraction of heavy metals

    Directory of Open Access Journals (Sweden)

    Šijačić-Nikolić Mirjana

    2012-01-01

    Full Text Available The research of heavy metals contents (Pb, Mn, Zn, Ni, Fe in soil in the area of the National Park „Fruška gora”, along the highway M21 shows lower values for manganese, zinc and iron than the maximum allowed quantity prescribed by law. For nickel and lead it shows higher values than maximum allowed quantity. The heavy metals contents in leaves of lime tree in 12 analyzed genotypes are far below average values in accordance with ECCE with all genotypes except genotype 7 for lead and genotypes 7 and 8 for iron. The results of analysis of variance components show that out of four components (locality, genotype, locality x genotype and error only the interaction between locality and genotype does not contribute to variance. The contents of Pb, Mn, Fe and Zn in leaves is primarily influenced by genotype while Ni contents may be considered a consequence of locality. The selection of genotypes which is able to uptake greater quantities of heavy metals than other genotypes may serve as a solid basis for phytoextraction of heavy metals as a technology by which heavy metals, metalloids and radionuclides are extracted from environment through usage of suitable species and plant genotypes able to uptake and accumulate the given pollutants in parts of plant tissue. [Projekat Ministarstva nauke Republike Srbije, br. 43007: Studying climate change and its influence on the environment: Impacts, adaptation and mitigation

  13. Natural and recombinant fungal laccases for paper pulp bleaching

    NARCIS (Netherlands)

    Sigoillot, C.; Record, E.; Belle, V.; Robert, J.L.; Levasseur, A.; Punt, P.J.; Hondel, C.A.M.J.J. van den; Fournel, A.; Sigoillot, J.C.; Asther, M.

    2004-01-01

    Three laccases, a natural form and two recombinant forms obtained from two different expression hosts, were characterized and compared for paper pulp bleaching. Laccase from Pycnoporus cinnabarinus, a well known lignolytic fungus, was selected as a reference for this study. The corresponding

  14. An overview on hepatitis C virus genotypes and its control

    Directory of Open Access Journals (Sweden)

    Faisal Nouroz

    2015-10-01

    Full Text Available Hepatitis C virus (HCV is a blood borne, circular and positive single stranded virus with high spread rates. With the passage of time the frequency of HCV is increasing in different parts of the world. HCV is a major cause, which may end in liver cirrhosis and hepatocellular carcinoma. HCV has six main genotypes with many subtypes, which have variable sequence homology with each other. Symptoms can appear anytime from 2 weeks to 6 months, which include jaundice, fatigue, gray-colored stool, joint pain, belly pain, weakness, anorexia, itchy skin and dark urine. Genotyping is more significant for planning of HCV treatment period and helps to cure HCV infections. For the quantification and identification of hepatitis C virus-ribonucleic acid, many molecular techniques are performed; the most significant are HCV ELISA, quantitative HCV-RNA PCR and recombinant immunoblot assay. PCR is the major technique targeting 5′ untranslated region (UTR. HCV can be transmitted by contaminated blood, ear and nose piercing and contaminated medical instruments. To overcome the rate of HCV, guidance should be provided to make aware the persons about risk factors, transmission and prevention. Discovery and designing of new therapies and vaccines to overcome this disease are the necessity of the present era. Four types of vaccines such as vector vaccines, peptide vaccines, DNA vaccines and recombinant protein vaccines are available in clinical trials.

  15. Recombinant canine coronaviruses in dogs, Europe.

    Science.gov (United States)

    Decaro, Nicola; Mari, Viviana; Elia, Gabriella; Addie, Diane D; Camero, Michele; Lucente, Maria Stella; Martella, Vito; Buonavoglia, Canio

    2010-01-01

    Coronaviruses of potential recombinant origin with porcine transmissible gastroenteritis virus (TGEV), referred to as a new subtype (IIb) of canine coronavirus (CCoV), were recently identified in dogs in Europe. To assess the distribution of the TGEV-like CCoV subtype, during 2001-2008 we tested fecal samples from dogs with gastroenteritis. Of 1,172 samples, 493 (42.06%) were positive for CCoV. CCoV-II was found in 218 samples, and CCoV-I and CCoV-II genotypes were found in 182. Approximately 20% of the samples with CCoV-II had the TGEV-like subtype; detection rates varied according to geographic origin. The highest and lowest rates of prevalence for CCoV-II infection were found in samples from Hungary and Greece (96.87% and 3.45%, respectively). Sequence and phylogenetic analyses showed that the CCoV-IIb strains were related to prototype TGEV-like strains in the 5' and the 3' ends of the spike protein gene.

  16. From genotype to apricot fruit quality: the antioxidant properties contribution.

    Science.gov (United States)

    Leccese, Annamaria; Bartolini, Susanna; Viti, Raffaella

    2012-12-01

    Apricot fruit (Prunus armeniaca L.) quality strictly relates to the eating quality of fresh produce. Since consumers are more and more interested in healthy food, and apricot germplasm shows a wide choice of new selections and cultivars, apricot nutraceutical properties are under evaluation in order to select outstanding genotypes, which may link breeding and marketing. In the present study, 18 apricot genotypes of the Italian and international germplasm were evaluated over three years according to pomological, total antioxidant and total phenols attributes using principal component and hierarchical cluster analyses. The antioxidant capacity ranged from 1.24 to 11.47 μmolTE gFW⁻¹ and total phenols from 0.22 to 1.58 mgGAE gFW⁻¹. Four outstanding genotypes stood out as healthy food for fresh consumption which may also be introduced in breeding programs to produce new cultivars with improved nutraceutical values in addition to fruit qualitative attributes.

  17. Rapid Cycling Genomic Selection in a Multiparental Tropical Maize Population.

    Science.gov (United States)

    Zhang, Xuecai; Pérez-Rodríguez, Paulino; Burgueño, Juan; Olsen, Michael; Buckler, Edward; Atlin, Gary; Prasanna, Boddupalli M; Vargas, Mateo; San Vicente, Félix; Crossa, José

    2017-07-05

    Genomic selection (GS) increases genetic gain by reducing the length of the selection cycle, as has been exemplified in maize using rapid cycling recombination of biparental populations. However, no results of GS applied to maize multi-parental populations have been reported so far. This study is the first to show realized genetic gains of rapid cycling genomic selection (RCGS) for four recombination cycles in a multi-parental tropical maize population. Eighteen elite tropical maize lines were intercrossed twice, and self-pollinated once, to form the cycle 0 (C 0 ) training population. A total of 1000 ear-to-row C 0 families was genotyped with 955,690 genotyping-by-sequencing SNP markers; their testcrosses were phenotyped at four optimal locations in Mexico to form the training population. Individuals from families with the best plant types, maturity, and grain yield were selected and intermated to form RCGS cycle 1 (C 1 ). Predictions of the genotyped individuals forming cycle C 1 were made, and the best predicted grain yielders were selected as parents of C 2 ; this was repeated for more cycles (C 2 , C 3 , and C 4 ), thereby achieving two cycles per year. Multi-environment trials of individuals from populations C 0, C 1 , C 2 , C 3 , and C 4 , together with four benchmark checks were evaluated at two locations in Mexico. Results indicated that realized grain yield from C 1 to C 4 reached 0.225 ton ha -1 per cycle, which is equivalent to 0.100 ton ha -1  yr -1 over a 4.5-yr breeding period from the initial cross to the last cycle. Compared with the original 18 parents used to form cycle 0 (C 0 ), genetic diversity narrowed only slightly during the last GS cycles (C 3 and C 4 ). Results indicate that, in tropical maize multi-parental breeding populations, RCGS can be an effective breeding strategy for simultaneously conserving genetic diversity and achieving high genetic gains in a short period of time. Copyright © 2017 Zhang et al.

  18. A SNP Genotyping Array for Hexaploid Oat

    Directory of Open Access Journals (Sweden)

    Nicholas A. Tinker

    2014-11-01

    Full Text Available Recognizing a need in cultivated hexaploid oat ( L. for a reliable set of reference single nucleotide polymorphisms (SNPs, we have developed a 6000 (6K BeadChip design containing 257 Infinium I and 5486 Infinium II designs corresponding to 5743 SNPs. Of those, 4975 SNPs yielded successful assays after array manufacturing. These SNPs were discovered based on a variety of bioinformatics pipelines in complementary DNA (cDNA and genomic DNA originating from 20 or more diverse oat cultivars. The array was validated in 1100 samples from six recombinant inbred line (RIL mapping populations and sets of diverse oat cultivars and breeding lines, and provided approximately 3500 discernible Mendelian polymorphisms. Here, we present an annotation of these SNPs, including methods of discovery, gene identification and orthology, population-genetic characteristics, and tentative positions on an oat consensus map. We also evaluate a new cluster-based method of calling SNPs. The SNP design sequences are made publicly available, and the full SNP genotyping platform is available for commercial purchase from an independent third party.

  19. Mineral Composition of Organically Grown Wheat Genotypes: Contribution to Daily Minerals Intake

    Science.gov (United States)

    Hussain, Abrar; Larsson, Hans; Kuktaite, Ramune; Johansson, Eva

    2010-01-01

    In this study, 321 winter and spring wheat genotypes were analysed for twelve nutritionally important minerals (B, Cu, Fe, Se, Mg, Zn, Ca, Mn, Mo, P, S and K). Some of the genotypes used were from multiple locations and years, resulting in a total number of 493 samples. Investigated genotypes were divided into six genotype groups i.e., selections, old landraces, primitive wheat, spelt, old cultivars and cultivars. For some of the investigated minerals higher concentrations were observed in selections, primitive wheat, and old cultivars as compared to more modern wheat material, e.g., cultivars and spelt wheat. Location was found to have a significant effect on mineral concentration for all genotype groups, although for primitive wheat, genotype had a higher impact than location. Spring wheat was observed to have significantly higher values for B, Cu, Fe, Zn, Ca, S and K as compared to winter wheat. Higher levels of several minerals were observed in the present study, as compared to previous studies carried out in inorganic systems, indicating that organic conditions with suitable genotypes may enhance mineral concentration in wheat grain. This study also showed that a very high mineral concentration, close to daily requirements, can be produced by growing specific primitive wheat genotypes in an organic farming system. Thus, by selecting genotypes for further breeding, nutritional value of the wheat flour for human consumption can be improved. PMID:20948934

  20. High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon.

    Science.gov (United States)

    Reddy, Umesh K; Nimmakayala, Padma; Levi, Amnon; Abburi, Venkata Lakshmi; Saminathan, Thangasamy; Tomason, Yan R; Vajja, Gopinath; Reddy, Rishi; Abburi, Lavanya; Wehner, Todd C; Ronin, Yefim; Karol, Abraham

    2014-09-15

    We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Collinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD), and selective sweep for wild, semi-wild, and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1563 SNPs obtained after LD pruning with minor allele frequency of 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild, and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima's D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication. Copyright © 2014 Reddy et al.

  1. Genotypic character relationship and phenotypic path coefficient analysis in chili pepper genotypes grown under tropical condition.

    Science.gov (United States)

    Usman, Magaji G; Rafii, Mohd Y; Martini, Mohammad Y; Oladosu, Yusuff; Kashiani, Pedram

    2017-03-01

    Studies on genotypic and phenotypic correlations among characters of crop plants are useful in planning, evaluating and setting selection criteria for the desired characters in a breeding program. The present study aimed to estimate the phenotypic correlation coefficients among yield and yield attributed characters and to work out the direct and indirect effects of yield-related characters on yield per plant using path coefficient analysis. Twenty-six genotypes of chili pepper were laid out in a randomized complete block design with three replications. Yield per plant showed positive and highly significant (P ≤ 0.01) correlations with most of the characters studied at both the phenotypic and genotypic levels. By contrast, disease incidence and days to flowering showed a significant negative association with yield. Fruit weight and number of fruits exerted positive direct effect on yield and also had a positive and significant (P ≤ 0.01) correlation with yield per plant. However, fruit length showed a low negative direct effect with a strong and positive indirect effect through fruit weight on yield and had a positive and significant association with yield. Longer fruits, heavy fruits and a high number of fruits are variables that are related to higher yields of chili pepper under tropical conditions and hence could be used as a reliable indicator in indirect selection for yield. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  2. K-selection, α-selection, effectiveness, and tolerance in competition ...

    Indian Academy of Sciences (India)

    Unknown

    In this formulation, N represents the total population size, regardless of genotype, whereas the r and K terms are genotype specific; consequently, these models have often been referred to as pure density-dependent selection models because there are no frequency-dependent inter- genotypic interactions. At the time these ...

  3. Genetic analysis of morphological traits in a new, versatile, rapid-cycling Brassica rapa recombinant inbred line population

    NARCIS (Netherlands)

    Bagheri, H.; El-Soda, M.; Oorschot, van I.; Hanhart, C.J.; Bonnema, A.B.; Jansen-van den Bosch, T.; Mank, R.; Keurentjes, J.J.B.; Meng, L.; Wu, Jian; Koornneef, M.; Aarts, M.G.M.

    2012-01-01

    A recombinant inbred line (RIL) population was produced based on a wide cross between the rapid-cycling and self-compatible genotypes L58, a Caixin vegetable type, and R-o-18, a yellow sarson oil type. A linkage map based on 160 F7 lines was constructed using 100 Single nucleotide polymorphisms

  4. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

    Directory of Open Access Journals (Sweden)

    Brian O'Farrell

    Full Text Available Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of 200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

  5. Adaptive mutations allow establishment of JFH1-based cell culture systems for hepatitis C virus genotype 4A

    DEFF Research Database (Denmark)

    2013-01-01

    The present inventors developed three 4a/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and all of or part of NS2 were replaced by the corresponding genes of the genotype 4a reference strain ED43. The 4a/2a junction in NS2 was placed after the first transm...

  6. Resistance Potential of Bread Wheat Genotypes Against Yellow Rust Disease Under Egyptian Climate

    Directory of Open Access Journals (Sweden)

    Amer F. Mahmoud

    2015-12-01

    Full Text Available Yellow rust (stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most destructive foliar diseases of wheat in Egypt and worldwide. In order to identify wheat genotypes resistant to yellow rust and develop molecular markers associated with the resistance, fifty F₈ recombinant inbred lines (RILs derived from a cross between resistant and susceptible bread wheat landraces were obtained. Artificial infection of Puccinia striiformis was performed under greenhouse conditions during two growing seasons and relative resistance index (RRI was calculated. Two Egyptian bread wheat cultivars i.e. Giza-168 (resistant and Sakha-69 (susceptible were also evaluated. RRI values of two-year trial showed that 10 RILs responded with RRI value >6 2 <6. However, only 7 RILs showed RRI value <2. Five RILs expressed hypersensitive type of resistance (R against the pathogen and showed the lowest Average Coefficient of Infection (ACI. Bulked segregant analysis (BSA with eight simple sequence repeat (SSR, eight sequence-related amplified polymorphism (SRAP and sixteen random amplified polymorphic DNA (RAPD markers revealed that three SSR, three SRAP and six RAPD markers were found to be associated with the resistance to yellow rust. However, further molecular analyses would be performed to confirm markers associated with the resistance and suitable for marker-assisted selection. Resistant RILs identified in the study could be efficiently used to improve the resistance to yellow rust in wheat.

  7. Univariate stability analysis methods for determining genotype ...

    African Journals Online (AJOL)

    Twenty two different stability statistics were used for analyzing genotype × environment (GE) interaction of durum wheat experimental data (20 genotypes in 15 environments). Combined analysis of variance indicated that GE interaction significantly influenced genotypes yield. According to type I stability concept, genotypes ...

  8. Evaluation of allelopathic potential of safflower genotypes (Carthamus tinctorius L.

    Directory of Open Access Journals (Sweden)

    Motamedi Marzieh

    2016-12-01

    Full Text Available Forty safflower genotypes were grown under normal irrigation and drought stress. In the first experiment, the allelopathic potential of shoot residues was evaluated using the sandwich method. Each genotype residue (0.4 g was placed in a sterile Petri dish and two layers of agar were poured on that. Radish seeds were placed on agar medium. The radish seeds were cultivated without safflower residues as the controls. The length of the radicle, hypocotyl, and fresh biomass weight and seed germination percentages were measured. A pot experiment was also done on two genotypes with the highest and two with the lowest allelopathic activity selected after screening genotypes in the first experiment. Before entering the reproductive phase, irrigation treatments (normal irrigation and drought stress were applied. Shoots were harvested, dried, milled and mixed with the topsoil of new pots and then radish seeds were sown. The pots with safflower genotypes were used to evaluate the effect of root residue allelopathy. The shoot length, fresh biomass weight, and germination percentage were measured. Different safflower genotypes showed varied allelopathic potential. The results of the first experiment showed that Egypt and Iran-Khorasan genotypes caused maximum inhibitory responses and Australia and Iran-Kerman genotypes resulted in minimum inhibitory responses on radish seedling growth. Fresh biomass weight had the most sensitivity to safflower residues. The results of the pot experiment were consistent with the results of in vitro experiments. Residues produced under drought stress had more inhibitory effects on the measured traits. Safflower root residue may have a higher level of allelochemicals or different allelochemicals than shoot residue.

  9. Associating Symptom Phenotype and Genotype in Preeclampsia.

    Science.gov (United States)

    Founds, Sandra A; Tsigas, Eleni; Ren, Dianxu; Barmada, M Michael

    2018-03-01

    Preeclampsia is a complex genetic disorder with an incompletely understood pathogenesis. Its phenotype may be better elucidated by integrating symptoms. This study aimed to identify symptoms by gestational age and associations with novel preeclampsia candidate genes. Women with a history of preeclampsia recruited from The Preeclampsia Registry completed clinical/demographic, symptom surveys and provided medical records. DNA extracted from saliva was processed with multiplexed assays for eight single-nucleotide polymorphisms (SNPs) selected to tag candidate genes and/or located in symptom susceptibility regions. Groups with versus without symptoms were compared using χ 2 . Associations between SNPs and symptoms were analyzed as genotype categories and presence/absence of the variant allele. Logistic regression modeling was conducted with exploratory p = .05. In 114 participants, 113 reported at least 1 of the 18 symptoms. Symptoms varied by trimester. Nine symptoms were associated with seven SNPs. Visual disturbances were associated with three SNPs and nausea/vomiting with two SNPs. Modeling adjustment for maternal age and parity resulted in 15 associations between 9 symptoms and 8 SNPs. Medical records demonstrated 100% concordance with self-reported diagnosis and 48% concordance with reported severity. Findings indicated novel symptom-genotype associations in preeclampsia. The small sample was self-selected, but results support future studies including medical records review. When validated, these results may lead to holistic phenotyping of women to characterize subsets of preeclampsia. This approach may optimize health in pregnancy and later life for mothers and offspring through prediction, prevention, and precision nursing care.

  10. Comparison and suitability of genotype by environment analysis ...

    African Journals Online (AJOL)

    Pearl millet (Pennisetum glaucum (L.) R. Br.) is an important food security and income crop for households living in semi-arid zones in Uganda. However, the genotype by environment interaction, in addition to the several methods used for its assessment, complicates selection of varieties adapted to such semi-arid areas.

  11. Short communication: Evaluation of the BovineSNP50 genotyping ...

    African Journals Online (AJOL)

    The BovineSNP50 genotyping array is a product with a wide range of applications in cattle such as genome-wide association studies, identification of copy number variation and investigation of genetic relationships among cattle breeds. It also holds potential for genomic selection, especially for traits that are expensive and ...

  12. Evaluation of bread wheat genotypes for salinity tolerance under ...

    African Journals Online (AJOL)

    In two consecutive seasons (2007-08 and 2008-09), field experiments were conducted at Soil Salinity Research Institute, Pindi Bhattian and Biosaline Agricultural Research Station, Pakka Aana, Pakistan. During 2007-08, 103 wheat landrace genotypes were evaluated for salinity tolerance. During 2008-09, 47 selected ...

  13. DNA landmarks for genetic diversity assessment in tea genotypes ...

    African Journals Online (AJOL)

    Tea (Camellia sinensis) is one of the most important non-alcoholic beverages of the world. Natural genetic diversity in tea has been reduced due to continue selection in favor of desirable traits. The present study was conducted to estimate genetic diversity in tea genotypes cultivated in Pakistan using 20 randomly amplified ...

  14. Genotype x environment interactions in three maturity groups of ...

    African Journals Online (AJOL)

    Genotype x environment (GE) interactions are of interest to plant breeders because of their influence on progress from selection. This study was conducted to examine the effects of GE interactions for grain yield in three maturity groups of maize (Zea mays L.) cultivars adapted to the lowland tropics. Nine early (90-95 days), ...

  15. genotype by environment interaction and grain yield stability

    African Journals Online (AJOL)

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    among environments, GXE interaction and Interaction Principal Component Analysis (IPCA-I) but ... value closer to zero, Genotype Selection Index (GSI) of 4 each and AMMI stability value (ASV) of 0.124 and. 0.087 ..... Analysis of variance for grain yield using Additive Mean Effect and Multiple Interactions (AMMI) model.

  16. Electric hydrogen recombiner special tests

    International Nuclear Information System (INIS)

    Wilson, J.F.

    1975-12-01

    Westinghouse has produced an electric hydrogen recombiner to control hydrogen levels in reactor containments following a postulated loss-of-coolant accident. The recombiner underwent extensive testing for NRC qualification (see WCAP 7709-L and Supplements 1, 2, 3, 4). As a result, WCAP 7709-L and Supplements 1, 2, 3, and 4 have been accepted by the NRC for reference in applications not committed to IEEE-323-1974. Supplement 5 and the next supplement will demonstrate conformance to IEEE-323-1974. This supplement describes additional tests, beyond those necessary to qualify the system, which will be referenced in supplement 6. Each test has demonstrated a considerable margin of safety over required performance. Concurrently, the test results increased the fund of technical information on the electric hydrogen recombiner

  17. Chromosome rearrangements, recombination suppression, and limited segregation distortion in hybrids between Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (O. mykiss).

    Science.gov (United States)

    Ostberg, Carl O; Hauser, Lorenz; Pritchard, Victoria L; Garza, John C; Naish, Kerry A

    2013-08-22

    Introgressive hybridization is an important evolutionary process that can lead to the creation of novel genome structures and thus potentially new genetic variation for selection to act upon. On the other hand, hybridization with introduced species can threaten native species, such as cutthroat trout (Oncorhynchus clarkii) following the introduction of rainbow trout (O. mykiss). Neither the evolutionary consequences nor conservation implications of rainbow trout introgression in cutthroat trout is well understood. Therefore, we generated a genetic linkage map for rainbow-Yellowstone cutthroat trout (O. clarkii bouvieri) hybrids to evaluate genome processes that may help explain how introgression affects hybrid genome evolution. The hybrid map closely aligned with the rainbow trout map (a cutthroat trout map does not exist), sharing all but one linkage group. This linkage group (RYHyb20) represented a fusion between an acrocentric (Omy28) and a metacentric chromosome (Omy20) in rainbow trout. Additional mapping in Yellowstone cutthroat trout indicated the two rainbow trout homologues were fused in the Yellowstone genome. Variation in the number of hybrid linkage groups (28 or 29) likely depended on a Robertsonian rearrangement polymorphism within the rainbow trout stock. Comparison between the female-merged F₁ map and a female consensus rainbow trout map revealed that introgression suppressed recombination across large genomic regions in 5 hybrid linkage groups. Two of these linkage groups (RYHyb20 and RYHyb25_29) contained confirmed chromosome rearrangements between rainbow and Yellowstone cutthroat trout indicating that rearrangements may suppress recombination. The frequency of allelic and genotypic segregation distortion varied among parents and families, suggesting few incompatibilities exist between rainbow and Yellowstone cutthroat trout genomes. Chromosome rearrangements suppressed recombination in the hybrids. This result supports several previous

  18. Chromosome rearrangements, recombination suppression, and limited segregation distortion in hybrids between Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (O. mykiss)

    Science.gov (United States)

    2013-01-01

    Background Introgressive hybridization is an important evolutionary process that can lead to the creation of novel genome structures and thus potentially new genetic variation for selection to act upon. On the other hand, hybridization with introduced species can threaten native species, such as cutthroat trout (Oncorhynchus clarkii) following the introduction of rainbow trout (O. mykiss). Neither the evolutionary consequences nor conservation implications of rainbow trout introgression in cutthroat trout is well understood. Therefore, we generated a genetic linkage map for rainbow-Yellowstone cutthroat trout (O. clarkii bouvieri) hybrids to evaluate genome processes that may help explain how introgression affects hybrid genome evolution. Results The hybrid map closely aligned with the rainbow trout map (a cutthroat trout map does not exist), sharing all but one linkage group. This linkage group (RYHyb20) represented a fusion between an acrocentric (Omy28) and a metacentric chromosome (Omy20) in rainbow trout. Additional mapping in Yellowstone cutthroat trout indicated the two rainbow trout homologues were fused in the Yellowstone genome. Variation in the number of hybrid linkage groups (28 or 29) likely depended on a Robertsonian rearrangement polymorphism within the rainbow trout stock. Comparison between the female-merged F1 map and a female consensus rainbow trout map revealed that introgression suppressed recombination across large genomic regions in 5 hybrid linkage groups. Two of these linkage groups (RYHyb20 and RYHyb25_29) contained confirmed chromosome rearrangements between rainbow and Yellowstone cutthroat trout indicating that rearrangements may suppress recombination. The frequency of allelic and genotypic segregation distortion varied among parents and families, suggesting few incompatibilities exist between rainbow and Yellowstone cutthroat trout genomes. Conclusions Chromosome rearrangements suppressed recombination in the hybrids. This result

  19. The effect of a single recombination event

    DEFF Research Database (Denmark)

    Schierup, Mikkel Heide; Jensen, Thomas Mailund; Wiuf, Carsten

    We investigate the variance in how visible a single recombination event is in a SNP data set as a function of the type of recombination event and its age. Data is simulated under the coalescent with recombination and inference is by the popular composite likelihood methods. The major determinant...... of the effect of a recombination event is the genealogical type of the event and whether SNP variation is present that can reveal the genealogical consequences of the recombination event. Recombination events that only change some branch lengths in the genealogy have a very small, but detectable, effect....... The more lineages left when the recombination event occurs, the larger effect it has, implying that it is mainly young recombination events that we detect when estimating the rate. If the population is growing, though, more lineages are present back in time and relatively more ancient recombination events...

  20. Dense genomic sampling identifies highways of pneumococcal recombination

    Science.gov (United States)

    Chewapreecha, Claire; Harris, Simon R; Croucher, Nicholas J; Turner, Claudia; Marttinen, Pekka; Cheng, Lu; Pessia, Alberto; Aanensen, David M; Mather, Alison E; Page, Andrew J; Salter, Susannah J.; Harris, David; Nosten, Francois; Goldblatt, David; Corander, Jukka; Parkhill, Julian

    2014-01-01

    Evasion of clinical interventions by Streptococcus pneumoniae occurs through selection of non-susceptible genomic variants. Here we use genome sequencing of 3,085 pneumococcal carriage isolates from a 2.4 km2 refugee camp to enable unprecedented resolution of the process of recombination, and highlight its impact on population evolution. Genomic recombination hotspots show remarkable consistency between lineages, indicating common selective pressures acting at certain loci, particularly those associated with antibiotic resistance. Temporal changes in antibiotic consumption are reflected in changes in recombination trends demonstrating rapid spread of resistance when selective pressure is high. The highest frequencies of receipt and donation of recombined DNA fragments were observed in non-encapsulated lineages, implying that this largely overlooked pneumococcal group, which is beyond the reach of current vaccines, may play a major role in genetic exchange and adaptation of the species as a whole. These findings advance our understanding of pneumococcal population dynamics and provide important information for the design of future intervention strategies. PMID:24509479

  1. Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress

    Science.gov (United States)

    2011-01-01

    Background Chickpea (Cicer arietinum L.) is an important grain-legume crop that is mainly grown in rainfed areas, where terminal drought is a major constraint to its productivity. We generated expressed sequence tags (ESTs) by suppression subtraction hybridization (SSH) to identify differentially expressed genes in drought-tolerant and -susceptible genotypes in chickpea. Results EST libraries were generated by SSH from root and shoot tissues of IC4958 (drought tolerant) and ICC 1882 (drought resistant) exposed to terminal drought conditions by the dry down method. SSH libraries were also constructed by using 2 sets of bulks prepared from the RNA of root tissues from selected recombinant inbred lines (RILs) (10 each) for the extreme high and low root biomass phenotype. A total of 3062 unigenes (638 contigs and 2424 singletons), 51.4% of which were novel in chickpea, were derived by cluster assembly and sequence alignment of 5949 ESTs. Only 2185 (71%) unigenes showed significant BLASTX similarity (<1E-06) in the NCBI non-redundant (nr) database. Gene ontology functional classification terms (BLASTX results and GO term), were retrieved for 2006 (92.0%) sequences, and 656 sequences were further annotated with 812 Enzyme Commission (EC) codes and were mapped to 108 different KEGG pathways. In addition, expression status of 830 unigenes in response to terminal drought stress was evaluated using macro-array (dot blots). The expression of few selected genes was validated by northern blotting and quantitative real-time PCR assay. Conclusion Our study compares not only genes that are up- and down-regulated in a drought-tolerant genotype under terminal drought stress and a drought susceptible genotype but also between the bulks of the selected RILs exhibiting extreme phenotypes. More than 50% of the genes identified have been shown to be associated with drought stress in chickpea for the first time. This study not only serves as resource for marker discovery, but can provide

  2. A Case Study of a Multiobjective Elitist Recombinative Genetic Algorithm with Coevolutionary Sharing

    NARCIS (Netherlands)

    Neef, R.M.; Thierens, D.; Arciszewski, H.F.R.

    1999-01-01

    We present a multiobjective genetic algorithm that incorporates various genetic algorithm techniques that have been proven to be efficient and robust in their problem domain. More specifically, we integrate rank based selection, adaptive niching through coevolutionary sharing, elitist recombination,

  3. A case study of a multiobjective recombinative genetic algorithm with coevolutionary sharing

    NARCIS (Netherlands)

    Neef, R.M.; Thierens, D.; Arciszewski, H.F.R.

    1999-01-01

    We present a multiobjective genetic algorithm that incorporates various genetic algorithm techniques that have been proven to be efficient and robust in their problem domain. More specifically, we integrate rank based selection, adaptive niching through coevolutionary sharing, elitist recombination,

  4. Chlamydia trachomatis Strain Types Have Diversified Regionally and Globally with Evidence for Recombination across Geographic Divides

    Directory of Open Access Journals (Sweden)

    Vitaly Smelov

    2017-11-01

    Full Text Available Chlamydia trachomatis (Ct is the leading cause of bacterial sexually transmitted diseases worldwide. The Ct Multi Locus Sequence Typing (MLST scheme is effective in differentiating strain types (ST, deciphering transmission patterns and treatment failure, and identifying recombinant strains. Here, we analyzed 323 reference and clinical samples, including 58 samples from Russia, an area that has not previously been represented in Ct typing schemes, to expand our knowledge of the global diversification of Ct STs. The 323 samples resolved into 84 unique STs, a 3.23 higher typing resolution compared to the gold standard single locus ompA genotyping. Our MLST scheme showed a high discriminatory index, D, of 0.98 (95% CI 0.97–0.99 confirming the validity of this method for typing. Phylogenetic analyses revealed distinct branches for the phenotypic diseases of lymphogranuloma venereum, urethritis and cervicitis, and a sub-branch for ocular trachoma. Consistent with these findings, single nucleotide polymorphisms were identified that significantly correlated with each phenotype. While the overall number of unique STs per region was comparable across geographies, the number of STs was greater for Russia with a significantly higher ST/sample ratio of 0.45 (95% CI: 0.35–0.53 compared to Europe or the Americas (p < 0.009, which may reflect a higher level of sexual mixing with the introduction of STs from other regions and/or reassortment of alleles. Four STs were found to be significantly associated with a particular geographic region. ST23 [p = 0.032 (95% CI: 1–23], ST34 [p = 0.019 (95% CI: 1.1–25]; and ST19 [p = 0.001 (95% CI: 1.7–34.7] were significantly associated with Netherlands compared to Russia or the Americas, while ST 30 [p = 0.031 (95% CI: 1.1–17.8] was significantly associated with the Americas. ST19 was significantly associated with Netherlands and Russia compared with the Americans [p = 0.001 (95% CI: 1.7–34.7 and p = 0.006 (95

  5. Efficient cell culture system for hepatitis C virus genotype 5A

    DEFF Research Database (Denmark)

    2013-01-01

    The present inventors developed 5a/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and all of or part of NS2 were replaced by the corresponding genes of the genotype 5a reference strain SA13. Compared to the J6/JFH control virus, after transfection of in vi......The present inventors developed 5a/2a intergenotypic recombinants in which the JFH1 structural genes (Core, E1 and E2), p7 and all of or part of NS2 were replaced by the corresponding genes of the genotype 5a reference strain SA13. Compared to the J6/JFH control virus, after transfection...

  6. Genotypic variability of morphological characteristics of English oak (Quercus robur L acorn

    Directory of Open Access Journals (Sweden)

    Nikolić Nataša P.

    2002-01-01

    Full Text Available This paper deals with the acorn morphology (length, diameter and mass analyzed in seventeen English oak genotypes (Quercus robur Lfrom the English Oak Clonal Seed Orchard Banov Brod (Srem,Vojvodina. The highest values of acorn mass and length were measured in genotype 5. The largest diameters were measured in genotypes 6 and 21. Genotype 35 had the lowest acorn mass, length and diameter. The results from this study should serve as guidelines for the selection of trees yielding fruits possessing the desirable morphological characteristics.

  7. The JP2 genotype of Aggregatibacter actinomycetemcomitans and marginal periodontitis in the mixed dentition

    DEFF Research Database (Denmark)

    Jensen, Anne Birkeholm; Ennibi, Oum Keltoum; Ismaili, Zouheir

    2016-01-01

    AIM: To perform a cross-sectional study on the carrier frequency of JP2 and non-JP2 genotypes of A. actinomycetemcomitans in Moroccan schoolchildren and relate the presence of these genotypes to the periodontal status in the mixed dentition. MATERIAL AND METHODS: A plaque sample from 513 children...... the JP2 genotype and 186 (36.3%) were positive for non-JP2 genotypes, whereas A. actinomycetemcomitans could not be detected in the remaining 281 subjects. Among 75 subjects with mixed dentition and selected for clinical examination, clinical attachment loss (CAL) ≥3 mm at two or more periodontal sites...

  8. Experimental study of para- and ortho-H3+ recombination

    Science.gov (United States)

    Plašil, R.; Varju, J.; Hejduk, M.; Dohnal, P.; Kotrík, T.; Glosík, J.

    2011-07-01

    Recombination of H3+ with electrons is a key process for many plasmatic environments. Recent experiments on storage ring devices used ion sources producing H3+ with enhanced populations of H3+ ions in the para nuclear spin configuration to shed light on the theoretically predicted faster recombination of para states. Although increased recombination rates were observed, no in situ characterization of recombining ions was performed. We present a state selective recombination study of para- and ortho-H3+ ions with electrons at 77 K in afterglow plasma in a He/Ar/H2 gas-mixture. Both spin configurations of H3+ have been observed in situ with a near infrared cavity ring down spectrometer (NIR-CRDS) using the two lowest energy levels of H3+. Using hydrogen with an enhanced population of H2 molecules in para states allowed us to influence the [para-H3+]/[ortho-H3+] ratio in the discharge and in the afterglow. We observed an increase in the measured effective recombination rate coefficients with the increase of the fraction of para-H3+. Measurements with different fractions of para-H3+ at otherwise identical conditions allowed us to determine the binary recombination rate coefficients for pure para-H3+ pαbin(77 K) = (2.0±0.4)×10-7 cm3s-1 and pure ortho-H3+ oαbin(77 K) = (4±3)×10-8 cm3s-1.

  9. Efficacy of NS5A Inhibitors Against Hepatitis C Virus Genotypes 1-7 and Escape Variants

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Pham, Long V; Mikkelsen, Lotte S

    2018-01-01

    NS5A inhibitors against HCV genotype 1-7 prototype isolates and resistant escape variants, and investigated the effects of pre-existing resistance-associated substitutions (RAS) on HCV escape from treatment. METHODS: We measured the efficacy of different concentrations of daclatasvir, ledipasvir......, ombitasvir, elbasvir, ruzasvir, velpatasvir, and pibrentasvir in cultured cells infected with HCV recombinants expressing genotype 1-7 NS5A proteins with or without RAS. We engineered HCV variants that included RAS identified in escape experiments, using recombinants with or without T/Y93H and daclatasvir......, or that contained RAS previously reported from patients. RESULTS: NS5A inhibitors had varying levels of efficacy against original and resistant viruses. Only velpatasvir and pibrentasvir had uniform high activity against all HCV genotypes tested. RAS hotspots in NS5A were found at amino acids 28, 30, 31, and 93...

  10. Recombinant protein hydrazides: application to site-specific protein PEGylation.

    Science.gov (United States)

    Thom, Jennifer; Anderson, David; McGregor, Joanne; Cotton, Graham

    2011-06-15

    Here, we describe a novel method for the site-specific C-terminal PEGylation of recombinant proteins. This general approach exploits chemical cleavage of precursor intein-fusion proteins with hydrazine to directly produce recombinant protein hydrazides. This unique functionality within the protein sequence then facilitates site-specific C-terminal modification by hydrazone-forming ligation reactions. This approach was used to generate folded, site-specifically C-terminal PEGylated IFNalpha2b and IFNbeta1b, which retained excellent antiviral activity, demonstrating the utility of this technology in the PEGylation of therapeutic proteins. As this methodology is straightforward to perform, is compatible with disulfide bonds, and is exclusively selective for the protein C-terminus, it shows great potential as general technology for the site-specific engineering and labeling of recombinant proteins.

  11. Seleção de genótipos de cana-de-açúcar para acúmulo de protoporfirina ix com uso de herbicidas inibidores da protox Selection of Sugarcane Genotypes for Protoporphyrin IX Accumulation using Protox-Inhibiting Herbicides

    Directory of Open Access Journals (Sweden)

    L.R.M. Barberis

    2009-01-01

    Full Text Available O objetivo do presente trabalho foi selecionar genótipos de cana-de-açúcar por meio de inibidores da PROTOX e antioxidantes para indução do acúmulo de protoporfirina IX (PROTO IX e/ou de seus precursores em plantas. Esses compostos podem ser utilizados como agentes sensibilizantes em terapia fotodinâmica (TFD, os quais possibilitam uma fonte de baixo custo para o tratamento de neoplasias e carcinomas. O experimento foi montado em câmara climatizada, com aplicação de nove tratamentos (1. oxyfluorfen + glutamato monossódico + vitaminas C e E; 2. oxyfluorfen + glutamato monossódico + vitaminas C e E + ácido levulênico; 3. oxyfluorfen; 4. carfentrazone + glutamato monossódico + vitaminas C e E; 5. carfentrazone + glutamato monossódico + vitaminas C e E + ácido levulênico; 6. carfentrazone; 7. testemunha + vitaminas C e E; 8. testemunha + vitaminas C e E + ácido levulênico; e 9. testemunha em oito genótipos de cana-de-açúcar (PO933499, RB806043, RB470355, PO830698, SP701143, PO901387, PO894414 e SP903414, dispostos em esquema fatorial 9 x 8, com quatro repetições. As repetições constituíram-se de folhas (20 cm destacadas de cada genótipo, sendo estas pulverizadas com os tratamentos mencionados, em simulador estacionário. Foram realizadas avaliações visuais de controle aos 2 DAA (dias após aplicação e, no fim do estudo, determinações analíticas via extração da biomassa fresca, verificando os teores de protoporfirina IX por cromatografia líquida de alta eficiência. Os resultados mostraram que em curto prazo foram detectados aumentos significativos nas concentrações de PROTO IX para os genótipos RB470355 e SP903414 submetidos ao tratamento 2 e para o genótipo SP701143 submetido ao tratamento 8, indicando que eles podem ser utilizados como fontes acumuladoras de protoporfirina IX.The objective of this study was to select sugarcane genotypes through PROTOX inhibitors and antioxidants to induce the accumulation

  12. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURCES...... circumference in response to weight loss intervention were not significantly different between FTO genotypes. Sensitivity analyses indicated that differential changes in body mass index, body weight, and waist circumference by FTO genotype did not differ by intervention type, intervention length, ethnicity......, sample size, sex, and baseline body mass index and age category. CONCLUSIONS: We have observed that carriage of the FTO minor allele was not associated with differential change in adiposity after weight loss interventions. These findings show that individuals carrying the minor allele respond equally...

  13. Genonets server-a web server for the construction, analysis and visualization of genotype networks.

    Science.gov (United States)

    Khalid, Fahad; Aguilar-Rodríguez, José; Wagner, Andreas; Payne, Joshua L

    2016-07-08

    A genotype network is a graph in which vertices represent genotypes that have the same phenotype. Edges connect vertices if their corresponding genotypes differ in a single small mutation. Genotype networks are used to study the organization of genotype spaces. They have shed light on the relationship between robustness and evolvability in biological systems as different as RNA macromolecules and transcriptional regulatory circuits. Despite the importance of genotype networks, no tool exists for their automatic construction, analysis and visualization. Here we fill this gap by presenting the Genonets Server, a tool that provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes from DNA, RNA, amino acid or binary sequences; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography and how it relates to the navigability of a genotype network via mutation and natural selection; (iii) multiple interactive visualizations that facilitate exploratory research and education. The Genonets Server is freely available at http://ieu-genonets.uzh.ch. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. BK polyomavirus genotypes Ia and Ib1 exhibit different biological properties in renal transplant recipients.

    Science.gov (United States)

    Varella, Rafael B; Zalona, Ana Carolina J; Diaz, Nuria C; Zalis, Mariano G; Santoro-Lopes, Guilherme

    2018-01-02

    BK polyomavirus (BKV) is an opportunist agent associated with nephropathy (BKVAN) in 1-10% of kidney transplant recipients. BKV is classified into genotypes or subgroups according to minor nucleotidic variations with unknown biological implications. Studies assessing the possible association between genotypes and the risk of BKVAN in kidney transplant patients have presented conflicting results. In these studies, genotype Ia, which is highly prevalent in Brazil, was less frequently found and, thus, comparative data on the biological properties of this genotype are lacking. In this study, BKV Ia and Ib1 genotypes were compared according to their viral load, genetic evolution (VP1 and NCCR) - in a cohort of renal transplant recipients. The patients infected with Ia (13/23; 56.5%) genotype exhibited higher viral loads in urine [>1.4 log over Ib1 (10/23; 43.5%); p=0.025]. In addition, genotype Ia was associated with diverse mutations at VP1 loops and sites under positive selection outside loops, which were totally absent in Ib1. Although the number of viremic patients was similar, the three patients who had BK nephropathy (BKVAN) were infected with Ia genotype. NCCR architecture (ww or rr) were not distinctive between Ia and Ib1 genotypes. Ia genotype, which is rare in other published BKV cohorts, presented some diverse biological properties in transplanted recipients in comparison to Ib1. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. The evolution of sex: A new hypothesis based on mitochondrial mutational erosion: Mitochondrial mutational erosion in ancestral eukaryotes would favor the evolution of sex, harnessing nuclear recombination to optimize compensatory nuclear coadaptation.

    Science.gov (United States)

    Havird, Justin C; Hall, Matthew D; Dowling, Damian K

    2015-09-01

    The evolution of sex in eukaryotes represents a paradox, given the "twofold" fitness cost it incurs. We hypothesize that the mutational dynamics of the mitochondrial genome would have favored the evolution of sexual reproduction. Mitochondrial DNA (mtDNA) exhibits a high-mutation rate across most eukaryote taxa, and several lines of evidence suggest that this high rate is an ancestral character. This seems inexplicable given that mtDNA-encoded genes underlie the expression of life's most salient functions, including energy conversion. We propose that negative metabolic effects linked to mitochondrial mutation accumulation would have invoked selection for sexual recombination between divergent host nuclear genomes in early eukaryote lineages. This would provide a mechanism by which recombinant host genotypes could be rapidly shuffled and screened for the presence of compensatory modifiers that offset mtDNA-induced harm. Under this hypothesis, recombination provides the genetic variation necessary for compensatory nuclear coadaptation to keep pace with mitochondrial mutation accumulation. © 2015 WILEY Periodicals, Inc.

  16. Shoot and Root Traits Contribute to Drought Resistance in Recombinant Inbred Lines of MD 23-24 × SEA 5 of Common Bean.

    Science.gov (United States)

    Polania, Jose; Rao, Idupulapati M; Cajiao, Cesar; Grajales, Miguel; Rivera, Mariela; Velasquez, Federico; Raatz, Bodo; Beebe, Stephen E

    2017-01-01

    Drought is the major abiotic stress factor limiting yield of common bean ( Phaseolus vulgaris L.) in smallholder systems in Latin America and eastern and southern Africa; where it is a main source of protein in the daily diet. Identification of shoot and root traits associated with drought resistance contributes to improving the process of designing bean genotypes adapted to drought. Field and greenhouse studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia to determine the relationship between grain yield and different shoot and root traits using a recombinant inbred lines (RILs) population (MD23-24 × SEA 5) of common bean. The main objectives of this study were to identify: (i) specific shoot and root morpho-physiological traits that contribute to improved resistance to drought and that could be useful as selection criteria in breeding beans for drought resistance; and (ii) superior genotypes with desirable shoot and root traits that could serve as parents in breeding programs that are aimed at improving drought resistance. A set of 121 bean genotypes (111 RILs, 2 parents, 8 checks) belonging to the Mesoamerican gene pool and one cowpea variety were evaluated under field conditions with two levels of water supply (irrigated and rainfed) over three seasons. To complement field studies, a greenhouse study was conducted using plastic cylinders with soil inserted into PVC pipes, to determine the