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Sample records for allelic exchange experiments

  1. Systematic review of allelic exchange experiments aimed at identifying mutations that confer drug resistance in Mycobacterium tuberculosis

    PubMed Central

    Nebenzahl-Guimaraes, Hanna; Jacobson, Karen R.; Farhat, Maha R.; Murray, Megan B.

    2014-01-01

    Background Improving our understanding of the relationship between the genotype and the drug resistance phenotype of Mycobacterium tuberculosis will aid the development of more accurate molecular diagnostics for drug-resistant tuberculosis. Studies that use direct genetic manipulation to identify the mutations that cause M. tuberculosis drug resistance are superior to associational studies in elucidating an individual mutation's contribution to the drug resistance phenotype. Methods We systematically reviewed the literature for publications reporting allelic exchange experiments in any of the resistance-associated M. tuberculosis genes. We included studies that introduced single point mutations using specialized linkage transduction or site-directed/in vitro mutagenesis and documented a change in the resistance phenotype. Results We summarize evidence supporting the causal relationship of 54 different mutations in eight genes (katG, inhA, kasA, embB, embC, rpoB, gyrA and gyrB) and one intergenic region (furA-katG) with resistance to isoniazid, the rifamycins, ethambutol and fluoroquinolones. We observed a significant role for the strain genomic background in modulating the resistance phenotype of 21 of these mutations and found examples of where the same drug resistance mutations caused varying levels of resistance to different members of the same drug class. Conclusions This systematic review highlights those mutations that have been shown to causally change phenotypic resistance in M. tuberculosis and brings attention to a notable lack of allelic exchange data for several of the genes known to be associated with drug resistance. PMID:24055765

  2. Do Heliconius butterfly species exchange mimicry alleles?

    PubMed Central

    Smith, Joel; Kronforst, Marcus R.

    2013-01-01

    Hybridization has the potential to transfer beneficial alleles across species boundaries, and there are a growing number of examples in which this has apparently occurred. Recent studies suggest that Heliconius butterflies have transferred wing pattern mimicry alleles between species via hybridization, but ancestral polymorphism could also produce a signature of shared ancestry around mimicry genes. To distinguish between these alternative hypotheses, we measured DNA sequence divergence around putatively introgressed mimicry loci and compared this with the rest of the genome. Our results reveal that putatively introgressed regions show strongly reduced sequence divergence between co-mimetic species, suggesting that their divergence times are younger than the rest of the genome. This is consistent with introgression and not ancestral variation. We further show that this signature of introgression occurs at sites throughout the genome, not just around mimicry genes. PMID:23864282

  3. Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange

    PubMed Central

    Hmelo, Laura R.; Borlee, Bradley R.; Almblad, Henrik; Love, Michelle E.; Randall, Trevor E.; Tseng, Boo Shan; Lin, Chuyang; Irie, Yasuhiko; Storek, Kelly M.; Yang, Jaeun Jane; Siehnel, Richard J.; Howell, P. Lynne; Singh, Pradeep K.; Tolker-Nielsen, Tim; Parsek, Matthew R.; Schweizer, Herbert P.; Harrison, Joe J.

    2016-01-01

    Allelic exchange is an efficient method of bacterial genome engineering. This protocol describes the use of this technique to make gene knockouts and knockins, as well as single nucleotide insertions, deletions and substitutions in Pseudomonas aeruginosa. Unlike other approaches to allelic exchange, this protocol does not require heterologous recombinases to insert or excise selective markers from the target chromosome. Rather, positive and negative selection are enabled solely by suicide vector-encoded functions and host cell proteins. Here, mutant alleles, which are flanked by regions of homology to the recipient chromosome, are synthesized in vitro and then cloned into allelic exchange vectors using standard procedures. These suicide vectors are then introduced into recipient cells by conjugation. Homologous recombination then results in antibiotic resistant single-crossover mutants in which the plasmid has integrated site-specifically into the chromosome. Subsequently, unmarked double-crossover mutants are isolated directly using sucrose-mediated counter-selection. This two-step process yields seamless mutations that are precise to a single base pair of DNA. The entire procedure requires ~2 weeks. PMID:26492139

  4. Gene Deletion by Fluorescence-Reported Allelic Exchange Mutagenesis in Chlamydia trachomatis

    PubMed Central

    Mueller, Konrad E.; Wolf, Katerina

    2016-01-01

    ABSTRACT Although progress in Chlamydia genetics has been rapid, genomic modification has previously been limited to point mutations and group II intron insertions which truncate protein products. The bacterium has thus far been intractable to gene deletion or more-complex genomic integrations such as allelic exchange. Herein, we present a novel suicide vector dependent on inducible expression of a chlamydial gene that renders Chlamydia trachomatis fully genetically tractable and permits rapid reverse genetics by fluorescence-reported allelic exchange mutagenesis (FRAEM). We describe the first available system of targeting chlamydial genes for deletion or allelic exchange as well as curing plasmids from C. trachomatis serovar L2. Furthermore, this approach permits the monitoring of mutagenesis by fluorescence microscopy without disturbing bacterial growth, a significant asset when manipulating obligate intracellular organisms. As proof of principle, trpA was successfully deleted and replaced with a sequence encoding both green fluorescent protein (GFP) and β-lactamase. The trpA-deficient strain was unable to grow in indole-containing medium, and this phenotype was reversed by complementation with trpA expressed in trans. To assess reproducibility at alternate sites, FRAEM was repeated for genes encoding type III secretion effectors CTL0063, CTL0064, and CTL0065. In all four cases, stable mutants were recovered one passage after the observation of transformants, and allelic exchange was limited to the specific target gene, as confirmed by whole-genome sequencing. Deleted sequences were not detected by quantitative real-time PCR (qPCR) from isogenic mutant populations. We demonstrate that utilization of the chlamydial suicide vector with FRAEM renders C. trachomatis highly amenable to versatile and efficient genetic manipulation. PMID:26787828

  5. A Colorful Ion Exchange Experiment

    NASA Astrophysics Data System (ADS)

    Mendes, Adélio

    1999-11-01

    A colorful ion-exchange experiment is described. The use of a resin with an adsorbed acid-base indicator allows students to follow the progress of the ion-exchange front along the column. In parallel, students can follow the ion-exchange breakthrough curve using a continuous conductometric cell at the column outlet. In the present example, K+ (KCl) exchanges with H+ (HCl) in a strong cationic resin (Amberlite IR 120). The adsorbed indicator is methyl violet. Sorption equilibrium is favorable to the K+ ions. Monovalent ions, used in this experiment, have the disadvantage of usually being colorless (except perhaps permanganate, but this is an extremely strong oxidant which attacks the resin). On the other hand, many divalent ions are colorful but the shape of the concentration front is hard to explain qualitatively as well as quantitatively. That is because the shape of the front depends on the total ionic concentration. However, color can be introduced in a monovalent ion-exchange system by adding an appropriate acid-base indicator to the resin. The text describes this experiment qualitatively. A simplified quantitative description, using the solute movement theory, can be found online.

  6. Exchange of astronomy teaching experiences

    NASA Astrophysics Data System (ADS)

    Ros, Rosa M.

    The Working Group of the European Association for Astronomy Education responsible for Teacher Training organises an annual Summer School for teachers under expert guidance. For a week the teachers participating can exchange experiences, increase their knowledge and discuss different ideas and perspectives. In general, the instructors are professional astronomers, professors and teachers from different countries. The papers presented offer very practical activities, paying special attention to didactic aspects, and take the form of general lectures to all 40 participants and workshops to reduced groups of 20 participants. There are also day and night observations, without expensive equipment or complicated procedures, that are easy to set up and based on topics that it is possible to use in the classroom. The Summer Schools promote a scientific astronomical education at all levels of astronomy teaching, reinforce the link between professional astronomers and teachers with experience of teaching astronomy, allow debates among the participants on their pedagogical activities already carried out in their own classroom and help them to organise activities outside it. Astronomy teachers need special training, access to specific research, to new educational materials and methods and the opportunity to exchange experiences. All these things are provided by the Summer School.

  7. Ion exchange - Simulation and experiment

    NASA Technical Reports Server (NTRS)

    Herrmann, Cal C.; Finn, John E.

    1991-01-01

    A FORTRAN program for simulating multicomponent adsorption by ion-exchange resins was adapted for use as both an ASPEN-callable module and as a free-standing simulator of the ion-exchange bed. Four polystyrene-divinylbenzene sulfonic acid resins have been characterized for three principal ions. It is concluded that a chelating resin appears appropriate as a heavy-metal trap. The same ASPEN-callable module is used to model this resin when Wilson parameters can be obtained.

  8. Microbial exchange experiment AR-002

    NASA Technical Reports Server (NTRS)

    Taylor, G. R.; Kropp, K. D.; Henney, M. R.; Ekblad, S. S.; Groves, T. O.; Molina, T. C.; Decelle, J. G.; Carmichael, C. F.; Gehring, N. J.; Young, E. L.

    1976-01-01

    Operational aspects associated with the experiment and the activities of medically important microorganisms recovered from the Apollo crewmen are evaluated. A variety of potential pathogens was recovered from each of the prime and backup crew members before and after flight. However, no disease events were reported. Candida albicans and Staphylococcus aureus were shown to be transferred from one crewmember to another during the flight. No other medically significant changes in the microbial population were observed.

  9. The 1980 stratospheric-tropospheric exchange experiment

    NASA Technical Reports Server (NTRS)

    Margozzi, A. P. (Editor)

    1983-01-01

    Data are presented from the Stratospheric-Tropospheric Water Vapor Exchange Experiment. Measurements were made during 11 flights of the NASA U-2 aircraft which provided data from horizontal traverser and samplings in and about the tops of extensive cirrus-anvil clouds produced by overshooting cumulus turrets. Aircraft measurements were made of water vapor, ozone, ambient and cloud top temperature, fluorocarbons, nitrous oxide, nitric acid, aerosols, and ice crystal populations. Balloonsondes were flown about twice daily providing data on ozone, wind fields, pressure and temperature to altitudes near 30 km. Satellite photography provided detailed cloud and cloud top temperature information. Descriptions of individual experiments and detailed compilations of all results are provided.

  10. Na{sup +}/H{sup +} exchanger-1 alleles: Strain distribution and correlation with activity

    SciTech Connect

    McClive, P.J.; Morahan, G.; Little, P.J.

    1996-12-31

    The Na{sup +}/H{sup +} exchanger-1 molecule (NHE1) regulates intracellular pH, cell volume, and cell growth. NHE1 is a phosphoprotein of approximately M{sub r} 110000 with 10 or 12 transmembrane domains. NHE1 is ubiquitously expressed. Three other family members have been identified which show close similarity to NHE1 but are significantly more restricted in their expression: all are found in the gastrointestinal tract, while NHE2 and NHE3 are also expressed in the kidney. 14 refs., 2 figs.

  11. Hydrogen Exchange Mass Spectrometry of Related Proteins with Divergent Sequences: A Comparative Study of HIV-1 Nef Allelic Variants

    NASA Astrophysics Data System (ADS)

    Wales, Thomas E.; Poe, Jerrod A.; Emert-Sedlak, Lori; Morgan, Christopher R.; Smithgall, Thomas E.; Engen, John R.

    2016-03-01

    Hydrogen exchange mass spectrometry can be used to compare the conformation and dynamics of proteins that are similar in tertiary structure. If relative deuterium levels are measured, differences in sequence, deuterium forward- and back-exchange, peptide retention time, and protease digestion patterns all complicate the data analysis. We illustrate what can be learned from such data sets by analyzing five variants (Consensus G2E, SF2, NL4-3, ELI, and LTNP4) of the HIV-1 Nef protein, both alone and when bound to the human Hck SH3 domain. Regions with similar sequence could be compared between variants. Although much of the hydrogen exchange features were preserved across the five proteins, the kinetics of Nef binding to Hck SH3 were not the same. These observations may be related to biological function, particularly for ELI Nef where we also observed an impaired ability to downregulate CD4 surface presentation. The data illustrate some of the caveats that must be considered for comparison experiments and provide a framework for investigations of other protein relatives, families, and superfamilies with HX MS.

  12. Hydrogen Exchange Mass Spectrometry of Related Proteins with Divergent Sequences: A Comparative Study of HIV-1 Nef Allelic Variants.

    PubMed

    Wales, Thomas E; Poe, Jerrod A; Emert-Sedlak, Lori; Morgan, Christopher R; Smithgall, Thomas E; Engen, John R

    2016-06-01

    Hydrogen exchange mass spectrometry can be used to compare the conformation and dynamics of proteins that are similar in tertiary structure. If relative deuterium levels are measured, differences in sequence, deuterium forward- and back-exchange, peptide retention time, and protease digestion patterns all complicate the data analysis. We illustrate what can be learned from such data sets by analyzing five variants (Consensus G2E, SF2, NL4-3, ELI, and LTNP4) of the HIV-1 Nef protein, both alone and when bound to the human Hck SH3 domain. Regions with similar sequence could be compared between variants. Although much of the hydrogen exchange features were preserved across the five proteins, the kinetics of Nef binding to Hck SH3 were not the same. These observations may be related to biological function, particularly for ELI Nef where we also observed an impaired ability to downregulate CD4 surface presentation. The data illustrate some of the caveats that must be considered for comparison experiments and provide a framework for investigations of other protein relatives, families, and superfamilies with HX MS. Graphical Abstract ᅟ. PMID:27032648

  13. Hydrogen Exchange Mass Spectrometry of Related Proteins with Divergent Sequences: A Comparative Study of HIV-1 Nef Allelic Variants

    NASA Astrophysics Data System (ADS)

    Wales, Thomas E.; Poe, Jerrod A.; Emert-Sedlak, Lori; Morgan, Christopher R.; Smithgall, Thomas E.; Engen, John R.

    2016-06-01

    Hydrogen exchange mass spectrometry can be used to compare the conformation and dynamics of proteins that are similar in tertiary structure. If relative deuterium levels are measured, differences in sequence, deuterium forward- and back-exchange, peptide retention time, and protease digestion patterns all complicate the data analysis. We illustrate what can be learned from such data sets by analyzing five variants (Consensus G2E, SF2, NL4-3, ELI, and LTNP4) of the HIV-1 Nef protein, both alone and when bound to the human Hck SH3 domain. Regions with similar sequence could be compared between variants. Although much of the hydrogen exchange features were preserved across the five proteins, the kinetics of Nef binding to Hck SH3 were not the same. These observations may be related to biological function, particularly for ELI Nef where we also observed an impaired ability to downregulate CD4 surface presentation. The data illustrate some of the caveats that must be considered for comparison experiments and provide a framework for investigations of other protein relatives, families, and superfamilies with HX MS.

  14. International Exchange as a Transformative Learning Experience: A Case Study

    ERIC Educational Resources Information Center

    Choi, Sheena; Slaubaugh, Michael; Kim, Ae-Sook

    2012-01-01

    This study examines the role of international exchange programs on the transformative learning of English-speaking students. A student exchange program at a South Korean university is used for this case study. It explores how learning experiences are translated by participants onto their perceptions about the host country. An analysis of a pre-…

  15. Ion Exchange Chromatography and Spectrophotometry: An Introductory Undergraduate Laboratory Experiment.

    ERIC Educational Resources Information Center

    Foster, N.; And Others

    1985-01-01

    Describes an experiment in which students use ion exchange chromatography to separate a mixture of chloro complexes of transition metal ions and then use spectrophotometry to define qualitatively the efficiency of the ion exchange columns. Background information, materials needed, and procedures used are included. (JN)

  16. Unbiased isotope equilibrium factors from partial isotope exchange experiments in 3-exchange site systems

    NASA Astrophysics Data System (ADS)

    Agrinier, Pierre; Javoy, Marc

    2016-09-01

    Two methods are available in order to evaluate the equilibrium isotope fractionation factors between exchange sites or phases from partial isotope exchange experiments. The first one developed by Northrop and Clayton (1966) is designed for isotope exchanges between two exchange sites (hereafter, the N&C method), the second one from Zheng et al. (1994) is a refinement of the first one to account for a third isotope exchanging site (hereafter, the Z method). In this paper, we use a simple model of isotope kinetic exchange for a 3-exchange site system (such as hydroxysilicates where oxygen occurs as OH and non-OH groups like in muscovite, chlorite, serpentine, or water or calcite) to explore the behavior of the N&C and Z methods. We show that these two methods lead to significant biases that cannot be detected with the usual graphical tests proposed by the authors. Our model shows that biases originate because isotopes are fractionated between all these exchanging sites. Actually, we point out that the variable mobility (or exchangeability) of isotopes in and between the exchange sites only controls the amplitude of the bias, but is not essential to the production of this bias as previously suggested. Setting a priori two of the three exchange sites at isotopic equilibrium remove the bias and thus is required for future partial exchange experiments to produce accurate and unbiased extrapolated equilibrium fractionation factors. Our modeling applied to published partial oxygen isotope exchange experiments for 3-exchange site systems (the muscovite-calcite (Chacko et al., 1996), the chlorite-water (Cole and Ripley, 1998) and the serpentine-water (Saccocia et al., 2009)) shows that the extrapolated equilibrium fractionation factors (reported as 1000 ln(α)) using either the N&C or the Z methods lead to bias that may reach several δ per mil in a few cases. These problematic cases, may be because experiments were conducted at low temperature and did not reach high

  17. The GL service: Web service to exchange GL string encoded HLA & KIR genotypes with complete and accurate allele and genotype ambiguity.

    PubMed

    Milius, Robert P; Heuer, Michael; George, Mike; Pollack, Jane; Hollenbach, Jill A; Mack, Steven J; Maiers, Martin

    2016-03-01

    Genotype list (GL) Strings use a set of hierarchical character delimiters to represent allele and genotype ambiguity in HLA and KIR genotypes in a complete and accurate fashion. A RESTful web service called genotype list service was created to allow users to register a GL string and receive a unique identifier for that string in the form of a URI. By exchanging URIs and dereferencing them through the GL service, users can easily transmit HLA genotypes in a variety of useful formats. The GL service was developed to be secure, scalable, and persistent. An instance of the GL service is configured with a nomenclature and can be run in strict or non-strict modes. Strict mode requires alleles used in the GL string to be present in the allele database using the fully qualified nomenclature. Non-strict mode allows any GL string to be registered as long as it is syntactically correct. The GL service source code is free and open source software, distributed under the GNU Lesser General Public License (LGPL) version 3 or later. PMID:26621609

  18. The CLAS Two Photon Exchange Experiment

    NASA Astrophysics Data System (ADS)

    Adikaram, Dasuni; Bennett, Robert; Weinstein, Larry; Rimal, Dipak; Khetarpal, Puneet; Raue, Brian

    2013-04-01

    There is a large discrepancy between the proton electron form factor (GE^p(Q^2)) measured using the Rosenbluth separation and polarization transfer methods. The most likely explanation of this discrepancy is the inclusion of two-photon exchange (TPE) amplitude contributions to the elastic electron-proton cross section. The TPE contribution can be extracted in a model-independent way from the measured ratio of the cross sections of positron-proton and electron-proton elastic scattering. This ratio was measured in Hall B at Jefferson Lab using a simultaneous mixed tertiary beam of electrons and positrons incident on a liquid hydrogen target in the center of the CLAS detector in 2010-2011. In this talk, the experimental techniques to produce e^+/e^- beam, the analysis techniques to identify the elastic scattering events, and some preliminary results will be presented.

  19. The CLAS Two Photon Exchange Experiment

    NASA Astrophysics Data System (ADS)

    Adikaram, Dasuni; CLAS Collaboration

    2013-10-01

    There is a large discrepancy between the proton electron form factor (GEp(Q2)) measured using the Rosenbluth separation and polarization transfer methods. The most likely explanation of this discrepancy is the inclusion of two-photon exchange (TPE) amplitude contributions to the elastic electron-proton cross section. The TPE contribution can be extracted in a model-independent way from the measured ratio of the cross sections of positron-proton and electron-proton elastic scattering. This ratio was measured in Hall B at Jefferson Lab using a simultaneous mixed tertiary beam of electrons and positrons incident on a liquid hydrogen target in the center of the CLAS detector in 2010-2011. This talk will present the analysis techniques used to identify the elastic scattering events, and some preliminary results at Q2 = 1.4 (GeV/c)2.

  20. DLA-DQB1 alleles and bone marrow transplantation experiments in narcoleptic dogs.

    PubMed

    Wagner, J L; Storb, R; Storer, B; Mignot, E

    2000-09-01

    Human narcolepsy is a neurological disorder known to be tightly associated with HLA-DQB1*0602. A clinically similar disorder has been described in various dog breeds. The canine form of the disease is inherited as an autosomal recessive disorder in Labrador retrievers and Doberman pinschers (canarc-1) but occurs sporadically in other breeds, most typically dachshunds and poodles. In this study, we have examined if there is a relationship between the development of narcolepsy and specific dog leukocyte antigen (DLA)-DQB1 alleles. Ninety-nine dogs were typed for DLA-DQB1-31 with narcolepsy and 68 control animals. Recent studies have linked the development of autosomal recessive canine narcolepsy to a disruption of the hypocretin receptor 2 (Hcrtr2) gene on the same chromosome as the canine MHC region (CFA12), but not close to the DLA. Four Hcrtr2-positive families (two Doberman pinscher families, one Labrador retriever family, one dachshund family) were analyzed at the DLA-DQ level. No relationship was found between narcolepsy and DLA in Hcrtr2-mediated narcolepsy but loose genetic linkage was observed (Zmax=2.3 at theta=25%, m= 40). Bone marrow transplantation between two DLA identical affected (Hcrtr2-/-) and unaffected (Hcrtr2+/-) siblings was also performed and found not to be successful neither in transmitting narcolepsy nor in relieving the symptoms in Doberman pinschers. DLA-DQB1 was next studied in 11 dogs with sporadic (non-familial) narcolepsy and in unrelated control animals of the same and different breeds. The allelic and carrier frequencies of various DLA-DQB1 alleles were analyzed. There was no strong positive or negative correlation between the development of narcolepsy and specific DLA-DQB1 alleles. These results do not support the involvement of DLA-DQ in canine narcolepsy, whether of sporadic or familial origin. PMID:11034558

  1. The urease locus of Mycobacterium tuberculosis and its utilization for the demonstration of allelic exchange in Mycobacterium bovis bacillus Calmette-Guérin.

    PubMed Central

    Reyrat, J M; Berthet, F X; Gicquel, B

    1995-01-01

    The ureABC genes of Mycobacterium tuberculosis were cloned. By using a set of degenerate primers corresponding to a conserved region of the urease enzyme (EC 3.5.1.5), a fragment of the expected size was amplified by PCR and was used to screen a M. tuberculosis cosmid library. Three open reading frames with extensive similarity to the urease genes from other organisms were found. The locus was mapped on the chromosome, using an ordered M. tuberculosis cosmid library. A suicide vector containing a ureC gene disrupted by a kanamycin marker (aph) was used to construct a urease-negative Mycobacterium bovis bacillus Calmette-Guérin mutant by allelic exchange involving replacement of the ureC gene with the aph::ureC construct. To our knowledge, allelic exchange has not been reported previously in the slow-growing mycobacteria. Homologous recombination will be an invaluable genetic tool for deciphering the mechanisms of tuberculosis pathogenesis, a disease that causes 3 x 10(6) deaths a year worldwide. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5 Fig. 6 Fig. 7 Fig. 8 PMID:7568014

  2. Utilization of a ts-sacB selection system for the generation of a Mycobacterium avium serovar-8 specific glycopeptidolipid allelic exchange mutant

    PubMed Central

    Irani, Vida R; Lee, Sun-Hwa; Eckstein, Torsten M; Inamine, Julia M; Belisle, John T; Maslow, Joel N

    2004-01-01

    Background Mycobacterium avium are ubiquitous environmental organisms and a cause of disseminated infection in patients with end-stage AIDS. The glycopeptidolipids (GPL) of M. avium are proposed to participate in the pathogenesis of this organism, however, establishment of a clear role for GPL in disease production has been limited by the inability to genetically manipulate M. avium. Methods To be able to study the role of the GPL in M. avium pathogenesis, a ts-sacB selection system, not previously used in M. avium, was employed as a means to achieve homologous recombination for the rhamnosyltransferase (rtfA) gene of a pathogenic serovar 8 strain of M. avium to prevent addition of serovar-specific sugars to rhamnose of the fatty acyl-peptide backbone of GPL. The genotype of the resultant rtfA mutant was confirmed by polymerase chain reaction and southern hybridization. Disruption in the proximal sugar of the haptenic oligosaccharide resulted in the loss of serovar specific GPL with no change in the pattern of non-serovar specific GPL moieties as shown by thin layer chromatography and gas chromatography/mass spectrometry. Complementation of wild type (wt) rtfA in trans through an integrative plasmid restored serovar-8 specific GPL expression identical to wt serovar 8 parent strain. Results In this study, we affirm our results that rtfA encodes an enzyme responsible for the transfer of Rha to 6d-Tal and provide evidence of a second allelic exchange mutagenesis system suitable for M. avium. Conclusion We report the second allelic exchange system for M. avium utilizing ts-sacB as double-negative and xylE as positive counter-selection markers, respectively. This system of allelic exchange would be especially useful for M. avium strains that demonstrate significant isoniazid (INH) resistance despite transformation with katG. Through the construction of mutants in GPL or other mycobacterial components, their roles in M. avium pathogenesis, biosynthesis, or drug

  3. Comparison of the Construction of Unmarked Deletion Mutations in Mycobacterium smegmatis, Mycobacterium bovis Bacillus Calmette-Guérin, and Mycobacterium tuberculosis H37Rv by Allelic Exchange

    PubMed Central

    Pavelka, Martin S.; Jacobs, William R.

    1999-01-01

    Until recently, genetic analysis of Mycobacterium tuberculosis, the causative agent of tuberculosis, was hindered by a lack of methods for gene disruptions and allelic exchange. Several groups have described different methods for disrupting genes marked with antibiotic resistance determinants in the slow-growing organisms Mycobacterium bovis bacillus Calmette-Guérin (BCG) and M. tuberculosis. In this study, we described the first report of using a mycobacterial suicidal plasmid bearing the counterselectable marker sacB for the allelic exchange of unmarked deletion mutations in the chromosomes of two substrains of M. bovis BCG and M. tuberculosis H37Rv. In addition, our comparison of the recombination frequencies in these two slow-growing species and that of the fast-growing organism Mycobacterium smegmatis suggests that the homologous recombination machinery of the three species is equally efficient. The mutants constructed here have deletions in the lysA gene, encoding meso-diaminopimelate decarboxylase, an enzyme catalyzing the last step in lysine biosynthesis. We observed striking differences in the lysine auxotrophic phenotypes of these three species of mycobacteria. The M. smegmatis mutant can grow on lysine-supplemented defined medium or complex rich medium, while the BCG mutants grow only on lysine-supplemented defined medium and are unable to form colonies on complex rich medium. The M. tuberculosis lysine auxotroph requires 25-fold more lysine on defined medium than do the other mutants and is dependent upon the detergent Tween 80. The mutants described in this work are potential vaccine candidates and can also be used for studies of cell wall biosynthesis and amino acid metabolism. PMID:10438745

  4. International exchange training in genetic counseling: an exploration of the value in exchange experiences.

    PubMed

    Alexander, Chelsea K A; Veach, Patricia McCarthy; Lian, Fengqin; LeRoy, Bonnie S

    2013-12-01

    International exchange training in genetic counseling is increasing, but research examining these experiences is lacking. In this study 309 genetic counseling students and genetic counselors completed an anonymous survey investigating six major research questions: (1) How prevalent are international genetic counseling experiences? (2) What types are pursued and why? (3) What supports and barriers exist? 3) What are the demographic characteristics of individuals accruing international experience? (5) Does international experience promote professional development? and (6) Do genetic counseling students and professionals perceive international experiences as beneficial? Most respondents were Caucasian females born in one of 25 countries. The most prevalent experiences involved either clinical observation or clinical training. Common motivations for pursuing international experience were personal growth, exposure to a different healthcare system, and travel opportunities. Outcomes included professionally-relevant experience and personal growth. Barriers included finances, limited availability of opportunities, and for those without international experience, family responsibilities. Additional findings, practice and training implications, and research recommendations are provided. PMID:23423708

  5. Combined Steady-State and Dynamic Heat Exchanger Experiment

    ERIC Educational Resources Information Center

    Luyben, William L.; Tuzla, Kemal; Bader, Paul N.

    2009-01-01

    This paper describes a heat-transfer experiment that combines steady-state analysis and dynamic control. A process-water stream is circulated through two tube-in-shell heat exchangers in series. In the first, the process water is heated by steam. In the second, it is cooled by cooling water. The equipment is pilot-plant size: heat-transfer areas…

  6. Japanese Exchange Students' Writing Experiences in a Canadian University.

    ERIC Educational Resources Information Center

    Shi, Ling; Beckett, Gulbahar H.

    2002-01-01

    Investigated the learning experiences of 23 Japanese students in a one-year academic exchange program in a Canadian university. Participants either wrote an opinion task or a summary task at the beginning of the program using preselected source texts. Analyses of interview data and comparisons of the original and revised texts indicate that…

  7. Minimizing back exchange in the hydrogen exchange-mass spectrometry experiment.

    PubMed

    Walters, Benjamin T; Ricciuti, Alec; Mayne, Leland; Englander, S Walter

    2012-12-01

    The addition of mass spectrometry (MS) analysis to the hydrogen exchange (HX) proteolytic fragmentation experiment extends powerful HX methodology to the study of large biologically important proteins. A persistent problem is the degradation of HX information due to back exchange of deuterium label during the fragmentation-separation process needed to prepare samples for MS measurement. This paper reports a systematic analysis of the factors that influence back exchange (solution pH, ionic strength, desolvation temperature, LC column interaction, flow rates, system volume). The many peptides exhibit a range of back exchange due to intrinsic amino acid HX rate differences. Accordingly, large back exchange leads to large variability in D-recovery from one residue to another as well as one peptide to another that cannot be corrected for by reference to any single peptide-level measurement. The usual effort to limit back exchange by limiting LC time provides little gain. Shortening the LC elution gradient by 3-fold only reduced back exchange by ~2%, while sacrificing S/N and peptide count. An unexpected dependence of back exchange on ionic strength as well as pH suggests a strategy in which solution conditions are changed during sample preparation. Higher salt should be used in the first stage of sample preparation (proteolysis and trapping) and lower salt (<20 mM) and pH in the second stage before electrospray injection. Adjustment of these and other factors together with recent advances in peptide fragment detection yields hundreds of peptide fragments with D-label recovery of 90% ± 5%. PMID:22965280

  8. Demonstration of Allelic Exchange in the Slow-Growing Bacterium Mycobacterium avium subsp. paratuberculosis, and Generation of Mutants with Deletions at the pknG, relA and lsr2 Loci

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mycobacterium avium subsp. paratuberculosis (Map) is the causative pathogen of Johne’s disease, a chronic inflammatory wasting disease in ruminants. The disease has been difficult to control because of the lack of an effective vaccine. To address this need, we developed an efficient allelic exchange...

  9. Inactivation of Serpulina hyodysenteriae flaA1 and flaB1 periplasmic flagellar genes by electroporation-mediated allelic exchange.

    PubMed Central

    Rosey, E L; Kennedy, M J; Petrella, D K; Ulrich, R G; Yancey, R J

    1995-01-01

    Serpulina hyodysenteriae, the etiologic agent of swine dysentery, contains complex periplasmic flagella which are composed of multiple class A and class B polypeptides. To examine the role these proteins play in flagellar synthesis, structure, and function and to develop strains which may provide insight into the importance of motility in the etiology of this pathogen, we constructed specific periplasmic flagellar mutations in S. hyodysenteriae B204. The cloned flaA1 and flaB1 genes were disrupted by replacement of internal fragments with chloramphenicol and/or kanamycin gene cassettes. Following delivery of these suicide plasmids into S. hyodysenteriae, homologous recombination and allelic exchange at the targeted chromosomal flaA1 and flaB1 genes was verified by PCR, sequence, and Southern analysis. The utility of a chloramphenicol resistance gene cassette for targeted gene disruption was demonstrated and found more amenable than kanamycin as a selective marker in S. hyodysenteriae. Immunoblots of cell lysates of the flagellar mutants with antiserum raised against purified FlaA or FlaB confirmed the absence of the corresponding sheath or core protein. Both mutations selectively abolished expression of the targeted gene without affecting synthesis of the other flagellar polypeptide. flaA1 and flaB1 mutant strains exhibited altered motility in vitro and were less efficient in movement through a liquid medium. Paradoxically, isogenic strains containing specifically disrupted flaA1 or flaB1 alleles were capable of assembling periplasmic flagella that were morphologically normal as evidenced by electron microscopy. This is the first report of specific inactivation of a motility-associated gene in spirochetes. PMID:7592350

  10. Student experiences with an international public health exchange project.

    PubMed

    Critchley, Kim A; Richardson, Eileen; Aarts, Clara; Campbell, Barbara; Hemmingway, Ann; Koskinen, Liisa; Mitchell, Maureen P; Nordstrom, Pam

    2009-01-01

    With growing interconnectivity of healthcare systems worldwide and increased immigration, inappropriate cultural and role assumptions are often seen when cultures clash within a country or when there is practice across country boundaries in times of disaster and during international travel. To increase students' multicultural awareness and work experiences abroad, the authors describe a 7-school, 5-country international student exchange project. The authors also share the students' evaluations of their experiences as they are challenged to erase boundaries and embrace nursing across countries. Participating faculty describe the process, challenges, and keys to success found in creating and living this international project. Students involved in the exchange process evaluate the learning opportunities and challenges and the joy of coming together as newfound colleagues and friends. PMID:20339334

  11. The SOLAS air-sea gas exchange experiment (SAGE) 2004

    NASA Astrophysics Data System (ADS)

    Harvey, Mike J.; Law, Cliff S.; Smith, Murray J.; Hall, Julie A.; Abraham, Edward R.; Stevens, Craig L.; Hadfield, Mark G.; Ho, David T.; Ward, Brian; Archer, Stephen D.; Cainey, Jill M.; Currie, Kim I.; Devries, Dawn; Ellwood, Michael J.; Hill, Peter; Jones, Graham B.; Katz, Dave; Kuparinen, Jorma; Macaskill, Burns; Main, William; Marriner, Andrew; McGregor, John; McNeil, Craig; Minnett, Peter J.; Nodder, Scott D.; Peloquin, Jill; Pickmere, Stuart; Pinkerton, Matthew H.; Safi, Karl A.; Thompson, Rona; Walkington, Matthew; Wright, Simon W.; Ziolkowski, Lori A.

    2011-03-01

    The SOLAS air-sea gas exchange experiment (SAGE) was a multiple-objective study investigating gas-transfer processes and the influence of iron fertilisation on biologically driven gas exchange in high-nitrate low-silicic acid low-chlorophyll (HNLSiLC) Sub-Antarctic waters characteristic of the expansive subpolar zone of the southern oceans. This paper provides a general introduction and summary of the main experimental findings. The release site was selected from a pre-voyage desktop study of environmental parameters to be in the south-west Bounty Trough (46.5°S 172.5°E) to the south-east of New Zealand and the experiment was conducted between mid-March and mid-April 2004. In common with other mesoscale iron addition experiments (FeAX's), SAGE was designed as a Lagrangian study, quantifying key biological and physical drivers influencing the air-sea gas exchange processes of CO 2, DMS and other biogenic gases associated with an iron-induced phytoplankton bloom. A dual tracer SF 6/ 3He release enabled quantification of both the lateral evolution of a labelled volume (patch) of ocean and the air-sea tracer exchange at tenths of kilometer scale, in conjunction with the iron fertilisation. Estimates from the dual-tracer experiment found a quadratic dependency of the gas exchange coefficient on windspeed that is widely applicable and describe air-sea gas exchange in strong wind regimes. Within the patch, local and micrometeorological gas exchange process studies (100 m scale) and physical variables such as near-surface turbulence, temperature microstructure at the interface, wave properties and windspeed were quantified to further assist the development of gas exchange models for high-wind environments. There was a significant increase in the photosynthetic competence ( Fv/ Fm) of resident phytoplankton within the first day following iron addition, but in contrast to other FeAX's, rates of net primary production and column-integrated chlorophyll a concentrations had

  12. Interactions between the apolipoprotein E ε4 allele status and adverse childhood experiences on depressive symptoms in older adults

    PubMed Central

    Park, Subin; Nam, Yoon-Young; Sim, Yoojin; Hong, Jin Pyo

    2015-01-01

    Background The influence of childhood adversity on depression is modulated by genetic vulnerability. The apolipoprotein E ε4 (APOE-ε4) allele is a strong genetic risk factor for Alzheimer's disease (AD). Because late-life depressive symptoms could be a part of the preclinical course of AD, the APOE-ε4 allele may contribute to depression in old age. Objective The aim of this study was to evaluate whether an APOE-ε4 carrier status was associated with depressive symptoms in older adults and to detect the gene–environment interaction between APOE-ε4 status and childhood adversity in relation to depressive symptoms in old age. Method The participants consisted of 137 older adults (age range 50–70) without any psychiatric history or clinically significant cognitive impairment. APOE genotypes and measures of childhood adversity and depressive symptoms were obtained. Results There was a significant positive association between adverse childhood experiences (ACE) scores and depressive symptoms (B=0.60; 95% CI=0.26, 0.93 for a 1 score increase in ACE scores; p=0.001). Although APOE-ε4 status per se was not associated with depressive symptoms, there was a significant interaction of the ACE scores with the APOE genotype in relation to depressive symptoms (B=0.78; 95% CI=0.02, 1.55; p=0.044). There was a significantly higher effect of childhood adversity on depressive symptoms in APOE-ε4 carriers than non-carriers (t=2.13, p=0.035). Conclusions Our results suggest that the APOE-ε4 may modulate the association between childhood adversity and depressive symptoms in older adults. However, more research in a larger sample is needed to gain a better understanding of the relationship between the APOE-ε4, childhood adversity, and depression. PMID:25630472

  13. Monitoring hyporheic exchanges during a dam controlled experiment

    NASA Astrophysics Data System (ADS)

    Houzé, Clémence; Varnède, Lucie; Durand, Véronique; Pessel, Marc

    2016-04-01

    Precise understanding of the hyporheic exchanges response to stream flow fluctuations remains a great challenge for many environmental and hydrological problems. Multiplication of natural stream restoration programs and anthropic structures removal highlight that a better understanding of the hydrodynamic and ecological functioning of hyporheic exchanges is critical . The objective of this field experiment was to monitor the dynamic exchanges within the hyporheic zone due to an artificial stream head variation. Various types of measurements were performed, using natural tracers and electrical resistivity tomography (ERT). The dam downstream the studied river reach was successively lowered during two days, and raised during three days, implying river heads variations of about 15cm. The studied area was equipped with CTD probes (measuring the head and the conductivity) within the river, 2 multi-depths water sampling tubes inserted up to one meter depth within the riverbed deposits and 3 ERT profiles with various electrode spacing (20 cm, 25 cm, 50 cm). During the 5 days experiment, water sampling and ERT profiles were done regularly. Estimations of the sediments hydraulic conductivity were obtained by several slug tests in plastic tubes at different depths within the streambed. First results showed that stream fluctuation leads to a rapid hyporheic response according to chloride variations between stream and riverbed sediments. Similar results between geochemical and geophysical tools were found. A decrease in stream head leads to reduce the depth of the mixing zone, as the river gaining conditions intensify. On the contrary, we observed that an increased river head tends to deepen the hyporheic exchange zone.

  14. Harnessing the Internet for International Exchanges on Learning Cities: The Pie Experience 2011-2013

    ERIC Educational Resources Information Center

    Kearns, Peter

    2014-01-01

    The PASCAL International Exchanges (PIE) project was developed to facilitate online exchanges of information and experience between learning cities around the world and, in doing this, to test the potential of the internet to enable such low-cost exchanges. The author provides a personal assessment of the PIE experience over the three years 2011…

  15. Global analysis of Plasmodium falciparum Na(+)/H(+) exchanger (pfnhe-1) allele polymorphism and its usefulness as a marker of in vitro resistance to quinine.

    PubMed

    Ménard, Didier; Andriantsoanirina, Valérie; Khim, Nimol; Ratsimbasoa, Arsène; Witkowski, Benoit; Benedet, Christophe; Canier, Lydie; Mercereau-Puijalon, Odile; Durand, Rémy

    2013-12-01

    The aim of this study was to provide a comprehensive analysis of the worldwide genetic polymorphism of ms4760 alleles of the pfnhe-1 gene and to discuss their usefulness as molecular marker of quinine resistance (QNR). A new numbering of ms4760 allele, classification grouping ms4760 alleles according to the number of DNNND and DDNHNDNHNND repeat motifs in blocks II and V was also proposed. A total of 1508 ms4760 sequences from isolates, culture-adapted parasites or reference strains from various geographical regions were retrieved from GenBank (last update on 15th June 2012) or from publications and were used for genetic analyses. The association of different alleles of pfnhe-1 with resistance to quinoline antimalarial drugs showed marked geographic disparities. The validity and reliability of candidate polymorphisms in pfnhe-1 gene as molecular markers of QNR appeared restricted to endemic areas from South Asia or possibly East African countries and needs to be confirmed. PMID:24533289

  16. Hydrogen isotope exchange experiments with Mt Mazama ash

    NASA Astrophysics Data System (ADS)

    Nolan, G. S.; Bindeman, I. N.; Palandri, J. L.

    2011-12-01

    minor (~20%) hydroxyl loss. 5) Native ash dried to <3% water and ~-145% ∂2H), and reacted with the 650 % prepared water evinces a much higher rate of 2H incorporation compared to rates with the native ash under all the same conditions. Given linearity of ∂2H exchange through time and modeling the reaction as (pseudo) first order in concentration of deuterium yields the following isotopic half life values: for 70° C 1.43 years, for 40° C 4.1 years, and for 25 °C 12.1 years. An Arrhenius treatment yields an activation energy of 32-38 kjoules. 6) A second order kinetic treatment can be used to follow the reaction. A calculation using the reaction constant k at 25 °C assuming native ash exposed to -60 % ∂2H water indicates it would take 2 years to rise from a starting value of -150 to approximately -100 % ∂2H. Results of these experiments put quantitative limits on reliability of ∂2H in ash in paleo-climate studies that are primarily controlled by the isotopic environments and temperatures. We hypothesize that hydrogen-deuterium exchange occurs in native ash exposed to isotopically labeled water. The effect is mediated through surface correlated water in addition to diffusion with both having a rate determining effect. There is nothing to suggest that deuterium-hydrogen exchange is selective for molecular or SiOH hydrogen in the ash.

  17. Measurements for the Jasper Program intermediate heat exchanger experiment

    SciTech Connect

    Muchkenthaler, F.J.; Spencer, R.R.; Hunter, H.T.; Hull, J.L.; Shono, A.

    1992-07-01

    The Intermediate Heat Exchanger (IHX) experiment was conducted at the Oak Ridge National Laboratory (ORNL) Tower shielding Facility (TSF) during the last three months of 1991 and the first two months of 1992 as part of a continuing series of eight experiments planned for the Japanese-American shielding Program for Experimental Research (JASPER) program that was started in 1986. This is the fifth experiment in that series, all of which are intended to provide support in the development of current reactor shield designs proposed for liquid metal reactor (LMR) systems both in Japan and the United States. The program is a cooperative effort between the United States Department of Energy (US DOE) and the japanese Power Reactor and Nuclear Development Corporation (PNC). The experimental configurations consisted of a neutron spectrum modifier followed by various shield mockups. For the PNC portion of the program the modifier was a large volume of sodium typical of the area in which their IHX vessel would be located radially from the reactor core. configurations studied in the US part of the program were preceded by the same modifier of iron, aluminum, boral, and sodium used with the Advanced Liquid Metal Reactor (ALMR) mockups in the previous In- Vessel Fuel Storage (IVFS) experiment. This modifier was followed by mockups representative of three different off-axial locations that were being considered for placement of the IHX vessel. The PNC plan was concerned with the effort of surrounding a mockup of the sodium containing IHX vessel by a partial or full component boron carbide (B{sub 4}C) shield.

  18. Achieving Maximal Speed of Solution Exchange for Patch Clamp Experiments

    PubMed Central

    Auzmendi, Jerónimo; Fernández Do Porto, Darío; Pallavicini, Carla; Moffatt, Luciano

    2012-01-01

    Background Resolving the kinetics of agonist binding events separately from the subsequent channel gating processes requires the ability of applying and removing the agonist before channel gating occurs. No reported system has yet achieved pulses shorter than 100 µs, necessary to study nicotinic ACh receptor or AMPA receptor activation. Methodology/Principal Findings Solution exchange systems deliver short agonist pulses by moving a sharp interface between a control and an experimental solution across a channel preparation. We achieved shorter pulses by means of an exchange system that combines a faster flow velocity, narrower partition between the two streams, and increased velocity and bandwidth of the movement of the interface. The measured response of the entire system was fed back to optimize the voltage signal applied to the piezoelectric actuator overcoming the spurious oscillations arising from the mechanical resonances when a high bandwidth driving function was applied. Optimization was accomplished by analyzing the transfer function of the solution exchange system. When driven by optimized command pulses the enhanced system provided pulses lasting 26 ± 1 µs and exchanging 93 ± 1% of the solution, as measured in the open tip of a patch pipette. Conclusions/Significance Pulses of this duration open the experimental study of the molecular events that occur between the agonist binding and the opening of the channel. PMID:22879927

  19. EXCHANGE

    SciTech Connect

    Boltz, J.C.

    1992-09-01

    EXCHANGE is published monthly by the Idaho National Engineering Laboratory (INEL), a multidisciplinary facility operated for the US Department of Energy (DOE). The purpose of EXCHANGE is to inform computer users about about recent changes and innovations in both the mainframe and personal computer environments and how these changes can affect work being performed at DOE facilities.

  20. Cloning and genetic characterization of the Helicobacter pylori and Helicobacter mustelae flaB flagellin genes and construction of H. pylori flaA- and flaB-negative mutants by electroporation-mediated allelic exchange.

    PubMed Central

    Suerbaum, S; Josenhans, C; Labigne, A

    1993-01-01

    Helicobacter pylori is one of the most common human pathogens. It causes chronic gastritis and is involved in the pathogenesis of gastroduodenal ulcer disease and possibly gastric carcinoma. Helicobacter mustelae is a bacterium closely related to H. pylori that causes gastritis and ulcer disease in ferrets and is therefore considered an important animal model of gastric Helicobacter infections. Motility, even in a viscous environment, is conferred to the bacteria by several sheathed flagella and is regarded as one of their principal virulence factors. The flagellar filament of H. pylori consists of two different flagellin species expressed in different amounts. The gene (flaA) encoding the major flagellin has recently been cloned and sequenced. Here we report the cloning and sequencing of two highly homologous new flagellin genes from H. pylori 85P and H. mustelae NCTC 12032. The nucleotide sequence of the H. pylori gene proved that it encoded the second flagellin molecule found in H. pylori flagellar filaments. The genes were named flaB. The H. mustelae and H. pylori flaB genes both coded for proteins with 514 amino acids and molecular masses of 54.0 and 53.9 kDa, respectively. The proteins shared 81.7% identical amino acids. The degree of conservation between H. pylori FlaB and the H. pylori FlaA major flagellin was much lower (58%). Both flaB genes were preceded by sigma 54-like promoter sequences. Mapping of the transcription start site for the H. pylori flaB gene by a primer extension experiment confirmed the functional activity of the sigma 54 promoter. To evaluate the importance of both genes for motility, flaA- and flaB-disrupted mutants of H. pylori N6 were constructed by electroporation-mediated allelic exchange and characterized by Western blot (immunoblot) analysis and motility testing. Both mutations selectively abolished the expression of the targeted gene without affecting the synthesis of the other flagellin molecule. Whereas flaA mutants were

  1. Acculturation Experiences of Taiwanese Students during Exchanges in the United States

    ERIC Educational Resources Information Center

    Lee, Annie (Ya-Ping); Bei, Lienti; DeVaney, Sharon A.

    2007-01-01

    This phenomenological study examined the acculturation experience of Taiwanese students who attended universities in the United States as exchange students. Hofstede's four dimensions of culture provided a framework for developing questions. Eight exchange students were interviewed. Taiwanese students realized there was a lower power distance…

  2. Academic and Social Experiences of Exchange Students from Japan Attending an American University

    ERIC Educational Resources Information Center

    Sato, Takahiro; Hodge, Samuel R.

    2015-01-01

    The purpose of this study was to identify and analyze the views of exchange students from Japan about their sojourn experiences at an American university. The participants were eight exchange students from Japan (four males and four females). This descriptive-qualitative study was conceptualized within sojourner theory (Siu, 1952). The data…

  3. NASA's experience in the international exchange of scientific and technical information in the aerospace field

    NASA Technical Reports Server (NTRS)

    Thibideau, Philip A.

    1990-01-01

    The early NASA international scientific and technical information exchange arrangements were usually detailed in correspondence with the librarians of the institutions involved. While this type of exchange grew to include some 200 organizations in 43 countries, NASA's main focus shifted to the relationship with the European Space Agency (ESA), which began in 1964. The NASA/ESA Tripartite Exchange Program provides more than 4000 technical reports from the NASA-produced Aerospace Database. The experience in the evolving cooperation between NASA and ESA has established the model for more recent exchange agreements with Israel, Australia, and Canada. The results of these agreements are made available to participating European organizations through the NASA File.

  4. Residue-specific NH exchange rates studied by NMR diffusion experiments

    NASA Astrophysics Data System (ADS)

    Brand, Torsten; Cabrita, Eurico J.; Morris, Gareth A.; Günther, Robert; Hofmann, Hans-Jörg; Berger, Stefan

    2007-07-01

    We present a novel approach to the investigation of rapid (>2 s -1) NH exchange rates in proteins, based on residue-specific diffusion measurements. 1H, 15N-DOSY-HSQC spectra are recorded in order to observe resolved amide proton signals for most residues of the protein. Human ubiquitin was used to demonstrate the proposed method. Exchange rates are derived directly from the decay data of the diffusion experiment by applying a model deduced from the assumption of a two-site exchange with water and the "pure" diffusion coefficients of water and protein. The "pure" diffusion coefficient of the protein is determined in an experiment with selective excitation of the amide protons in order to suppress the influence of magnetization transfer from water to amide protons on the decay data. For rapidly exchanging residues a comparison of our results with the exchange rates obtained in a MEXICO experiment showed good agreement. Molecular dynamics (MD) and quantum mechanical calculations were performed to find molecular parameters correlating with the exchangeability of the NH protons. The RMS fluctuations of the amide protons, obtained from the MD simulations, together with the NH coupling constants provide a bilinear model which shows a good correlation with the experimental NH exchange rates.

  5. Exchange transfusion in severe hyperbilirubinemia: an experience in northwest Iran.

    PubMed

    Hosseinpour Sakha, Seddigheh; Gharehbaghi, Manizheh Mostafa

    2010-01-01

    Our goal was to determine the indications for exchange transfusion (ECT) and the rates of ECT-related adverse events in neonatal hyperbilirubinemia. We reviewed retrospectively the medical charts of all newborns that had undergone ECT over three years from January 2006 to December 2008. Causes of jaundice, demographic data of the patients, and details of ECT and ECT-related adverse events were recorded. A total of 176 ECT procedures were performed in 150 neonates in the three-year study period. The mean total serum bilirubin before ECT was 29.59 +/- 6.88 mg/dl. Those infants requiring more than one ECT had higher total serum bilirubin than neonates with single ECT, but the difference was not significant (35.66 +/- 12.21 vs. 29.12 +/- 6.30 mg/dl, p = 0.09). The most common cause of ECT was ABO incompatibility (49.3%), Rh disease (7.3%) and idiopathic (28%). Among the adverse events related to ECT, thrombocytopenia (36.4%), hypocalcemia (25.5%), apnea (20%), and infection (10.9%) were noted commonly. No case of ECT-related mortality was observed. All of the adverse events resolved completely before discharge. ABO isoimmunization was the most common cause of ECT in this study. The majority of adverse events associated with ECT are asymptomatic and reversible. PMID:21043381

  6. A Classroom Experiment on Exchange Rate Determination with Purchasing Power Parity

    ERIC Educational Resources Information Center

    Mitchell, David T.; Rebelein, Robert P.; Schneider, Patricia H.; Simpson, Nicole B.; Fisher, Eric

    2009-01-01

    The authors developed a classroom experiment on exchange rate determination appropriate for undergraduate courses in macroeconomics and international economics. In the experiment, students represent citizens from different countries and need to obtain currency to purchase goods. By participating in an auction to buy currency, students gain a…

  7. The International Association for the Exchange of Students for Technical Experience. 34th Annual Report 1981.

    ERIC Educational Resources Information Center

    International Association for the Exchange of Students for Technical Experience/United States, Columbia, MD.

    The 1981 annual report of the International Association for the Exchange of Students for Technical Experience (IAESTE) is presented. IAESTE seeks to provide students at institutions of higher education with technical experience abroad relative to their studies and to promote international understanding among all students. An international report…

  8. The use of ion exchange membranes for isotope analyses on soil water sulfate: laboratory experiments.

    PubMed

    Kwon, Jang-Soon; Mayer, Bernhard; Yun, Seong-Taek; Nightingale, Michael

    2008-01-01

    To investigate the potential use of anion exchange membranes (plant root simulator [PRS] probes) for isotope investigations of the soil sulfur cycle, laboratory experiments were performed to examine the sulfate exchange characteristics and to determine the extent of sulfur and oxygen isotope fractionation during sulfate sorption and desorption on the probes in aqueous solutions and simulated soil solutions. The sulfate-exchange tests in aqueous solutions under varying experimental conditions indicated that the amount of sulfate exchanged onto PRS probes increased with increasing reaction time, initial sulfate concentration, and the number of probes used (= surface area), whereas the percentage of removal of available sulfate was constant irrespective of the initial sulfate concentration. The competition of nitrate and chloride in the solution lowered the amount of exchanged sulfate. The exchange experiments in a simulated soil under water-saturated and water-unsaturated conditions showed that a considerable proportion of the soil sulfate was exchanged by the PRS probes after about 10 d. There was no evidence for significant sulfur and oxygen isotope fractionation between soil sulfate and sulfate recovered from the PRS probes. Therefore, we recommend the use of PRS probes as an efficient and easy way to collect soil water sulfate for determination of its isotope composition. PMID:18268314

  9. Materials experience and selection for nuclear materials production reactor heat exchangers

    SciTech Connect

    Marra, J.E.; Louthan, M.R. Jr.

    1990-01-01

    The primary coolant systems for the heavy-water nuclear materials production reactors at the Savannah River Site are coupled to the secondary coolant systems through shell and tube heat exchangers. The head, shell, and tube sheets of these heat exchangers are fabricated from AISI Type 304 grades of austenitic stainless steel. The 8,957 tubes in each heat exchanger were originally fabricated from Type 304 stainless steel, but service experience has lead to the use of Sea Cure tubing in newer systems. The design includes double tube sheets, core rods, and 33,410 square feet of heat transfer surface. Tubes are rolled into the tube sheets and seal welded after rolling. The tubes contain Type 304 stainless steel rods which are positioned in the center of each tube axis to increase the fraction of the cooling water contacting the heat transfer surface. Each reactor utilizes twelve heat exchangers; thus the 120+ reactor-years of operating experience provide approximately 1,440 heat exchanger-years of service. Fatigue, stress corrosion cracking, crevice corrosion, and pitting have been observed during the service life. This paper describes the observed degradation processes and uses the operational experience to recommend materials for the Heavy Water -- New Production Reactor (HW-NPR).

  10. The International Association for the Exchange of Students for Technical Experience. 32nd Annual Report 1979.

    ERIC Educational Resources Information Center

    International Association for the Exchange of Students for Technical Experience/United States, Columbia, MD.

    After a general outline of the organization of the International Association for the Exchange of Students for Technical Experience and a brief introduction to its functions and activities, this annual report contains the international report. This includes: the report of the General Secretary; a list of international visits and visitors; publicity…

  11. EPR Studies of Spin-Spin Exchange Processes: A Physical Chemistry Experiment.

    ERIC Educational Resources Information Center

    Eastman, Michael P.

    1982-01-01

    Theoretical background, experimental procedures, and analysis of experimental results are provided for an undergraduate physical chemistry experiment on electron paramagnetic resonance (EPR) linewidths. Source of line broadening observed in a spin-spin exchange process between radicals formed in aqueous solutions of potassium peroxylamine…

  12. International Exchange with a Disability: Enhancing Experiences Abroad through Advising and Mentoring (Practice Brief)

    ERIC Educational Resources Information Center

    Holben, Ashley; Özel, Claire

    2015-01-01

    Through interaction with an advisor or peer mentor and through exposure to the experiences of role models, students with disabilities gain an appreciation of the potential challenges and benefits of international exchange and make informed choices about whether, where, and how to go abroad. By adopting strategies for inclusive advising and role…

  13. Two dimensional exchange NMR experiments of natural porous media with portable Halbach-Magnets

    NASA Astrophysics Data System (ADS)

    Haber, Agnes; Haber-Pohlmeier, Sabina; Casanova, Federico; Blümich, Bernhard

    2010-05-01

    The characterization of pore space and connectivity in soils of different textures is one topic within Cluster A, Partial Project A1. For this purpose low field mobile NMR became a powerful tool following the development of portable NMR sensors for well logging. By now there are numerous applications of mobile NMR in materials analysis and chemical engineering where, for example, unique information about the structure, morphology and dynamics of polymers is obtained, and new opportunities are provided for geophysical investigations [1]. In particular, dynamic information can be retrieved by two-dimensional Laplace exchange NMR, where the initial NMR relaxation environment is correlated with the final relaxation environment of molecules migrating from one environment to the other within a so-called NMR mixing time tm [2]. Relaxation-relaxation exchange experiments were performed with saturated and un-saturated soil samples at low and moderately inhomogeneous magnetic field with a simple, portable Halbach-Magnet. By conducting NMR transverse relaxation exchange experiments for several mixing times and inverting the results to 2D T2 distributions (similar to joint probability densities of transverse relaxation times T2) with the help of inverse 2D Laplace Transformation (ILT), we observed characteristic exchange processes: Soils consisting mainly of silt and clay components show predominantly exchange between the smaller pores at mixing times of some milliseconds. In addition, there exists also weaker exchange with the larger pores observable for longer mixing time. In contrast to that fine sand exhibits 2D T2 distributions with no exchange processes which can be interpreted that water molecules move within pores of the same size class. These results will be compared to the exchange behaviour under unsaturated conditions. References: 1. B. Blümich, J. Mauler, A. Haber, J. Perlo, E. Danieli, F. Casanova, Mobile NMR for geophysical analysis and material testing

  14. Relaxation-relaxation exchange experiments in porous media with portable Halbach-Magnets.

    NASA Astrophysics Data System (ADS)

    Haber, A.; Haber-Pohlmeier, S.; Casanova, F.; Blümich, B.

    2009-04-01

    Mobile NMR became a powerful tool following the development of portable NMR sensors for well logging. By now there are numerous applications of mobile NMR in materials analysis and chemical engineering where, for example, unique information about the structure, morphology and dynamics of polymers is obtained, and new opportunities are provided for geo-physical investigations [1]. In particular, dynamic information can be retrieved by two-dimensional Laplace exchange NMR, where the initial NMR relaxation environment is correlated with the final relaxation environment of molecules migrating from one environment to the other within a so-called NMR mixing time tm [2]. Relaxation-relaxation exchange experiments of water in inorganic porous media were performed at low and moderately inhomogeneous magnetic field with a simple, portable Halbach-Magnet. By conducting NMR transverse relaxation exchange experiments for several mixing times and converting the results to 2D T2 distributions (joint probability densities of transverse relaxation times T2) with the help of the inverse 2D Laplace Transformation (ILT), we obtained characteristic exchange times for different pore sizes. The results of first experiments on soil samples are reported, which reveal information about the complex pore structure of soil and the moisture content. References: 1. B. Blümich, J. Mauler, A. Haber, J. Perlo, E. Danieli, F. Casanova, Mobile NMR for Geo-Physical Analysis and Material Testing, Petroleum Science, xx (2009) xxx - xxx. 2. K. E. Washburn, P.T. Callaghan, Tracking pore to pore exchange using relaxation exchange spectroscopy, Phys. Rev. Lett. 97 (2006) 175502.

  15. Cesium migration in Hanford sediment: a multisite cation exchange model based on laboratory transport experiments

    NASA Astrophysics Data System (ADS)

    Steefel, Carl I.; Carroll, Susan; Zhao, Pihong; Roberts, Sarah

    2003-12-01

    Cs + transport experiments carried out in columns packed with uncontaminated Hanford formation sediment from the SX tank farm provide strong support for the use of a multisite, multicomponent cation exchange model to describe Cs + migration in the Hanford vadose zone. The experimental results indicate a strong dependence of the effective Cs +Kd on the concentrations of other cations, including Na + that is present at high to extremely high concentrations in fluids leaking from the Hanford SX tanks. A strong dependence of the Cs +Kd on the aqueous Cs + concentration is also apparent, with retardation of Cs + increasing from a value of 41 at a Cs + concentration of 10 -4 M in the feed solution to as much as 282 at a Cs + concentration of 5×10 -7 M, all in a background of 1 M NaNO 3. The total cation exchange capacity (CEC) of the Hanford sediment was determined using 22Na isotopic equilibrium exchange in a flow-through column experiment. The value for the CEC of 120 μeq/g determined with this method is compatible with a value of 121.9 μeq/g determined by multi-cation elution. While two distinct exchange sites were proposed by Zachara et al. [Geochim. Cosmochim. Acta 66 (2002) 193] based on binary batch exchange experiments, a third site is proposed in this study to improve the fit of the Cs +-Na + and Cs +-Ca + exchange data and to capture self-sharpened Cs + breakthrough curves at low concentrations of Cs +. Two of the proposed exchange sites represent frayed edge sites (FES) on weathered micas and constitute 0.02% and 0.22% of the total CEC. Both of the FES show a very strong selectivity for Cs + over Na + ( KNa-Cs=10 7.22 and 10 4.93, respectively). The third site, accounting for over 99% of the total CEC, is associated with planar sites on expansible clays and shows a smaller Na +-Cs + selectivity coefficient of 10 1.99. Parameters derived from a fit of binary batch experiments alone tend to under predict Cs + retardation in the column experiments. The

  16. Cesium migration in Hanford sediment: a multisite cation exchange model based on laboratory transport experiments.

    PubMed

    Steefel, Carl I; Carroll, Susan; Zhao, Pihong; Roberts, Sarah

    2003-12-01

    Cs+ transport experiments carried out in columns packed with uncontaminated Hanford formation sediment from the SX tank farm provide strong support for the use of a multisite, multicomponent cation exchange model to describe Cs+ migration in the Hanford vadose zone. The experimental results indicate a strong dependence of the effective Cs+ Kd on the concentrations of other cations, including Na+ that is present at high to extremely high concentrations in fluids leaking from the Hanford SX tanks. A strong dependence of the Cs+ Kd on the aqueous Cs+ concentration is also apparent, with retardation of Cs+ increasing from a value of 41 at a Cs+ concentration of 10(-4) M in the feed solution to as much as 282 at a Cs+ concentration of 5x10(-7) M, all in a background of 1 M NaNO3. The total cation exchange capacity (CEC) of the Hanford sediment was determined using 22Na isotopic equilibrium exchange in a flow-through column experiment. The value for the CEC of 120 microeq/g determined with this method is compatible with a value of 121.9 microeq/g determined by multi-cation elution. While two distinct exchange sites were proposed by Zachara et al. [Geochim. Cosmochim. Acta 66 (2002) 193] based on binary batch exchange experiments, a third site is proposed in this study to improve the fit of the Cs+-Na+ and Cs+-Ca+ exchange data and to capture self-sharpened Cs+ breakthrough curves at low concentrations of Cs+. Two of the proposed exchange sites represent frayed edge sites (FES) on weathered micas and constitute 0.02% and 0.22% of the total CEC. Both of the FES show a very strong selectivity for Cs+ over Na+ (K(Na-Cs)=10(7.22) and 10(4.93), respectively). The third site, accounting for over 99% of the total CEC, is associated with planar sites on expansible clays and shows a smaller Na+-Cs+ selectivity coefficient of 10(1.99). Parameters derived from a fit of binary batch experiments alone tend to under predict Cs+ retardation in the column experiments. The transport

  17. Charge exchange contamination of CRIT-II barium CIV experiment. [critical ionization velocity in ionosphere

    NASA Technical Reports Server (NTRS)

    Swenson, G. R.; Mende, S. B.; Meyerott, R. E.; Rairden, R. L.

    1991-01-01

    Experiments have been recently performed which attempted to confirm critical ionization velocity (CIV) ionization by deploying chemicals at high velocity in the ionosphere. Specifically, the CRIT-II rocket performed a barium release in the ionosphere, where observations of Ba(+) resonant emissions following the release are believed to have resulted from the CIV process. Calculations are presented which suggest a significant fraction (if not all) of the Ba(+) observed likely resulted from charge exchange with the thermosphere ions and not through CIV processes. The results presented here are pertinent to other CIV experiments performed in the ionosphere. It is recommended that laboratory measurements should be made of the charge exchange cross section between O(+) and Ba as well as other metal vapors used in CIV experiments.

  18. Standardization of XML Database Exchanges and the James Webb Space Telescope Experience

    NASA Technical Reports Server (NTRS)

    Gal-Edd, Jonathan; Detter, Ryan; Jones, Ron; Fatig, Curtis C.

    2007-01-01

    Personnel from the National Aeronautics and Space Administration (NASA) James Webb Space Telescope (JWST) Project have been working with various standard communities such the Object Management Group (OMG) and the Consultative Committee for Space Data Systems (CCSDS) to assist in the definition of a common extensible Markup Language (XML) for database exchange format. The CCSDS and OMG standards are intended for the exchange of core command and telemetry information, not for all database information needed to exercise a NASA space mission. The mission-specific database, containing all the information needed for a space mission, is translated from/to the standard using a translator. The standard is meant to provide a system that encompasses 90% of the information needed for command and telemetry processing. This paper will discuss standardization of the XML database exchange format, tools used, and the JWST experience, as well as future work with XML standard groups both commercial and government.

  19. Experiments probing the influence of air exchange rates on secondary organic aerosols derived from indoor chemistry

    NASA Astrophysics Data System (ADS)

    Weschler, Charles J.; Shields, Helen C.

    Reactions between ozone and terpenes have been shown to increase the concentrations of submicron particles in indoor settings. The present study was designed to examine the influence of air exchange rates on the concentrations of these secondary organic aerosols as well as on the evolution of their particle size distributions. The experiments were performed in a manipulated office setting containing a constant source of d-limonene and an ozone generator that was remotely turned "on" or "off" at 6 h intervals. The particle number concentrations were monitored using an optical particle counter with eight-channels ranging from 0.1-0.2 to>2.0 μm diameter. The air exchange rates during the experiments were either high (working hours) or low (non-working hours) and ranged from 1.6 to>12 h -1, with intermediate exchange rates. Given the emission rates of ozone and d-limonene used in these studies, at an air exchange rate of 1.6 h -1 particle number concentration in the 0.1-0.2 μm size-range peaked 1.2 h after the ozone generator was switched on. In the ensuing 4.8 h particle counts increased in successive size-ranges up to the 0.5-0.7 μm diameter range. At higher air exchange rates, the resulting concentrations of total particles and particle mass (calculated from particle counts) were smaller, and at exchange rates exceeding 12 h -1, no excess particle formation was detectable with the instrument used in this study. Particle size evolved through accretion and, in some cases, coagulation. There was evidence for coagulation among particles in the smallest size-range at low air exchange rates (high particle concentrations) but no evidence of coagulation was apparent at higher air exchange rates (lower particle concentrations). At higher air exchange rates the particle count or size distributions were shifted towards smaller particle diameters and less time was required to achieve the maximum concentration in each of the size-ranges where discernable particle growth

  20. Review of Current Experience on Intermediate Heat Exchanger (IHX) and A Recommended Code Approach

    SciTech Connect

    Duane Spencer; Kevin McCoy

    2010-02-02

    The purpose of the ASME/DOE Gen IV Task 7 Part I is to review the current experience on various high temperature reactor intermediate heat exchanger (IHX) concepts. There are several different IHX concepts that could be envisioned for HTR/VHTR applications in a range of temperature from 850C to 950C. The concepts that will be primarily discussed herein are: (1) Tubular Helical Coil Heat Exchanger (THCHE); (2) Plate-Stamped Heat Exchanger (PSHE); (3) Plate-Fin Heat Exchanger (PFHE); and (4) Plate-Machined Heat Exchanger (PMHE). The primary coolant of the NGNP is potentially subject to radioactive contamination by the core as well as contamination from the secondary loop fluid. To isolate the radioactivity to minimize radiation doses to personnel, and protect the primary circuit from contamination, intermediate heat exchangers (IHXs) have been proposed as a means for separating the primary circuit of the NGNP (Next Generation Nuclear Plant) or other process heat application from the remainder of the plant. This task will first review the different concepts of IHX that could be envisioned for HTR/VHTR applications in a range of temperature from 850 to 950 C. This will cover shell-and-tube and compact designs (including the platefin concept). The review will then discuss the maturity of the concepts in terms of design, fabricability and component testing (or feedback from experience when applicable). Particular attention will be paid to the feasibility of developing the IHX concepts for the NGNP with operation expected in 2018-2021. This report will also discuss material candidates for IHX applications and will discuss specific issues that will have to be addressed in the context of the HTR design (thermal aging, corrosion, creep, creep-fatigue, etc). Particular attention will be paid to specific issues associated with operation at the upper end of the creep regime.

  1. Nested heat tracer experiments for identifying heterogeneity of aquifer-river exchange at multiple scales

    NASA Astrophysics Data System (ADS)

    Krause, Stefan; Hannah, David; Blume, Theresa; Angermann, Lisa; Lewandowski, Joerg; Cassidy, Nigel

    2016-04-01

    This study presents the nested application of three heat tracing methods for identifying aquifer-river exchange fluxes at multiple scales ranging from centimeter to stream reach-scale. The investigations focus on a UK lowland river where hotspots of redox-reactivity were found to coincide with locations of increased streambed residence times underneath flow confining streambed peat and clay structures. In order to identify the spatial extend and patterns of reactivity hot spots associated with these streambed structures, reach-scale patterns of aquifer-river exchange fluxes have been analysed by Fibre-Optic Distributed Temperature Sensing (FO-DTS) along a cable buried in the streambed of a 250 m reach in combination with 2D thermocouple arrays in a 12 m long pool-riffle-pool sequence and small-scale heat pulse injections for tracing shallow hyporheic flow paths within the uppermost 20cm streambed sediments. FO-DTS observed streambed temperature anomalies caused by the mixing of different temperatures of GW and SW end-members were used to infer information on exchange fluxes at the aquifer-river interface. FO-DTS survey results indicate that patterns of up to 2C colder (Summer) and 3.5C warmer (Winter) temperatures in investigated streambed sediments can be attributed to fast GW up-welling in sandy and gravely sediments. Contrasting conditions were found at locations where streambed temperatures equal SW temperatures and GW-SW exchange was inhibited by the existence of peat or clay lenses within the streambed. FO-DTS observations of regional GW up-welling patterns were complemented by heat pulse injection experiments which provided essential information of the shallow aquifer- river exchange fluxes and confirmed increased SW infiltration and lateral flow in riffle crests and at locations with highly conductive streambed sediments above flow confining low conductivity structures. The propagation of diurnal temperature oscillations from the surface to streambed depths

  2. Nested heat tracer experiments for identifying heterogeneity of aquifer-river exchange at multiple scales

    NASA Astrophysics Data System (ADS)

    Krause, S.; Hannah, D. M.; Blume, T.; Angermann, L.; Lewandowski, J.; Cassidy, N. J.

    2012-04-01

    This study presents the nested application of three heat tracing methods for identifying aquifer-river exchange fluxes at multiple scales ranging from centimeter to stream reach-scale. The investigations focus on a UK lowland river where hotspots of redox-reactivity were found to coincide with locations of increased streambed residence times underneath flow confining streambed peat and clay structures. In order to identify the spatial extend and patterns of reactivity hot spots associated with these streambed structures, reach-scale patterns of aquifer-river exchange fluxes have been analysed by Fibre-Optic Distributed Temperature Sensing (FO-DTS) along a cable buried in the streambed of a 250 m reach in combination with 2D thermocouple arrays in a 12 m long pool-riffle-pool sequence and small-scale heat pulse injections for tracing shallow hyporheic flow paths within the uppermost 20cm streambed sediments. FO-DTS observed streambed temperature anomalies caused by the mixing of different temperatures of GW and SW end-members were used to infer information on exchange fluxes at the aquifer-river interface. FO-DTS survey results indicate that patterns of up to 2C colder (Summer) and 3.5C warmer (Winter) temperatures in investigated streambed sediments can be attributed to fast GW up-welling in sandy and gravely sediments. Contrasting conditions were found at locations where streambed temperatures equal SW temperatures and GW-SW exchange was inhibited by the existence of peat or clay lenses within the streambed. FO-DTS observations of regional GW up-welling patterns were complemented by heat pulse injection experiments which provided essential information of the shallow aquifer- river exchange fluxes and confirmed increased SW infiltration and lateral flow in riffle crests and at locations with highly conductive streambed sediments above flow confining low conductivity structures. The propagation of diurnal temperature oscillations from the surface to streambed depths

  3. Effect of diffusion potential, osmosis and ion-exchange on transdermal drug delivery: theory and experiments.

    PubMed

    Hirvonen, J; Murtomäki, L; Kontturi, K

    1998-12-01

    Equations expressing the effect of the diffusion potential on the trace ion transfer across a porous charged membrane have been derived. These equations have been tested with experiments with human cadaver skin. The transfer of sotalol and salicylate was measured varying the salt (NaCl) concentration in the donor and receiver compartments. It appears that osmotic pressure and ion-exchange make a significant contribution to the flux enhancement by the diffusion potential. PMID:9801427

  4. Uncertainties in gas exchange parameterization during the SAGE dual-tracer experiment

    NASA Astrophysics Data System (ADS)

    Smith, Murray J.; Ho, David T.; Law, Cliff S.; McGregor, John; Popinet, Stéphane; Schlosser, Peter

    2011-03-01

    A dual tracer experiment was carried out during the SAGE experiment using the inert tracers SF 6 and 3He, in order to determine the gas transfer velocity, k, at high wind speeds in the Southern Ocean. Wind speed/gas exchange parameterization is characterised by significant variability and we examine the major measurement uncertainties that contribute to that scatter. Correction for the airflow distortion over the research vessel, as determined by computational fluid dynamics (CFD) modelling, had the effect of increasing the calculated value of k by 30%. On the short time scales of such experiments, the spatial variability of the wind field resulted in differences between ship and satellite QuikSCAT winds, which produced significant differences in transfer velocity. With such variability between wind estimates, the comparison between gas exchange parameterizations from diverse experiments should clearly be made on the basis of the same wind product. Uncertainty in mixed layer depth of ˜10% arose from mixed layer deepening at high wind speed and limited resolution of vertical sampling. However the assumption of equal mixing of the two tracers is borne out by the experiment. Two dual tracer releases were carried out during SAGE, and showed no significant difference in transfer velocities using QuikSCAT winds, despite the differences in wind history. In the SAGE experiment, duration limitation on the development of waves was shown to be an important factor for Southern Ocean waves, despite the presence of long fetches.

  5. Perspectives of an interdisciplinaryg research team to engage practice: lessons from a knowledge exchange trainee experience.

    PubMed

    Urquhart, Robin L; Johnston, Grace M; McVorran, Shauna M; Burge, Fred I

    2010-05-01

    End-of-life (EOL) care is an area of health services that will ultimately affect us all. To share the knowledge emerging from EOL research and to address inequities in the quality of EOL care in Nova Scotia, a knowledge exchange (KE) trainee was hired to translate research and surveillance into a Surveillance Report. The purpose of this paper is to reflect upon this initiative and share the research team's perspectives on their KE experiences. We describe four key competencies of the KE trainee selected, and discuss lessons learned from this KE trainee experience, to expand our understanding of KE. PMID:21532769

  6. Preliminary findings of the Viking gas exchange experiment and a model for Martian surface chemistry

    NASA Technical Reports Server (NTRS)

    Oyama, V. I.; Berdahl, B. J.; Carle, G. C.

    1977-01-01

    Earlier results reported from the Viking Lander-1 experiment are reexamined and interpreted in terms of a model of the Martian soil surface morphology and chemistry. Major events in the gas exchange experiment (GEX) first cycle are tabulated and data are presented on the sample processing and transport environments experienced by the soil samples. Oxygen and CO2 evolved from humidified Martian soil in GEX and slight changes in N2 present are investigated. A soil model involving iron oxide coating on silicate material is entertained to yield a mechanistic explanation of the experimental findings, and invocation of biotic processes is eschewed.

  7. The Gas Exchange Experiment for life detection - The Viking Mars Lander.

    NASA Technical Reports Server (NTRS)

    Oyama, V. I.

    1972-01-01

    The Gas Exchange Experiment of the Viking mission accepts a sample of Martian soil, incubates this soil with nutrient medium, and periodically samples the enclosed atmosphere over this soil for the gases H2, N2, O2, Kr, and CO2. These gases are analyzed by an automated gas chromatograph, and the data are transmitted to earth. The design of the experiment and the qualitative and quantitative changes, if any, of gas composition should allow conclusions to be made on the presence of life on Mars. Data and theory substantiating this approach are presented.

  8. NASA's experience in the international exchange of scientific and technical information in the aerospace field

    NASA Technical Reports Server (NTRS)

    Thibideau, Philip A.

    1989-01-01

    The early NASA international scientific and technical information (STI) exchange arrangements were usually detailed in correspondence with the librarians of the institutions involved. While this type of exchange, which involved only hardcopy (paper) products, grew to include some 220 organization in 43 countries, NASA's main focus shifted substantially to the STI relationship with the European Space Agency (ESA) which began in 1964. The NASA/ESA Tripartite Exchange Program, which now has more than 500 participants, provides more than 4,000 highly-relevant technical reports, fully processed, for the NASA produced 'Aerospace Database'. In turn, NASA provides an updated copy of this Database, known in Europe as the 'NASA File', for access, through ESA's Information Retrieval Service, by participating European organizations. Our experience in the evolving cooperation with ESA has established the 'model' for our more recent exchange agreements with Israel, Australia, Canada, and one under negotiation with Japan. The results of these agreements are made available to participating European organizations through the NASA File.

  9. Correlation between JAK2 allele burden and pulmonary arterial hypertension and hematological parameters in Philadelphia negative JAK2 positive myeloproliferative neoplasms. An Egyptian experience.

    PubMed

    Mattar, Mervat M; Morad, Mohammed Abdel Kader; El Husseiny, Noha M; Ali, Noha H; El Demerdash, Doaa M

    2016-10-01

    Myeloproliferative neoplasms are characterized by a common stem cell-derived clonal proliferation, but are phenotypically diverse. JAK2 is mutated (V617F) in more than 90 % of patients with polycythemia vera (PV) and approximately 60 % of patients with essential thrombocythemia (ET) or primary myelofibrosis (PMF). Pulmonary arterial hypertension (PAH) is a major complication of several hematological disorders. Chronic myeloproliferative disorders associated with PAH have been included in group five for which the etiology is unclear and/or multifactorial. The aim of this study is to screen Egyptian Philadelphia negative JAK2 positive myeloproliferative neoplasm patients for the presence of PAH and its correlation with JAK2 allele burden. We also made a review for correlation of JAK2 allele with hematological parameters comparing our results to others. We enrolled 60 patients with Philadelphia negative myeloproliferative neoplasms. All patients enrolled in the study were subjected to laboratory and imaging workup in the form of CBC, liver, kidney profile, bone marrow examination, abdominal ultrasonography, and transthoracic echocardiography. Our results revealed that 7 patients out of 60 (11.67 %) had pulmonary arterial hypertension, 3 patients with PMF, 2 patients with PRV, and 2 patients with ET, and its correlation with JAK2 allele burden was not statistically significant. Correlation analysis between JAK2 V617F allele burden and other parameters revealed: statistical significant correlation with age, HB, HCT, PLT, UA, LDH, and splenic diameter but insignificant correlation with WBCs and PAH. Pulmonary arterial hypertension prevalence in our study was 11.67 % and no significant correlation with JAK 2 allele burden. Our study is the largest one up to our knowledge that studies the association between its prevalence and JAK2 burden. PMID:27468853

  10. The Experience Of Massachusetts Shows That Consumers Will Need Help In Navigating Insurance Exchanges

    PubMed Central

    Sinaiko, Anna D.; Ross-Degnan, Dennis; Soumerai, Stephen B.; Lieu, Tracy; Galbraith, Alison

    2014-01-01

    In 2022 twenty-five million people are expected to purchase health insurance through exchanges to be established under the Affordable Care Act. Understanding how people seek information and make decisions about the insurance plans that are available to them may improve their ability to select a plan and their satisfaction with it. We conducted a survey in 2010 of enrollees in one plan offered through Massachusetts’s unsubsidized health insurance exchange to analyze how a sample of consumers selected their plans. More than 40 percent found plan information difficult to understand. Approximately one-third of respondents had help selecting plans—most commonly from friends or family members. However, one-fifth of respondents wished they had had help narrowing plan choices; these enrollees were more likely to report negative experiences related to plan understanding, satisfaction with affordability and coverage, and unexpected costs. Some may have been eligible for subsidized plans. Exchanges may need to provide more resources and decision-support tools to improve consumers’ experiences in selecting a health plan. PMID:23297274

  11. The experience of Massachusetts shows that consumers will need help in navigating insurance exchanges.

    PubMed

    Sinaiko, Anna D; Ross-Degnan, Dennis; Soumerai, Stephen B; Lieu, Tracy; Galbraith, Alison

    2013-01-01

    In 2022 twenty-five million people are expected to purchase health insurance through exchanges to be established under the Affordable Care Act. Understanding how people seek information and make decisions about the insurance plans that are available to them may improve their ability to select a plan and their satisfaction with it. We conducted a survey in 2010 of enrollees in one plan offered through Massachusetts's unsubsidized health insurance exchange to analyze how a sample of consumers selected their plans. More than 40 percent found plan information difficult to understand. Approximately one-third of respondents had help selecting plans-most commonly from friends or family members. However, one-fifth of respondents wished they had had help narrowing plan choices; these enrollees were more likely to report negative experiences related to plan understanding, satisfaction with affordability and coverage, and unexpected costs. Some may have been eligible for subsidized plans. Exchanges may need to provide more resources and decision-support tools to improve consumers' experiences in selecting a health plan. PMID:23297274

  12. Field experiments yield new insights into gas exchange and excess air formation in natural porous media

    NASA Astrophysics Data System (ADS)

    Klump, Stephan; Tomonaga, Yama; Kienzler, Peter; Kinzelbach, Wolfgang; Baumann, Thomas; Imboden, Dieter M.; Kipfer, Rolf

    2007-03-01

    Gas exchange between seepage water and soil air within the unsaturated and quasi-saturated zones is fundamentally different from gas exchange between water and gas across a free boundary layer, e.g., in lakes or rivers. In addition to the atmospheric equilibrium fraction, most groundwater samples contain an excess of dissolved atmospheric gases which is called "excess air". Excess air in groundwater is not only of crucial importance for the interpretation of gaseous environmental tracer data, but also for other aspects of groundwater hydrology, e.g., for oxygen availability in bio-remediation and in connection with changes in transport dynamics caused by the presence of entrapped air bubbles. Whereas atmospheric solubility equilibrium is controlled mainly by local soil temperature, the excess air component is characterized by the (hydrostatic) pressure acting on entrapped air bubbles within the quasi-saturated zone. Here we present the results of preliminary field experiments in which we investigated gas exchange and excess air formation in natural porous media. The experimental data suggest that the formation of excess air depends significantly on soil properties and on infiltration mechanisms. Excess air was produced by the partial dissolution of entrapped air bubbles during a sprinkling experiment in fine-grained sediments, whereas similar experiments conducted in coarse sand and gravel did not lead to the formation of excess air in the infiltrating water. Furthermore, the experiments revealed that the noble gas temperatures determined from noble gases dissolved in seepage water at different depths are identical to the corresponding in situ soil temperatures. This finding is important for all applications of noble gases as a paleotemperature indicator in groundwater since these applications are always based on the assumption that the noble gas temperature is identical to the (past) soil temperature.

  13. Nested heat tracer experiments for identifying heterogeneity of aquifer-river exchange at multiple scales

    NASA Astrophysics Data System (ADS)

    Krause, S.; Blume, T.; Angermann, L.; Hannah, D. M.; Weatherill, J.; Cassidy, N. J.

    2011-12-01

    injection experiments which provided essential information of the shallow aquifer- river exchange fluxes and confirmed increased SW infiltration and lateral flow in riffle crests and at locations with highly conductive streambed sediments above flow confining low conductivity structures. The propagation of diurnal temperature oscillations from the surface to streambed depths of up to 40cm was observed at thermocouple profiles along a pool-riffle-pool sequence in order to analyse the potential masking of FO-DTS observed temperature patterns by topography induced hyporheic exchange fluxes. The cross-correlation functions based analysis of the depth dampening and offset of diurnal temperature amplitudes revealed that streambed temperature variation due to topography induced hyporheic exchange flow was an order of magnitude lower than the FO-DTS signal strength. The investigations supported the development of a conceptual model of aquifer-river exchange and hyporheic reactivity in lowland rivers including temperature traceable hyporheic exchange fluxes at multiple scales.

  14. Influence of soil erosion on CO2 exchange within the CarboZALF manipulation experiment

    NASA Astrophysics Data System (ADS)

    Hoffmann, Mathias; Augustin, Jürgen; Sommer, Michael

    2014-05-01

    Agriculture in the hummocky ground moraine landscape of NE-Germany is characterized by an increase in energy crop cultivation, like maize or sorghum. Both enhance lateral C fluxes by erosion and induce feedbacks on C dynamics of agroecosystems as a result of the time limited land cover and the vigorous crop growth. However, the actual impact of these phenomena on the CO2-sink/-source function of agricultural landscapes, is still not clear. Therefore we established the interdisciplinary project 'CarboZALF' in 2009. In our field experiment CarboZALF-D we are monitoring CO2 fluxes for soil-plant systems, which cover all landscape relevant soil states in respect to erosion and deposition, like Albic Cutanic Luvisol, Calcic Cutanic Luvisol, Calcaric Regosol and Endogleyic Colluvic Regosol. Furthermore, we induced erosion / deposition in a manipulation experiment. Automated chamber systems (2.5 m, basal area 1 m2, transparent) are placed at the manipulated sites as well as at one site neither influenced by erosion, nor by deposition. CO2 flux modelling of high temporal resolution includes ecosystem respiration (Reco), gross primary productivity (GPP) and net ecosystem exchange (NEE) based on parallel and continuous measurements of the CO2 exchange, soil and air temperatures as well as photosynthetic active radiation (PAR). Modelling includes gap filling which is needed in case of chamber malfunctions and abrupt disturbances by farming practice. In our presentation we would like to show results of the CO2 exchange measurements for one year. Differences are most pronounced between the non-eroded and the colluvial soil: The Endogleyic Colluvic Regosol showed higher flux rates for Reco and NEE compared to the Albic Cutanic Luvisol. The eroded soil (Calcic Cutanic Luvisol) demonstrated CO2fluxes intermediate between the non-affected and depositional site. Site-specific consequences for the soil C stocks will be also discussed in the presentation.

  15. A Personnel Exchange Model for Vocational Education, Business, and Industry. Skills/Experience Exchange Program. Project Report.

    ERIC Educational Resources Information Center

    Hutcheson, Peggy G.

    This project was begun to explore the feasibility of instituting a personnel exchange program for vocational education--at both the secondary and postsecondary levels--and business and industry in the metropolitan Atlanta area. Following a literature search for other programs and interviews with representatives of business and industry and of…

  16. Experimental Background Studies in the Two Photon Exchange (TPE) Experiment at Jefferson Lab

    SciTech Connect

    Pena, Cristian; Brooks, W. K.; Hakobyan, Hayk

    2010-08-04

    This work is based on the improvement of an existing simulation for the two photon exchange (TPE) experiment at Jefferson Lab developed within the GEANT4 framework. This experiment will determine the ratio of the positron-proton elastic scattering cross section and the electron-proton elastic scattering cross section with high precision. To accomplish this measurement requires the use of a variety of devices and complex arrangements, creating background particles that manage to reach the detector system (CLAS). A number of test runs have identified the sources of background in the detector guided by previous simulations. Even so, the remaining background can be reduced considerably by the microscopic identification and locating of the background sources performed by our new simulation.

  17. Experimental Background Studies in the Two Photon Exchange (TPE) Experiment at Jefferson Lab

    SciTech Connect

    Cristian Peña, W. K. Brooks, Hayk Hakobyan

    2010-08-01

    This work is based on the improvement of an existing simulation for the two photon exchange (TPE) experiment at Jefferson Lab developed within the GEANT4 framework. This experiment will determine the ratio of the positron-proton elastic scattering cross section and the electron-proton elastic scattering cross section with high precision. To accomplish this measurement requires the use of a variety of devices and complex arrangements, creating background particles that manage to reach the detector system (CLAS). A number of test runs have identified the sources of background in the detector guided by previous simulations. Even so, the remaining background can be reduced considerably by the microscopic identification and locating of the background sources performed by our new simulation.

  18. Building a national electronic medical record exchange system - experiences in Taiwan.

    PubMed

    Li, Yu-Chuan Jack; Yen, Ju-Chuan; Chiu, Wen-Ta; Jian, Wen-Shan; Syed-Abdul, Shabbir; Hsu, Min-Huei

    2015-08-01

    Architecture (CDA) standards to generate clinical documents and Integrating the Healthcare Enterprise (IHE) Cross-enterprise Document Sharing (XDS) profile for the communication infrastructure. By December of 2014, the number of hospitals that provide an inter-institution EMR exchange service had reached 321. Hospitals that had not joined the service were all smaller ones with less than 100 beds. Inter-institution EMR exchange can make it much easier for people to access their own medical records, reduce the waste of medical resources, and improve the quality of medical care. The implementation of an inter-institution EMR exchange system faces many challenges. This article provides Taiwan's experiences as a reference. PMID:26001420

  19. Transfer Rate Edited experiment for the selective detection of Chemical Exchange via Saturation Transfer (TRE-CEST)

    NASA Astrophysics Data System (ADS)

    Friedman, Joshua I.; Xia, Ding; Regatte, Ravinder R.; Jerschow, Alexej

    2015-07-01

    Chemical Exchange Saturation Transfer (CEST) magnetic resonance experiments have become valuable tools in magnetic resonance for the detection of low concentration solutes with far greater sensitivity than direct detection methods. Accurate measures of rates of chemical exchange provided by CEST are of particular interest to biomedical imaging communities where variations in chemical exchange can be related to subtle variations in biomarker concentration, temperature and pH within tissues using MRI. Despite their name, however, traditional CEST methods are not truly selective for chemical exchange and instead detect all forms of magnetization transfer including through-space NOE. This ambiguity crowds CEST spectra and greatly complicates subsequent data analysis. We have developed a Transfer Rate Edited CEST experiment (TRE-CEST) that uses two different types of solute labeling in order to selectively amplify signals of rapidly exchanging proton species while simultaneously suppressing 'slower' NOE-dominated magnetization transfer processes. This approach is demonstrated in the context of both NMR and MRI, where it is used to detect the labile amide protons of proteins undergoing chemical exchange (at rates ⩾ 30 s-1) while simultaneously eliminating signals originating from slower (∼5 s-1) NOE-mediated magnetization transfer processes. TRE-CEST greatly expands the utility of CEST experiments in complex systems, and in-vivo, in particular, where it is expected to improve the quantification of chemical exchange and magnetization transfer rates while enabling new forms of imaging contrast.

  20. Experiments and Simulations on a Heat Exchanger of an Automotive Exhaust Thermoelectric Generation System Under Coupling Conditions

    NASA Astrophysics Data System (ADS)

    Liu, X.; Yu, C. G.; Chen, S.; Wang, Y. P.; Su, C. Q.

    2014-06-01

    The present experimental and computational study investigates an exhaust gas waste heat recovery system for vehicles, using thermoelectric modules and a heat exchanger to produce electric power. It proposes a new plane heat exchanger of a thermoelectric generation (TEG) system, producing electricity from a limited hot surface area. To investigate the new plane heat exchanger, we make a coupling condition of heat-flow and flow-solid coupling analysis on it to obtain the temperature, heat, and pressure field of the heat exchanger, and compared it with the old heat exchanger. These fields couple together to solve the multi-field coupling of the flow, solid, and heat, and then the simulation result is compared with the test bench experiment of TEG, providing a theoretical and experimental basis for the present exhaust gas waste heat recovery system.

  1. H/D exchange of a 15N labelled Tau fragment as measured by a simple Relax-EXSY experiment

    NASA Astrophysics Data System (ADS)

    Lopez, Juan; Ahuja, Puneet; Landrieu, Isabelle; Cantrelle, François-Xavier; Huvent, Isabelle; Lippens, Guy

    2014-12-01

    We present an equilibrium H/D exchange experiment to measure the exchange rates of labile amide protons in intrinsically unfolded proteins. By measuring the contribution of the H/D exchange to the apparent T1 relaxation rates in solvents of different D2O content, we can easily derive the rates of exchange for rapidly exchanging amide protons. The method does not require double isotope labelling, is sensitive, and requires limited fitting of the data. We demonstrate it on a functional fragment of Tau, and provide evidence for the hydrogen bond formation of the phosphate moiety of Ser214 with its own amide proton in the same fragment phosphorylated by the PKA kinase.

  2. Many overlapping peptides for protein hydrogen exchange experiments by the fragment separation-mass spectrometry method.

    PubMed

    Mayne, Leland; Kan, Zhong-Yuan; Chetty, Palaniappan Sevugan; Ricciuti, Alec; Walters, Benjamin T; Englander, S Walter

    2011-11-01

    Measurement of the naturally occurring hydrogen exchange (HX) behavior of proteins can in principle provide highly resolved thermodynamic and kinetic information on protein structure, dynamics, and interactions. The HX fragment separation-mass spectrometry method (HX-MS) is able to measure hydrogen exchange in biologically important protein systems that are not accessible to NMR methods. In order to achieve high structural resolution in HX-MS experiments, it will be necessary to obtain many sequentially overlapping peptide fragments and be able to identify and analyze them efficiently and accurately by mass spectrometry. This paper describes operations which, when applied to four different proteins ranging in size from 140 to 908 residues, routinely provides hundreds of useful unique peptides, covering the entire protein length many times over. Coverage in terms of the average number of peptide fragments that span each amino acid exceeds 10. The ability to achieve these results required the integrated application of experimental methods that are described here and a computer analysis program, called ExMS, described in a following paper. PMID:21952777

  3. Adsorption of iodine on hydrogen-reduced silver-exchanged mordenite: Experiments and modeling

    DOE PAGESBeta

    Nan, Yue; Tavlarides, Lawrence L.; DePaoli, David W.

    2016-08-03

    The adsorption process of iodine, a major volatile radionuclide in the off-gas streams of spent nuclear fuel reprocessing, on hydrogen-reduced silver-exchanged mordenite (Ag0Z) was studied at the micro-scale. The gas-solid mass transfer and reaction involved in the adsorption process were investigated and evaluated with appropriate models. Optimal conditions for reducing the silver-exchanged mordenite (AgZ) in a hydrogen stream were determined. Kinetic and equilibrium data of iodine adsorption on Ag0Z were obtained by performing single-layer adsorption experiments with experimental systems of high precision at 373–473 K over various iodine concentrations. Results indicate approximately 91% to 97% of the iodine adsorption wasmore » through the silver-iodine reaction. The effect of temperature on the iodine loading capacity of Ag0Z was discussed. In conclusion, the Shrinking Core model describes the data well, and the primary rate controlling mechanisms were macro-pore diffusion and silver-iodine reaction. © 2016 American Institute of Chemical Engineers AIChE J, 2016« less

  4. The Viking gas exchange experiment results from Chryse and Utopia surface samples

    NASA Technical Reports Server (NTRS)

    Oyama, V. I.; Berdahl, B. J.

    1977-01-01

    Immediate gas changes occurred when untreated Martian surface samples were humidified and/or wet by an aqueous nutrient medium in the Viking lander gas exchange experiment. The evolutions of N2, CO2, and Ar are mainly associated with soil surface desorption caused by water vapor, while O2 evolution is primarily associated with decomposition of superoxides inferred to be present on Mars. On recharges with fresh nutrient and test gas, only CO2 was given off, and its rate of evolution decreased with each recharge. This CO2 evolution is thought to come from the oxidation of organics present in the nutrient by gamma Fe2O3 in the surface samples. Atmospheric analyses were also performed at both sites. The mean atmospheric composition from four analyses is N2, 2.3%; O2, not greater than 0.15%; Ar, 1.5% and CO2, 96.2%.

  5. Injection of dust into the Martian atmosphere - Evidence from the Viking Gas Exchange experiment

    NASA Technical Reports Server (NTRS)

    Huguenin, R. L.; Harris, S. L.; Carter, R.

    1986-01-01

    The hypothesis that predawn midlatitude storms are triggered by a soil humidification process is examined. A freeze/thaw model of the process is evaluated in the Viking Gas Exchange experiments conducted on Mars. The humidification-driven desorption and desiccation state of Martian soil samples are analyzed. The periodic humidification of equatorial regolith soil is studied in terms of pore space pressure during desorption events and soil diffusivity; the thermal properties of the regolith surface layer are modeled using the program of Clifford (1984). Consideration is given to the diurnal and seasonal cycles of the humidification process, the permanent, low-albedo features in the midlatitudes, and the production of H2SO4 and HCl aerosols.

  6. In-channel Restoration Structures and the Implications on Hyporheic Exchange: a Laboratory Experiment

    NASA Astrophysics Data System (ADS)

    Han, B.; Chu, H. H.; Endreny, T. A.

    2014-12-01

    In-channel structures, i.e. cross-vanes and J-hooks, are commonly installed in river restoration projects to modify the streambed morphology and stream water surface profile, and are known to change hyporhiec exchange flux and habitats for riverine animals. However, few studies have continuous and accurate pre- and post-treatment data to evaluate the impact of these structures on channel hydraulic gradients and morphology. To quantify the effects of in-channel structures, we developed a scaled physical model of a meandering stream with a cross-vane and 6 J-hooks on a mobile-bed river table. Close-range photogrammetry technique was applied to obtain 3-D water and ground surface profiles with sub-millimeter vertical accuracy and horizontal resolution. The experiment was compared with a control experiment without structures while maintaining the same initial conditions of river bed, floodplain and stream flow. Results indicated that the cross-vane caused an average local head loss that represented 16% of the total stream reach head loss, and a 74% increase in channel load in the entire stream reach. Most J-hooks can create stepwise patterns in stream longitudinal profile, and cross-vane can create even more significant ones. Hydraulic gradients across the intra-meander zone also increased with in-channel structures, i.e. from 2.5% to 3.5% at the meander neck. Scour pools developed downstream of the cross-vane, and mostly around the 4 meander apex J-hooks at their hooked tip. Backwater caused by the cross-vane steepened the local water table profile by an additional 4.2%, and was the primary driver of statistically significant hydraulic gradient increase. Reach scale water and streambed surface profiles from our study provided detailed data to improve the understanding of in-channel structure effects, and may serve as reliable data source in computational modeling of hyporheic exchange.

  7. Clinical expression of facioscapulohumeral muscular dystrophy in carriers of 1–3 D4Z4 reduced alleles: experience of the FSHD Italian National Registry

    PubMed Central

    Nikolic, Ana; Ricci, Giulia; Sera, Francesco; Bucci, Elisabetta; Govi, Monica; Mele, Fabiano; Rossi, Marta; Ruggiero, Lucia; Vercelli, Liliana; Ravaglia, Sabrina; Brisca, Giacomo; Fiorillo, Chiara; Villa, Luisa; Maggi, Lorenzo; Cao, Michelangelo; D'Amico, Maria Chiara; Siciliano, Gabriele; Antonini, Giovanni; Santoro, Lucio; Mongini, Tiziana; Moggio, Maurizio; Morandi, Lucia; Pegoraro, Elena; Angelini, Corrado; Di Muzio, Antonio; Rodolico, Carmelo; Tomelleri, Giuliano; Grazia D'Angelo, Maria; Bruno, Claudio; Berardinelli, Angela; Tupler, Rossella

    2016-01-01

    Objectives Facioscapulohumeral muscular dystrophy type 1 (FSHD1) has been genetically linked to reduced numbers (≤8) of D4Z4 repeats at 4q35. Particularly severe FSHD cases, characterised by an infantile onset and presence of additional extra-muscular features, have been associated with the shortest D4Z4 reduced alleles with 1–3 repeats (1–3 DRA). We searched for signs of perinatal onset and evaluated disease outcome through the systematic collection of clinical and anamnestic records of de novo and familial index cases and their relatives, carrying 1–3 DRA. Setting Italy. Participants 66 index cases and 33 relatives carrying 1–3 DRA. Outcomes The clinical examination was performed using the standardised FSHD evaluation form with validated inter-rater reliability. To investigate the earliest signs of disease, we designed the Infantile Anamnestic Questionnaire (IAQ). Comparison of age at onset was performed using the non-parametric Wilcoxon rank-sum or Kruskal-Wallis test. Comparison of the FSHD score was performed using a general linear model and Wald test. Kaplan-Meier survival analysis was used to estimate the age-specific cumulative motor impairment risk. Results No patients had perinatal onset. Among index cases, 36 (54.5%) showed the first signs by 10 years of age. The large majority of patients with early disease onset (26 out of 36, 72.2%) were de novo; whereas the majority of patients with disease onset after 10 years of age were familial (16, 53.3%). Comparison of the disease severity outcome between index cases with age at onset before and over 10 years of age, failed to detect statistical significance (Wald test p value=0.064). Of 61 index cases, only 17 (27.9%) presented extra-muscular conditions. Relatives carrying 1–3 DRA showed a large clinical variability ranging from healthy subjects, to patients with severe motor impairment. Conclusions The size of the D4Z4 allele is not always predictive of severe clinical outcome. The high

  8. Verification of the AWA Photoinjector Beam Parameters Required for a Transverse-to-Longitudinal Emittance Exchange Experiment

    SciTech Connect

    Rihaoui, M.M.; Piot, P.; Power, J.G.; Mihalcea, D.; Gai, W.; /Argonne

    2009-05-01

    A transverse-to-longitudinal emittance exchange experiment is in preparation at the Argonne Wakefield Accelerator (AWA). The experiment aims at exchanging a low ({var_epsilon}{sub z} < 5 {micro}m) longitudinal emittance with a large ({var_epsilon}{sub x} > 15 {micro}m) transverse horizontal emittance for a bunch charge of {approx}100 pC. Achieving such initial emittance partitioning, though demonstrated via numerical simulations, is a challenging task and needs to be experimentally verified. In this paper, we report preliminary emittance measurements of the beam in the transverse and longitudinal planes performed at {approx}12 MeV. The measurements are compared with numerical simulations.

  9. Exchange Transfusion for Severe Neonatal Hyperbilirubinemia: 17 Years' Experience from Vojvodina, Serbia.

    PubMed

    Bujandric, Nevenka; Grujic, Jasmina

    2016-06-01

    This study aimed to evaluate the frequency of the main risk factors for severe neonatal hyperbilirubinemia, to determine the incidence of exchange transfusion (ET) in the Autonomous Province of Vojvodina (the northern part of Serbia) and to describe the experience with ET performed in premature and term infants during the past 17 years. We performed a retrospective data analysis of 398 newborn infants who underwent a double volume ET from 1997 to 2013. During the 17 year study period, a decreasing incidence of ET, expressed per thousand newborns, was observed. A total of 468 double volume ET were performed: 328 (82.4 %) infants had one treatment and 70 (17.6 %) had repeated treatments. A total of 262,830 mLs of blood were transfused, an average of 660 mLs per child. There were 221 male and 177 female infants, with a sex ratio 1.25:1. The frequencies of risk factors for developing hyperbilirubinemia were as follows: (1) 38 % RhD incompatibility; (2) 38 % ABO incompatibility (26 % group A infant of group O mother, 12 % group B infant of group O mother); (3) 7 % low birth weight/preterm birth; (4) 17 % other factors. Risk factors for neurotoxicity were identified in 56.3 % of infants. No deaths or complications were reported arising from the treatment. ABO and Rh incompatibilities were found to be the main risk factors for severe neonatal hyperbilirubinemia in Vojvodina. Exchange transfusion, used as therapy for severe hyperbilirubinemia, trended downwards over the period of this study. PMID:27065585

  10. Methods for Leveraging a Health Information Exchange for Public Health: Lessons Learned from the NW-PHIE Experience

    PubMed Central

    Trebatoski, M; Davies, J; Revere, D; Dobbs, D

    2010-01-01

    The intent of this article is to provide public health and health information exchanges (HIEs) insight into activities and processes for connecting public health with clinical care through HIEs. In 2007 the CDC issued a Request for Proposal (RFP) for the “Situational Awareness through Health Information Exchange” project. The project’s goals are to connect public health with health information exchanges (HIEs) to improve public health’s real-time understanding of communities’ population health and healthcare facility status. This article describes the approach and methodology used by the Northwest Public Health Information Exchange to achieve the project’s goals. The experience of the NWPHIE Collaboration provides an organizational and operational roadmap for implementing a successful regional HIE that ensures secure exchange and use of electronic health information between local and state public health and health care entities. PMID:23569587

  11. Design of Plant Gas Exchange Experiments in a Variable Pressure Growth Chamber

    NASA Technical Reports Server (NTRS)

    Corey, Kenneth A.

    1996-01-01

    Sustainable human presence in extreme environments such as lunar and martian bases will require bioregenerative components to human life support systems where plants are used for generation of oxygen, food, and water. Reduced atmospheric pressures will be used to minimize mass and engineering requirements. Few studies have assessed the metabolic and developmental responses of plants to reduced pressure and varied oxygen atmospheres. The first tests of hypobaric pressures on plant gas exchange and biomass production at the Johnson Space Center will be initiated in January 1996 in the Variable Pressure Growth Chamber (VPGC), a large, closed plant growth chamber rated for 10.2 psi. Experiments were designed and protocols detailed for two complete growouts each of lettuce and wheat to generate a general database for human life support requirements and to answer questions about plant growth processes in reduced pressure and varied oxygen environments. The central objective of crop growth studies in the VPGC is to determine the influence of reduced pressure and reduced oxygen on the rates of photosynthesis, dark respiration, evapotranspiration and biomass production of lettuce and wheat. Due to the constraint of one experimental unit, internal controls, called pressure transients, will be used to evaluate rates of CO2 uptake, O2 evolution, and H2O generation. Pressure transients will give interpretive power to the results of repeated growouts at both reduced and ambient pressures. Other experiments involve the generation of response functions to partial pressures of O2 and CO2 and to light intensity. Protocol for determining and calculating rates of gas exchange have been detailed. In order to build these databases and implement the necessary treatment combinations in short time periods, specific requirements for gas injections and removals have been defined. A set of system capability checks will include determination of leakage rates conducted prior to the actual crop

  12. The Tropical Experiment of the Stratosphere-Troposphere Exchange Project (STEP): Science objectives, operations, and summary findings

    SciTech Connect

    Russell, P.B.; Pfister, L. ); Selkirk, H.B. )

    1993-05-20

    The authors provide an overview of the objectives, operation, and findings of the Stratosphere-Troposphere Exchange Project (STEP). This project had two main objectives. First was to study the mechanisms and exchange rates associated with the exchange of mass, gases, and aerosols between the troposphere and stratosphere. Second was to try to explain the extreme dryness observed in stratospheric air masses. This series of studies comprises the STEP Tropical Experiment, which was carried out in January and February, 1987. Most data was collected by a high flying ER-2 aircraft, outfitted with an array of data collection instrumentation. This experiment found the driest air just at or above the cloud tops, and in conjunction with other measurements concludes that temperatures, and ice crystal growth and transport contribute to local dehydration in these cloud systems. Significant convection is also evident in the clouds. Temperatures at the top of the monsoonal clouds, and their height contribute to mixing dry air into the lower stratosphere.

  13. Culture, Identity, and Structure in Social Exchange: A Web-Based Trust Experiment in the United States and Japan

    ERIC Educational Resources Information Center

    Kuwabara, Ko; Willer, Robb; Macy, Michael W.; Mashima, Rie; Terai, Shigeru; Yamagishi, Toshio

    2007-01-01

    Cross-cultural trust and cooperation are important concerns for international markets, political cooperation, and cultural exchange. Until recently, this problem was difficult to study under controlled conditions due to the inability to conduct experiments involving interaction between participants located in physically distant locations. We…

  14. Calcium-ammonium exchange experiments on clay minerals using a (45)Ca tracer technique in marine pore water.

    PubMed

    Ockert, Charlotte; Wehrmann, Laura M; Kaufhold, Stephan; Ferdelman, Tim G; Teichert, Barbara M A; Gussone, Nikolaus

    2014-01-01

    Understanding cation exchange processes is important for evaluating early diagenetic and synsedimentary processes taking place in marine sediments. To quantify calcium (Ca) exchange and Ca-ammonium exchange in a seawater environment, we performed experiments with a radioactive (45)Ca tracer on clay mineral standards (Fithian illite, montmorillonite and kaolinite) and marine sediments from the North Atlantic Integrated Ocean Drilling Program Site U1306A in artificial seawater (ASW). The results show that equilibrium during the initial attachment of Ca as well as the exchange of Ca by [Formula: see text] is attained in less than 2 min. On average 8-20% of the exchangeable sites of the clay minerals were occupied by Ca in a seawater medium. The conditional selectivity coefficient, describing the [Formula: see text] exchange in ASW is mineral specific and it was determined to be 0.07 for montmorillonite, 0.05 for a natural marine sediment and 0.013 for Fithian illite. PMID:24437731

  15. "Gene-swap knock-in" cassette in mice to study allelic differences in human genes.

    PubMed

    Nebert, D W; Dalton, T P; Stuart, G W; Carvan, M J

    2000-01-01

    Genetic differences in environmental toxicity and cancer susceptibility among individuals in a human population often reflect polymorphisms in the genes encoding drug-metabolizing enzymes (DMEs), drug transporters, and receptors that control DME levels. This field of study is called "ecogenetics", and a subset of this field--concerning genetic variability in response to drugs--is termed "pharmacogenetics". Although human-mouse differences might be 3- to perhaps 10-fold, human interindividual differences can be as great as 20-fold or more than 40-fold. It would be helpful, therefore, to study toxicokinetics/pharmacokinetics of particular environmental agents and drugs in mice containing these "high-" and "low-extreme" human alleles. We hope to use transgenic "knock-in" technology in order to insert human alleles in place of the orthologous mouse gene. However, the knock-in of each gene has normally been a separate event requiring the following: (a) construction of the targeting vector, (b) transfection into embryonic stem (ES) cells, (c) generation of a targeted mouse having germline transmission of the construct, and (d) backcross breeding of the knock-in mouse (at least 6-8 times) to produce a suitable genetically homogeneous background (i.e., to decrease "experimental noise"). These experiments require 1 1/2 to 2 years to complete, making this very powerful technology inefficient for routine applications. If, on the other hand, the initial knock-in targeting vector might include sequences that would allow the knocked-in gene to be exchanged (quickly and repeatedly) for one new allele after another, then testing distinctly different human polymorphic alleles in transgenic mice could be accomplished in a few months instead of several years. This "gene-swapping" technique will soon be done by zygotic injection of a "human allele cassette" into the sperm or fertilized ovum of the parental knock-in mouse inbred strain or by the cloning of whole mice from cumulus

  16. Educational Exchanges: Essays on the Sino-American Experience. Research Papers and Policy Studies 21.

    ERIC Educational Resources Information Center

    Kallgren, Joyce K., Ed.; Simon, Denis Fred, Ed.

    The essays in this monograph (except one) were originally presented and discussed at the Conference on Sino-American Cultural and Scientific Exchanges held in Honolulu, Hawaii in February 1985. Frank Ninkovich presents some of the thoughts that characterized the U.S. approach to cultural exchanges before 1940. In her essay on the pre-World War II…

  17. An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange

    PubMed Central

    Baldwin, Andrew J.

    2014-01-01

    The Carr–Purcell–Meiboom–Gill (CPMG) experiment is widely used to quantitatively analyse the effects of chemical exchange on NMR spectra. In a CPMG experiment, the effective transverse relaxation rate, R2,eff, is typically measured as a function of the pulse frequency, νCPMG. Here, an exact expression for how R2,eff varies with νCPMG is derived for the commonly encountered scenario of two-site chemical exchange of in-phase magnetisation. This result, summarised in Appendix A, generalises a frequently used equation derived by Carver and Richards, published in 1972. The expression enables more rapid analysis of CPMG data by both speeding up calculation of R2,eff over numerical methods by a factor of ca. 130, and yields exact derivatives for use in data analysis. Moreover, the derivation provides insight into the physical principles behind the experiment. PMID:24852115

  18. Open inquiry-based learning experiences: a case study in the context of energy exchange by thermal radiation

    NASA Astrophysics Data System (ADS)

    Pizzolato, Nicola; Fazio, Claudio; Rosario Battaglia, Onofrio

    2014-01-01

    An open inquiry (OI)-based teaching/learning experience, regarding a scientific investigation of the process of energy exchange by thermal radiation, is presented. A sample of upper secondary school physics teachers carried out this experience at the University of Palermo, Italy, in the framework of ESTABLISH, a FP7 European Project aimed at promoting and developing inquiry-based science education. The teachers had the opportunity to personally experience an OI-based learning activity, with the aim of exploring the pedagogical potentialities of this teaching approach to promote both the understanding of difficult concepts and a deeper view of scientific practices. The teachers were firstly engaged in discussions concerning real-life problematic situations, and then stimulated to design and carry out their own laboratory activities, aimed at investigating the process of energy exchange by thermal radiation. A scientific study on the energy exchange between a powered resistor and its surrounding environment, during the heating and cooling processes, was designed and performed. Here we report the phases of this experiment by following the teachers' perspective. A structured interview conducted both before and after the OI experience allowed us to analyze and point out the teachers' feedback from a pedagogical point of view. The advantages and limits of an OI-based approach to promote the development of more student-centred inquiry-oriented teaching strategies are finally discussed.

  19. Fixation probability with multiple alleles and projected average allelic effect on selection.

    PubMed

    Lessard, Sabin; Lahaie, Philippe

    2009-06-01

    The first-order effect of selection on the probability of fixation of an allele, with respect to an intensity of selection s>0 in a diploid population of fixed finite size N, undergoing discrete, non-overlapping generations, is shown to be given by the sum of the average effects of that allele on the coefficient of selection in the current generation and all future generations, given the population state in the current generation. This projected average allelic effect is a weighted sum of average allelic effects in allozygous and autozygous offspring in the initial generation, with weights given in terms of expected coalescence times, under neutrality, for the lineages of two or three gametes chosen at random in the same generation. This is shown in the framework of multiple alleles at one locus, with genotypic values determining either viability or fertility differences, and with either multinomial or exchangeable reproduction schemes. In the limit of weak selection in a large population such that Ns tends to zero, the initial average allelic effects in allozygous offspring and autozygous offspring have the same weight on the fixation probability only in the domain of application of the Kingman coalescent. With frequency-dependent selection in a linear-game-theoretic context with two phenotypes determined by additive gene action, the first-order effect on the fixation probability is a combination of two effects of frequency-independent selection, one in a haploid population, the other in a diploid population. In the domain of application of the Kingman coalescent as the population size goes to infinity and Ns to zero, the first effect is three times more important than the second effect. This explains the one-third law of evolutionary dynamics in this domain, and shows how this law can be extended beyond this domain. PMID:19249322

  20. Analysis of one-dimensional pure-exchange NMR experiments for studying dynamics with broad distributions of correlation times.

    PubMed

    deAzevedo, E R; Tozoni, J R; Schmidt-Rohr, K; Bonagamba, T J

    2005-04-15

    One-dimensional (1D) exchange NMR experiments can elucidate the geometry, time scale, memory, and heterogeneity of slow molecular motions (1 ms-1 s) in solids. The one-dimensional version of pure-exchange (PUREX) solid-state exchange NMR, which is applied to static samples and uses the chemical shift anisotropy as a probe for molecular motion, is particularly promising and convenient in applications where site resolution is not a problem, i.e., in systems with few chemical sites. In this work, some important aspects of the 1D PUREX experiment applied to systems with complex molecular motions are analyzed. The influence of intermediate-regime (10 micros-1 ms) motions and of the distribution of reorientation angles on the pure-exchange intensity are discussed, together with a simple method for estimating the activation energy of motions occurring with a single correlation time. In addition, it is demonstrated that detailed information on the motional geometry can be obtained from 1D PUREX spectral line shapes. Experiments on a molecular crystal, dimethyl sulfone, confirm the analysis quantitatively. In two amorphous polymers, atactic polypropylene (aPP) and polyisobutylene (PIB), which differ only by one methyl group in the repeat unit, the height of the normalized exchange intensity clearly reveals a striking difference in the width of the distribution of correlation times slightly above the glass transition. The aPP shows the broad distribution and Williams-Landel-Ferry temperature dependence of correlation times typical of polymers and other "fragile" glass formers. In contrast, the dynamics in PIB occur essentially with a single correlation time and exhibits Arrhenius behavior, which is more typical of "strong" glass formers; this is somewhat surprising given the weak intermolecular forces in PIB. PMID:15945644

  1. Long-Term (4 mo) Oxygen Isotope Exchange Experiment between Zircon and Hydrothermal Fluid

    NASA Astrophysics Data System (ADS)

    Bindeman, I. N.; Schmitt, A. K.; Lundstrom, C.; Golledge, S.

    2013-12-01

    Knowing oxygen diffusivity in zircon has several critical applications: 1) establishing zircon stability and solubility in hot silica-saturated hydrothermal solutions; 2) deriving metamorphic and magmatic heating timescales from intra-crystal oxygen isotopic gradients; 3) assessing the survivability of oxygen isotopic signatures in Hadean zircons. We report results of a microanalytical investigation of an isotope exchange experiment using a cold-seal pressure apparatus at 850°C and 500 MPa over 4 months duration. Natural zircon, quartz and rutile were sealed with a silica-rich solution doped with 18-O, D, 7-Li and 10-B in a gold capsule. The diffusion length-scales were examined by depth profiling using time-of-flight (TOF) and high-sensitivity dynamic secondary ionization mass spectrometry (SIMS). Starting materials had distinct and homogeneous δ18O: zircon from Mesa Falls tuff of Yellowstone (+3.6‰), rutile from Karelia (-29‰), Bishop Tuff Quartz (+8.4‰), and δ18O doped water (+400‰). Starting material zircon showed invariant 18O/16O during depth profiling. After the 4 month experiment, rutile crystal surfaces displayed etching (100's of nm), while zircon exteriors lacked visible change. Quartz was completely dissolved and reprecipitated in a minor residue. Rutile developed ~2 μm long Fickian diffusion profiles largely consistent with the wet diffusion coefficients for rutile previously reported [1]. Surface U-Pb dating of zircon detected no significant Pb loss from the outermost ~300 nm of the crystal face and returned identical core-face ages. We performed δ18O depth profiling of zircon in two directions. First, forward profiles (crystal rim inwards) by dynamic SIMS (no surface treatment besides Au-coating; Cs+ beam of 20 kV impact energy) showed initially high and decreasing 18O/16O over ~130 nm; TOF-SIMS forward profiles using a 2 kV Cs+ sputter beam and 25 kV Bi3+ primary ions on uncoated zircon surfaces (cleaned for 2 min with HF) yielded

  2. Hydrogen isotope exchange in beryllium co-deposits: modelling and experiment

    NASA Astrophysics Data System (ADS)

    Kogut, D.; Douai, D.; Baldwin, M. J.; Doerner, R. P.; Sinelnikov, D.; Mamedov, N.; Kurnaev, V.; Becker, H. W.; Schwarz-Selinger, T.

    2016-02-01

    In order to understand the interaction mechanisms between hydrogenic species and beryllium co-deposits, a 1D Diffusion Trapping Model of Isotopic eXchange in Be (DITMIX) is developed. Hydrogen depth profiles from DITMIX are in good agreement with those measured by 15N-NRA on pre-characterised 600 nm thick Be:H layers (H/Be = 0.04), which were irradiated by D ions with a low flux of 1017 m-2 s-1 and an energy of 5 keV D-1, for different fluences and surface temperatures. Hence DITMIX provides a qualitative understanding of the isotope exchange mechanisms, although modelled versus measured D profiles show less agreement in the bulk, casting some doubt on the processes involved. For such low fluxes, DITMIX shows that the main factors determining isotopic exchange are the irradiation fluence and the surface temperature.

  3. Deuterium Exchange in Ethyl Acetoacetate: An Undergraduate GC-MS [Gas Chromatography-Mass Spectroscopy] Experiment

    ERIC Educational Resources Information Center

    Heinson, C. D.; Williams, J. M.; Tinnerman, W. N.; Malloy, T. B.

    2005-01-01

    The role of ethanol O-d in nullifying the deuterolysis may be demonstrated by determining that transesterification of methyl acetoacetate of the ethyl ester occurs as well as deuterium exchange of the five acetoacetate hydrogens. The significant acidity of the methylene protons in the acetoacetate group, the efficacy of base catalysis, the role of…

  4. Experiences from Cross-Institutional Exchanges of Undergraduate Business Student Written Cases

    ERIC Educational Resources Information Center

    Ross, Douglas N.; Zufan, Pavel; Rosenbloom, Al

    2008-01-01

    This article describes an undergraduate course assignment that required 134 students in 52 student teams from three universities, two in the United States and one in the Czech Republic, to write, exchange, and give constructive feedback on a student-written strategic management or international business case and its accompanying teaching note. The…

  5. Electron self-exchange kinetics determined by MARY spectroscopy: theory and experiment.

    PubMed

    Justinek, M; Grampp, G; Landgraf, S; Hore, P J; Lukzen, N N

    2004-05-01

    The electron self-exchange between a neutral molecule and its charged radical, which is part of a spin-correlated radical ion pair, gives rise to line width effects in the fluorescence-detected MARY (magnetic field effect on reaction yield) spectrum similar to those observed in EPR spectroscopy. An increasing self-exchange rate (i.e., a higher concentration of the neutral molecule) leads to broadening and subsequent narrowing of the spectrum. Along with a series of MARY spectra recorded for several systems (the fluorophores pyrene, pyrene-d(10) and N-methylcarbazole in combination with 1,2- and 1,4-dicyanobenzene) in various solvents, a theoretical model is developed that describes the spin evolution and the diffusive recombination of the radical pair under the influence of the external magnetic field and electron self-exchange, thereby allowing the simulation of MARY spectra of the systems investigated experimentally. The spin evolution of the radicals in the pair is calculated separately using spin correlation tensors, thereby allowing rigorous quantum mechanical calculations for real spin systems. It is shown that the combination of these simulations with high resolution, low noise experimental spectra makes the MARY technique a novel, quantitative method for the determination of self-exchange rate constants. In comparison to a simple analytical formula which estimates the self-exchange rate constant from the slope of the linear part of a line width vs concentration plot, the simulation method yields more reliable and accurate results. The correctness of the results obtained by the MARY method is proved by a comparison with corresponding data from the well-established EPR line broadening technique. With its less stringent restrictions on radical lifetime and stability, the MARY technique provides an alternative to the classical EPR method, in particular for systems involving short-lived and unstable radicals. PMID:15113235

  6. What Is a Recessive Allele?

    ERIC Educational Resources Information Center

    American Biology Teacher, 1991

    1991-01-01

    Presents four misconceptions students have concerning the concepts of recessive and dominant alleles. Discusses the spectrum of dominant-recessive relationships, different levels of analysis between phenotype and genotype, possible causes of dominance, and an example involving wrinkled peas. (MDH)

  7. The use of some ion-exchange sorbing tracer cations in in-situ experiments in high saline groundwaters

    SciTech Connect

    Byegaard, J.; Skarnemark, G.; Skaalberg, M.

    1995-12-31

    The possibility to use alkali metals and alkaline earth metals as slightly sorbing tracers in in-situ sorption experiments in high saline groundwaters has been investigated. The cation exchange characteristics of granite and some fracture minerals (chlorite and calcite) have been studied using the proposed cations as tracers. The results show low Kd`s for Na, Ca and Sr ({approximately}0.1 ml/g), while the sorption is higher for the more electropositive cations (Rb, Cs and Ba). A higher contribution of irreversible sorption can also be observed for the latter group of cations. For calcite the sorption of all the tracers, except Ca, is lower compared to the corresponding sorption to granite and chlorite. Differences in selectivity coefficients and cation exchange capacity are obtained when using different size fractions of crushed granite. The difference is even more pronounced when comparing crushed granite to intact granite.

  8. Do Students Share the Same Experience in an Online Language Exchange Programme?--The Chinese-French eTandem Case

    ERIC Educational Resources Information Center

    Szilas, Jue Wang; Zhang, Ling; Berger, Claudia

    2013-01-01

    This article presents the findings of an eTandem Chinese-French exchange course during two academic years, the year 2010-2011 when the course was not credited, and the year 2011-2012 when the course was credited in one university but not in the other. It focuses on the students' perspective about the language exchange experience. The participants…

  9. Aspartate beta-decarboxylase from Alcaligenes faecalis: carbon-13 kinetic isotope effect and deuterium exchange experiments

    SciTech Connect

    Rosenberg, R.M.; O'Leary, M.H.

    1985-03-26

    The authors have measured the /sup 13/C kinetic isotope effect at pH 4.0, 5.0, 6.0, and 6.5 and in D/sub 2/O at pH 5.0 and the rate of D-H exchange of the alpha and beta protons of aspartic acid in D/sub 2/O at pH 5.0 for the reaction catalyzed by the enzyme aspartate beta-decarboxylase from Alcaligenes faecalis. The /sup 13/C kinetic isotope effect, with a value of 1.0099 +/- 0.0002 at pH 5.0, is less than the intrinsic isotope effect for the decarboxylation step, indicating that the decarboxylation step is not entirely rate limiting. The authors have been able to estimate probable values of the relative free energies of the transition states of the enzymatic reaction up to and including the decarboxylation step from the /sup 13/C kinetic isotope effect and the rate of D-H exchange of alpha-H. The pH dependence of the kinetic isotope effect reflects the pKa of the pyridine nitrogen of the coenzyme pyridoxal 5'-phosphate but not that of the imine nitrogen. A mechanism is proposed for the exchange of aspartate beta-H that is consistent with the stereochemistry suggested earlier.

  10. How do client and therapists in online text therapy experience their exchanges and relationship?

    PubMed

    Reynolds, D'Arcy J

    2014-01-01

    The impact of online therapy text exchanges and the client-therapist alliance was compared to previously published means and standard deviations on face-to-face therapy using an aggregate benchmarking strategy. Further, the moderating effects of 4 participant factors found significant in the face-to-face therapy literature was investigated using mixed modeling analytic techniques. Thirty therapists and 30 clients visited an online site to report weekly to complete session impact and therapeutic alliance measures for a minimum of six weeks, which allowed for a naturalistic and nuanced examination of the process of online text psychotherapy. The impact of exchanges and client-therapist alliance in text therapy were similar to but in some respects more positive than previous evaluations of face-to-face therapy. A notable exception was substantially lower Arousal scores replicating the previously-observed online calming effect. The significance of participant factors previously found to influence impact and alliance in face-to-face therapy was not replicated except that therapists with the more symptomatic clients rated their text exchanges as less smooth and comfortable. PMID:24875704

  11. Unified superresolution experiments and stochastic theory provide mechanistic insight into protein ion-exchange adsorptive separations

    PubMed Central

    Kisley, Lydia; Chen, Jixin; Mansur, Andrea P.; Shuang, Bo; Kourentzi, Katerina; Poongavanam, Mohan-Vivekanandan; Chen, Wen-Hsiang; Dhamane, Sagar; Willson, Richard C.; Landes, Christy F.

    2014-01-01

    Chromatographic protein separations, immunoassays, and biosensing all typically involve the adsorption of proteins to surfaces decorated with charged, hydrophobic, or affinity ligands. Despite increasingly widespread use throughout the pharmaceutical industry, mechanistic detail about the interactions of proteins with individual chromatographic adsorbent sites is available only via inference from ensemble measurements such as binding isotherms, calorimetry, and chromatography. In this work, we present the direct superresolution mapping and kinetic characterization of functional sites on ion-exchange ligands based on agarose, a support matrix routinely used in protein chromatography. By quantifying the interactions of single proteins with individual charged ligands, we demonstrate that clusters of charges are necessary to create detectable adsorption sites and that even chemically identical ligands create adsorption sites of varying kinetic properties that depend on steric availability at the interface. Additionally, we relate experimental results to the stochastic theory of chromatography. Simulated elution profiles calculated from the molecular-scale data suggest that, if it were possible to engineer uniform optimal interactions into ion-exchange systems, separation efficiencies could be improved by as much as a factor of five by deliberately exploiting clustered interactions that currently dominate the ion-exchange process only accidentally. PMID:24459184

  12. Leveraging Health Information Exchange to Support Public Health Situational Awareness: The Indiana Experience

    PubMed Central

    Grannis, Shaun J.; Stevens, Kevin C.; Merriwether, Ricardo

    2010-01-01

    Public health situational awareness is contingent upon timely, comprehensive and accurate information from clinical systems. Ad-hoc models for sending non-standard clinical information directly to public health are inefficient and increasingly unsustainable. Information sharing models that leverage Health Information Exchanges (HIEs) are emerging. HIEs standardize, aggregate and streamline information sharing among data partners, including public health stakeholders, and HIE has supported public health practice in Indiana for more than 10 years. To accelerate nationwide adoption of HIE-supported situational awareness processes, the CDC awarded three HIEs across the nation, including Indiana, New York and Washington/Idaho. The Indiana partners included Indiana University School of Medicine, Regenstrief Institute, Indiana Health Information Exchange, Indiana State Department of Health, Health & Hospital Corporation of Marion County, and Children’s Hospital Boston. Activities included augmenting biosurveillance processes, enabling bi-directional communication, enhancing automated detection of notifiable conditions, and demonstrating technological advances at national forums. HIE transactions destined for public health were enhanced with standardized clinical vocabulary and more complete physician contact information. During the 2009 H1N1 flu outbreak, the HIE delivered targeted public health broadcast messages to providers in Marion County, Indiana. We will review the partnership characteristics, activities, accomplishments and future directions for our health information exchange. PMID:23569586

  13. Sodium Concentration Measurement during Hemodialysis through Ion-Exchange Resin and Conductivity Measure Approach: In Vitro Experiments

    PubMed Central

    Tura, Andrea; Sbrignadello, Stefano; Mambelli, Emanuele; Ravazzani, Paolo; Santoro, Antonio; Pacini, Giovanni

    2013-01-01

    Sodium measurement during hemodialysis treatment is important to preserve the patient from clinical events related to hypo- or hyper-natremia Usually, sodium measurement is performed through laboratory equipment which is typically expensive, and requires manual intervention. We propose a new method, based on conductivity measurement after treatment of dialysate solution through ion-exchange resin. To test this method, we performed in vitro experiments. We prepared 40 ml sodium chloride (NaCl) samples at 280, 140, 70, 35, 17.5, 8.75, 4.375 mEq/l, and some “mixed samples”, i.e., with added potassium chloride (KCl) at different concentrations (4.375-17.5 mEq/l), to simulate the confounding factors in a conductivity-based sodium measurement. We measured the conductivity of all samples. Afterwards, each sample was treated for 1 min with 1 g of Dowex G-26 resin, and conductivity was measured again. On average, the difference in the conductivity between mixed samples and corresponding pure NaCl samples (at the same NaCl concentration) was 20.9%. After treatment with the exchange resin, it was 14.7%, i.e., 42% lower. Similar experiments were performed with calcium chloride and magnesium chloride as confounding factors, with similar results. We also performed some experiments on actual dialysate solution during hemodialysis sessions in 15 patients, and found that the correlation between conductivity measures and sodium concentration improved after resin treatment (R=0.839 before treatment, R=0.924 after treatment, P<0.0001). We conclude that ion-exchange resin treatment coupled with conductivity measures may improve the measurement of sodium compared to conductivity measures alone, and may become a possible simple approach for continuous and automatic sodium measurement during hemodialysis. PMID:23844253

  14. Delimiting Allelic Imbalance of TYMS by Allele-Specific Analysis

    PubMed Central

    Balboa-Beltrán, Emilia; Cruz, Raquel; Carracedo, Angel; Barros, Francisco

    2015-01-01

    Abstract Allelic imbalance of thymidylate synthase (TYMS) is attributed to polymorphisms in the 5′- and 3′-untranslated region (UTR). These polymorphisms have been related to the risk of suffering different cancers, for example leukemia, breast or gastric cancer, and response to different drugs, among which are methotrexate glutamates, stavudine, and specifically 5-fluorouracil (5-FU), as TYMS is its direct target. A vast literature has been published in relation to 5-FU, even suggesting the sole use of these polymorphisms to effectively manage 5-FU dosage. Estimates of the extent to which these polymorphisms influence in TYMS expression have in the past been based on functional analysis by luciferase assays and quantification of TYMS mRNA, but both these studies, as the association studies with cancer risk or with toxicity or response to 5-FU, are very contradictory. Regarding functional assays, the artificial genetic environment created in luciferase assay and the problems derived from quantitative polymerase chain reactions (qPCRs), for example the use of a reference gene, may have distorted the results. To avoid these sources of interference, we have analyzed the allelic imbalance of TYMS by allelic-specific analysis in peripheral blood mononuclear cells (PBMCs) from patients. Allelic imbalance in PBMCs, taken from 40 patients with suspected myeloproliferative haematological diseases, was determined by fluorescent fragment analysis (for the 3′-UTR polymorphism), Sanger sequencing and allelic-specific qPCR in multiplex (for the 5′-UTR polymorphisms). For neither the 3′- nor the 5′-UTR polymorphisms did the observed allelic imbalance exceed 1.5 fold. None of the TYMS polymorphisms is statistically associated with allelic imbalance. The results acquired allow us to deny the previously established assertion of an influence of 2 to 4 fold of the rs45445694 and rs2853542 polymorphisms in the expression of TYMS and narrow its allelic imbalance to 1.5 fold

  15. Lagrangian evolution of DMS during the Southern Ocean gas exchange experiment: The effects of vertical mixing and biological community shift

    NASA Astrophysics Data System (ADS)

    Yang, M.; Archer, S. D.; Blomquist, B. W.; Ho, D. T.; Lance, V. P.; Torres, R. J.

    2013-12-01

    Concentrations of dimethylsulfide (DMS) and its precursor dimethylsulfoniopropionate (DMSP) are highly variable in time and space. What is driving the variability in DMS(P), and can those variability be explained by physical processes and changes in the biological community? During the Southern Ocean Gas Exchange Experiment (SO GasEx) in the austral fall of 2008, two 3He/SF6 labeled patches were created in the surface water. SF6 and DMS were surveyed continuously in a Lagrangian framework, while direct measurements of air-sea exchange further constrained the gas budgets. Turbulent diffusivity at the base of the mixed layer was estimated from SF6 profiles and used to calculate the vertical fluxes of DMS and nutrients. Increasing mixed layer nutrient concentrations due to mixing were associated with a shift in the phytoplankton community structure, which in turned likely affected the sulfur dynamics on timescales of days. DMS concentration as well as air-sea DMS flux appeared to be decoupled from the DMSP concentration, possibly due to grazing and bacterial DMS production. Contrary to expectations, in an environment with high winds and modest productivity, physical processes (air-sea exchange, photochemistry, vertical mixing) only accounted for a small fraction of DMS loss from the surface water. Among the DMS sinks, inferred biological consumption most likely dominated during SO GasEx.

  16. Influence of Waves, Whitecaps, and Turbulence on the Gas Transfer during the Southern Ocean Gas Exchange Experiment

    NASA Astrophysics Data System (ADS)

    Zappa, C. J.; Cifuentes-Lorenzen, A.; Edson, J. B.; McGillis, W. R.; Bariteau, L.; Fairall, C. W.

    2008-12-01

    The exchange of carbon dioxide and other trace gases across the air-sea interface plays an important role in global and regional biogeochemical cycles. The gas transfer velocity (k) is thought to be controlled by near- surface turbulence at low to moderate wind speeds and by bubble-mediated processes at higher wind speeds. At low to moderate wind speeds, small-scale waves including microbreaking disrupt the diffusive boundary layer, contribute to mixing at the surface, and enhance exchange. Likewise, at higher wind speeds, large-scale wave breaking, or whitecapping, generates mixing and additionally enhances gas transfer via bubble-mediated exchange. The parameterization for k based on the direct covariance fluxes is shown to have a cubic dependence on wind speed. This result supports the hypothesis that, if bubble mediated exchange is important, the transfer velocity should increase proportionally with whitecap coverage, since whitecap coverage been shown to increase with at least a cubic dependence on wind speed. However, the very large uncertainties under high wind speed conditions limit the universality of this result and the role of breaking waves and bubble modulated transfer. Here, we present results of the combination of turbulence, deep-ocean wave statistics, whitecapping, and CO2 gas exchange measured during the Southern Ocean Gas Exchange Experiment (SO GasEx) with sustained conditions between 10-20 m s-1. Directional ocean wave spectra, significant wave height, peak wave period, and peak wave direction were obtained with a Wave and Surface Current Monitoring System (WaMoS® II). WaMoS® II also has the capability to resolve two-dimensional maps of surface elevation snapshots with the significant advantage of continuous availability of wave data in rough seas. In addition, significant wave height was measured using a laser altimeter as well as a nadir-looking microwave system. Oceanic turbulent kinetic energy dissipation rates were measured using a pulse

  17. Stoichiometry determined exchange interactions in amorphous ternary transition metal oxides: Theory and experiment

    SciTech Connect

    Hu, Shu-jun; Yan, Shi-shen Zhang, Yun-peng; Zhao, Ming-wen; Kang, Shi-shou; Mei, Liang-mo

    2014-07-28

    Amorphous transition metal oxides exhibit exotic transport and magnetic properties, while the absence of periodic structure has long been a major obstacle for the understanding of their electronic structure and exchange interaction. In this paper, we have formulated a theoretical approach, which combines the melt-quench approach and the spin dynamic Monte-Carlo simulations, and based on it, we explored amorphous Co{sub 0.5}Zn{sub 0.5}O{sub 1−y} ternary transition metal oxides. Our theoretical results reveal that the microstructure, the magnetic properties, and the exchange interactions of Co{sub 0.5}Zn{sub 0.5}O{sub 1−y} are strongly determined by the oxygen stoichiometry. In the oxygen-deficient sample (y > 0), we have observed the long-range ferromagnetic spin ordering which is associated with the non-stoichiometric cobalt-rich region rather than metallic clusters. On the other hand, the microstructure of stoichiometric sample takes the form of continuous random networks, and no long-range ferromagnetism has been observed in it. Magnetization characterization of experimental synthesized Co{sub 0.61}Zn{sub 0.39}O{sub 1−y} films verifies the relation between the spin ordering and the oxygen stoichiometry. Furthermore, the temperature dependence of electrical transport shows a typical feature of semiconductors, in agreement with our theoretical results.

  18. Systemic Thrombolysis Versus Device Exchange for Pump Thrombosis Management: A Single-Center Experience.

    PubMed

    Oezpeker, Cenk; Zittermann, Armin; Ensminger, Stephan; Kizner, Lukas; Koster, Andreas; Sayin, Ali; Schoenbrodt, Michael; Milting, Hendrik; Gummert, Jan F; Morshuis, Michiel

    2016-01-01

    In patients with left ventricular assist device (LVAD) implants, pump thrombosis is a potential life-threatening complication. In a retrospective data analysis, we compared clinical outcomes in 50 patients with HeartWare (HW) or HeartMate II implants undergoing device exchange (DEx; n = 21) or systemic thrombolysis (STL; n = 29) for pump thrombosis. Primary end-point was survival up to 90 days postintervention. Secondary end-points were the need for blood products postintervention, duration of intensive care unit stay, in-hospital stay, 90 day and 2 year therapy failure (the need for additional surgical or nonsurgical intervention because of pump thrombosis), and 2 year survival. Ninety-day survival was 89.3% in the STL group and 91.0% in the DEx group (p = 0.901). Compared with the DEx group, the average use of different blood products was lower (p < 0.001), and duration of intensive care unit stay and in-hospital stay tended to be shorter in the STL group (p values = 0.086 and 0.048, respectively). However, 90 day freedom from therapy failure was significantly lower in the STL group than in the DEx exchange group (p = 0.027) and so was 2 year freedom from therapy failure (p = 0.006). Two-year survival was comparable between groups (p = 0.267). Our data indicate that STL can be considered as a therapeutic option in LVAD patients with pump thrombosis. PMID:26771393

  19. Beam dynamics simulations of the transverse-to-longitudinal emittance exchange proof-of-principle experiment at the Argonne Wakefield Accelerator

    SciTech Connect

    Rihaoui, M.; Gai, W.; Kim, K.J.; Piot, Philippe; Power, John Gorham; Sun, Y.E.; /Fermilab

    2009-01-01

    Transverse-to-longitudinal emittance exchange has promising applications in various advanced acceleration and light source concepts. A proof-of-principle experiment to demonstrate this phase space manipulation method is currently being planned at the Argonne Wakefield Accelerator. The experiment focuses on exchanging a low longitudinal emittance with a high transverse horizontal emittance and also incorporates room for possible parametric studies e.g. using an incoming flat beam with tunable horizontal emittance. In this paper, we present realistic start-to-end beam dynamics simulation of the scheme, explore the limitations of this phase space exchange.

  20. Beam dynamics simulations of the transverse-to-longitudinal emittance exchange proof-of-principle experiment at the Argonne Wakefield Accelerator.

    SciTech Connect

    Gao, F.; Gai, W.; Power, J. G.; Kim, K. J.; Sun, Y. E.; Piot, P.; Rihaoui, M.; High Energy Physics; Northern Illinois Univ.; FNAL

    2009-01-01

    Transverse-to-longitudinal emittance exchange has promising applications in various advanced acceleration and light source concepts. A proof-of-principle experiment to demonstrate this phase space manipulation method is currently being planned at the Argonne Wakefield Accelerator. The experiment focuses on exchanging a low longitudinal emittance with a high transverse horizontal emittance and also incorporates room for possible parametric studies e.g. using an incoming flat beam with tunable horizontal emittance. In this paper, we present realistic start-to-end beam dynamics simulation of the scheme, explore the limitations of this phase space exchange.

  1. Beam dynamics simulations of the transverse-to-longitudinal emittance exchange proof-of-principle experiment at the Argonne Wakefield Accelerator

    SciTech Connect

    Rihaoui, M.; Gai, W.; Kim, K.-J.; Power, J. G.; Piot, P.; Sun, Y.-E.

    2009-01-22

    Transverse-to-longitudinal emittance exchange has promising applications in various advanced acceleration and light source concepts. A proof-of-principle experiment to demonstrate this phase space manipulation method is currently being planned at the Argonne Wakefield Accelerator. The experiment focuses on exchanging a low longitudinal emittance with a high transverse horizontal emittance and also incorporates room for possible parametric studies e.g. using an incoming flat beam with tunable horizontal emittance. In this paper, we present realistic start-to-end beam dynamics simulation of the scheme, explore the limitations of this phase space exchange.

  2. Allelic Interactions Heritably Alter the Activity of a Metastable Maize Pl Allele

    PubMed Central

    Hollick, J. B.; Patterson, G. I.; Coe-Jr., E. H.; Cone, K. C.; Chandler, V. L.

    1995-01-01

    The maize pl locus encodes a transcriptional activator of anthocyanin biosynthetic genes. The Pl-Rhoades (Pl-Rh) allele confers robust purple anthocyanin pigment in several tissues. Spontaneous derivatives of Pl-Rh, termed Pl'-mahogany (Pl'-mah), arise that confer reduced pigment and are meiotically heritable. These derivatives influence other Pl-Rh alleles such that only Pl'-mah alleles are transmitted from a Pl-Rh/Pl'-mah heterozygote. Genetic crosses establish that chromosomal segregation distortion does not explain this exclusive transmission and suggest that Pl-Rh invariably changes to Pl'-mah when exposed to Pl'-mah. Such behavior is a hallmark of paramutation. Cosegregation experiments demonstrate that this paramutagenic activity is genetically linked to the pl locus. By visually quantifying pl action through successive crosses, we find that phenotypic expression is inversely related to paramutagenic strength. In addition, the paramutagenic state is metastable; reversion to a nonparamutagenic Pl-Rh state can occur. The behavior of Pl-Rh is unique, yet it shares characteristics with paramutation at two other maize loci, b and r. Previous analysis of b and r paramutation revealed extensive differences and led to suggestions of distinct molecular mechanisms. Consideration of the common features of all three systems reinvigorates the interpretation that the mechanistic processes of these three allelic interactions are similar. PMID:8647404

  3. An overview of the regional experiments for land-atmosphere exchanges 2012 (REFLEX 2012) campaign

    NASA Astrophysics Data System (ADS)

    Timmermans, Wim; Van der Tol, Christiaan; Timmermans, Joris; Ucer, Murat; Chen, Xuelong; Alonso, Luis; Moreno, Jose; Carrara, Arnaud; Lopez, Ramon; de la Cruz Tercero, Fernando; Corcoles, Horacio L.; de Miguel, Eduardo; Sanchez, Jose A. G.; Pérez, Irene; Franch, Belen; Munoz, Juan-Carlos J.; Skokovic, Drazen; Sobrino, Jose; Soria, Guillem; MacArthur, Alasdair; Vescovo, Loris; Reusen, Ils; Andreu, Ana; Burkart, Andreas; Cilia, Chiara; Contreras, Sergio; Corbari, Chiara; Calleja, Javier F.; Guzinski, Radoslaw; Hellmann, Christine; Herrmann, Ittai; Kerr, Gregoire; Lazar, Adina-Laura; Leutner, Benjamin; Mendiguren, Gorka; Nasilowska, Sylwia; Nieto, Hector; Pachego-Labrador, Javier; Pulanekar, Survana; Raj, Rahul; Schikling, Anke; Siegmann, Bastian; von Bueren, Stefanie; Su, Zhongbo (Bob)

    2014-12-01

    The REFLEX 2012 campaign was initiated as part of a training course on the organization of an airborne campaign to support advancement of the understanding of land-atmosphere interaction processes. This article describes the campaign, its objectives and observations, remote as well as in situ. The observations took place at the experimental Las Tiesas farm in an agricultural area in the south of Spain. During the period of ten days, measurements were made to capture the main processes controlling the local and regional land-atmosphere exchanges. Apart from multi-temporal, multi-directional and multi-spatial space-borne and airborne observations, measurements of the local meteorology, energy fluxes, soil temperature profiles, soil moisture profiles, surface temperature, canopy structure as well as leaf-level measurements were carried out. Additional thermo-dynamical monitoring took place at selected sites. After presenting the different types of measurements, some examples are given to illustrate the potential of the observations made.

  4. An Overview of the Regional Experiments for Land-Atmosphere Exchanges 2012 (Reflex 2012) Campaign

    NASA Astrophysics Data System (ADS)

    Timmermans, Wim J.; Tol, Christiaan van der; Timmermans, Joris; Ucer, Murat; Chen, Xuelong; Alonso, Luis; Moreno, Jose; Carrara, Arnaud; Lopez, Ramon; de la Cruz Tercero, Fernando; Corcoles, Horacio L.; De Miguel, Eduardo; Sanchez, Jose A. G.; Pérez, Irene; Franch, Belen; Munoz, Juan-Carlos J.; Skokovic, Drazen; Sobrino, Jose; Soria, Guillem; MacArthur, Alasdair; Vescovo, Loris; Reusen, Ils; Andreu, Ana; Burkart, Andreas; Cilia, Chiara; Contreras, Sergio; Corbari, Chiara; Calleja, Javier F.; Guzinski, Radoslaw; Hellmann, Christine; Herrmann, Ittai; Kerr, Gregoire; Lazar, Adina-Laura; Leutner, Benjamin; Mendiguren, Gorka; Nasilowska, Sylwia; Nieto, Hector; Pachego-Labrador, Javier; Pulanekar, Survana; Raj, Rahul; Schikling, Anke; Siegmann, Bastian; von Bueren, Stefanie; Su, Zhongbo

    2015-12-01

    The REFLEX 2012 campaign was initiated as part of a training course on the organization of an airborne campaign to support advancement of the understanding of land-atmosphere interaction processes. This article describes the campaign, its objectives and observations, remote as well as in situ. The observations took place at the experimental Las Tiesas farm in an agricultural area in the south of Spain. During the period of ten days, measurements were made to capture the main processes controlling the local and regional land-atmosphere exchanges. Apart from multi-temporal, multi-directional and multi-spatial space-borne and airborne observations, measurements of the local meteorology, energy fluxes, soil temperature profiles, soil moisture profiles, surface temperature, canopy structure as well as leaf-level measurements were carried out. Additional thermo-dynamical monitoring took place at selected sites. After presenting the different types of measurements, some examples are given to illustrate the potential of the observations made.

  5. Solute exchange at the fracture-matrix wall involving significant buoyancy effects - an analog experiment

    NASA Astrophysics Data System (ADS)

    Michel, L.; Meheust, Y.; Bouquain, J.; Caudal, J.; de Bremond D'Ars, J.; de Dreuzy, J.; Davy, P.

    2008-12-01

    Contaminant transport in heterogeneous fractured aquifers occurs mostly through the networks of intersecting fractures. The physical mechanisms of solute transport in a single fracture with impermeable walls are well identified: advection, micro-dispersion (including molecular diffusion) Taylor-Aris dispersion, roughness dispersion, and aperture-variation dispersion. The description of the mass transfert coefficient between the region of high permeability (the fracture) and that of low permeability (the surrounding matrix), when the permeability of the latter cannot be neglected, is in contrast poorly understood. We address here solute transport through a synthetic fracture with a porous wall placed under the fracture, and for which buoyancy effects significantly promote solute exchange at the porous wall. We have developed an analog experimental setup in which the planar horizontal fracture is 1 m long, 5 cm wide and its mean aperture is 5 mm. It is bounded by either two smooth parallel Plexiglass plates (impermeable walls configuration), or by one such plate and a porous medium consisting of 1 mm glass beads ("semi-permeable" configuration). A permanent laminar water flow is forced through the fracture at controlled mean velocity (~ 1mm/s). The flow conditions inside the experimental fracture have been characterized using three-dimensional finite volume numerical simulations of the flow. A dye (patent blue) injection system simulates a point source of contaminant along the center plane of the experimental fracture. The tracer plume is tracked using a visualization system based on (i) lasers illuminating a series of vertical linear optical sensor arrays, and (ii) 4 cameras positioned side by side and providing a composite image of the fracture length, viewed from the side. The two measurement systems yield consistent quantitative temporal descriptions of the tracer concentration, integrated over the fracture width and at several positions along the fracture length

  6. Bomb radiocarbon in the Red Sea: A medium-scale gas exchange experiment

    SciTech Connect

    Cember, R.

    1989-02-15

    The history of bomb-produced radiocarbon in the surface waters of the Red Sea and the western Gulf of Aden was reconstructed from annual growth bands of corals. Gulf of Aden surface water entering the Red Sea and flowing to the north at the surface of the Red Sea becomes progressively enriched in bomb /sup 14/C by air-sea exchange of carbon dioxide. With physical oceanographic observations and analysis as the basis of a simple model, this progressive northward enrichment can be used to calculate a mean invasionn flux for CO/sub 2/ across the Red Sea surface. The CO/sub 2/ invasion flux so calculated is 8 mol/m/sup 2//yr with an uncertainty of approximately 2 mol/m/sup 2//yr. When combined with the extensive historical observations of wind speeds in the Red Sea, the calculated CO/sub 2/ invasion flux supports the empirical relationship between CO/sub 2/ invasion and wind speed proposed by other workers. Sea surface pCO/sub 2/ was measured at seven stations along the length of the Red Sea in January 1985. These pCO/sub 2/ data show that in midwinter the net flux of CO/sub 2/ across the Red Sea surface (i.e. the difference between the invasion and evasion fluxes) is approximately zero for the Red Sea as a whole. copyright American Geophysical Union 1989

  7. Vapor Compression and Thermoelectric Heat Pump Heat Exchangers for a Condensate Distillation System: Design and Experiment

    NASA Technical Reports Server (NTRS)

    Erickson, Lisa R.; Ungar, Eugene K.

    2013-01-01

    Maximizing the reuse of wastewater while minimizing the use of consumables is critical in long duration space exploration. One of the more promising methods of reclaiming urine is the distillation/condensation process used in the cascade distillation system (CDS). This system accepts a mixture of urine and toxic stabilizing agents, heats it to vaporize the water and condenses and cools the resulting water vapor. The CDS wastewater flow requires heating and its condensate flow requires cooling. Performing the heating and cooling processes separately requires two separate units, each of which would require large amounts of electrical power. By heating the wastewater and cooling the condensate in a single heat pump unit, mass, volume, and power efficiencies can be obtained. The present work describes and compares two competing heat pump methodologies that meet the needs of the CDS: 1) a series of mini compressor vapor compression cycles and 2) a thermoelectric heat exchanger. In the paper, the system level requirements are outlined, the designs of the two heat pumps are described in detail, and the results of heat pump performance tests are provided. A summary is provided of the heat pump mass, volume and power trades and a selection recommendation is made.

  8. qcML: an exchange format for quality control metrics from mass spectrometry experiments.

    PubMed

    Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W P; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A; Kelstrup, Christian D; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S; Olsen, Jesper V; Heck, Albert J R; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

    2014-08-01

    Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml. PMID:24760958

  9. qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments*

    PubMed Central

    Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W. P.; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A.; Kelstrup, Christian D.; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S.; Olsen, Jesper V.; Heck, Albert J. R.; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

    2014-01-01

    Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml. PMID:24760958

  10. Experiments on vibration of heat-exchanger tube arrays in cross flow

    SciTech Connect

    Blevins, R.D.; Gibert, R.J.; Villard, B.

    1981-04-01

    A series of tests has been made at the Commissariat a L Energie Atomique, Saclay, France, in cooperation with General Atomic Company, San Diego, on flow-induced vibration of simulated heat exchanger tube bundles in a cross flow of air. The tests were of two types. In the first type, a tube instrumented with pressure transducers was inserted at various locations in a tube bundle. Measurements were made of pressure spectra, coherence, and lift force. It was found that the turbulence-induced pressures rise from a low value at the bundle entrance to a relatively high value within the bundle. In the second type of test, tube bundles were fabricated from flexible plastic tubes, cantilevered off a tube sheet, and the vibration induced by cross flow was observed. An investigation was made of the effect of tube-to-tube frequency difference and spacing on the onset of instability. It was found that while present theory often qualitatively predicts the correct trends, it may not be quantitatively accurate in many cases.

  11. Transatlantic Student Exchange between Canada and Europe: Experiences from the CEIHPAL Project

    ERIC Educational Resources Information Center

    Sherriff, Nigel Stuart; Jeffery, Amanda; Davies, John Kenneth; Hills, Marcia; Carroll, Simon; Jackson, Suzanne; Krupa, Gene; Goepel, Eberhard; Hofmeister, Arnd; Tountas, Yannis; Attorp, Adrienne

    2012-01-01

    International student mobility amongst and between countries has become increasingly common and forms a central feature of the global higher education system. This paper examines the key learning experiences relating to the student mobility component of the Canadian-European Initiative for Health Promotion Advanced Learning (CEIHPAL) project.…

  12. Charge-exchange and fusion reaction measurements during compression experiments with neutral beam heating in the Tokamak Fusion Test Reactor

    SciTech Connect

    Kaita, R.; Heidbrink, W.W.; Hammett, G.W.; Chan, A.A.; England, A.C.; Hendel, H.W.; Medley, S.S.; Nieschmidt, E.; Roquemore, A.L.; Scott, S.D.

    1986-04-01

    Adiabatic toroidal compression experiments were performed in conjunction with high power neutral beam injection in the Tokamak Fusion Test Reactor (TFTR). Acceleration of beam ions to energies nearly twice the injection energy was measured with a charge-exchange neutral particle analyzer. Measurements were also made of 2.5 MeV neutrons and 15 MeV protons produced in fusion reactions between the deuterium beam ions and the thermal deuterium and /sup 3/He ions, respectively. When the plasma was compressed, the d(d,n)/sup 3/He fusion reaction rate increased a factor of five, and the /sup 3/He(d,p)/sup 4/He rate by a factor of twenty. These data were simulated with a bounce-averaged Fokker-Planck program, which assumed conservation of angular momentum and magnetic moment during compression. The results indicate that the beam ion acceleration was consistent with adiabatic scaling.

  13. Proton Form Factor Puzzle and the CEBAF Large Acceptance Spectrometer (CLAS) two-photon exchange experiment

    NASA Astrophysics Data System (ADS)

    Rimal, Dipak

    The electromagnetic form factors are the most fundamental observables that encode information about the internal structure of the nucleon. The electric (GE) and the magnetic ( GM) form factors contain information about the spatial distribution of the charge and magnetization inside the nucleon. A significant discrepancy exists between the Rosenbluth and the polarization transfer measurements of the electromagnetic form factors of the proton. One possible explanation for the discrepancy is the contributions of two-photon exchange (TPE) effects. Theoretical calculations estimating the magnitude of the TPE effect are highly model dependent, and limited experimental evidence for such effects exists. Experimentally, the TPE effect can be measured by comparing the ratio of positron-proton elastic scattering cross section to that of the electron-proton [R = sigma(e +p)/sigma(e+p)]. The ratio R was measured over a wide range of kinematics, utilizing a 5.6 GeV primary electron beam produced by the Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Lab. This dissertation explored dependence of R on kinematic variables such as squared four-momentum transfer (Q2) and the virtual photon polarization parameter (epsilon). A mixed electron-positron beam was produced from the primary electron beam in experimental Hall B. The mixed beam was scattered from a liquid hydrogen (LH2) target. Both the scattered lepton and the recoil proton were detected by the CEBAF Large Acceptance Spectrometer (CLAS). The elastic events were then identified by using elastic scattering kinematics. This work extracted the Q2 dependence of R at high epsilon(epsilon > 0.8) and the $epsilon dependence of R at approx 0.85 GeV2. In these kinematics, our data confirm the validity of the hadronic calculations of the TPE effect by Blunden, Melnitchouk, and Tjon. This hadronic TPE effect, with additional corrections contributed by higher excitations of the intermediate state nucleon, largely

  14. Proteus - An experimenter's view. [of spacecraft carrying exchangable Explorer scientific experiments

    NASA Technical Reports Server (NTRS)

    Hibbard, W. D.

    1984-01-01

    The scientific experiments package to be carried by the Proteus system takes the form of an Instrument Load carried into orbit by a Space Shuttle, and there mated to a Proteus spacecraft with the Shuttle's Remote Manipulator System. The Proteus system extends to ground support equipment, development tools, and communications, as well as the orbiting satellites. It is expected that Proteus will be able to triple the number of Explorer missions while staying within the current budgetary allocation for such missions. The Proteus spacecraft encompasses a system interface assembly plug, a data handling module, remote interface units, and a power distribution module.

  15. Experiences of women with breast cancer: exchanging social support over the CHESS computer network.

    PubMed

    Shaw, B R; McTavish, F; Hawkins, R; Gustafson, D H; Pingree, S

    2000-01-01

    Using an existential-phenomenological approach, this paper describes how women with breast cancer experience the giving and receiving of social support in a computer-mediated context. Women viewed their experiences with the computer-mediated support group as an additional and unique source of support in facing their illness. Anonymity within the support group fostered equalized participation and allowed women to communicate in ways that would have been more difficult in a face-to-face context. The asynchronous communication was a frustration to some participants, but some indicated that the format allowed for more thoughtful interaction. Motivations for seeking social support appeared to be a dynamic process, with a consistent progression from a position of receiving support to that of giving support. The primary benefits women received from participation in the group were communicating with other people who shared similar problems and helping others, which allowed them to change their focus from a preoccupation with their own sickness to thinking of others. Consistent with past research is the finding that women in this study expressed that social support is a multidimensional phenomenon and that their computer-mediated support group provided abundant emotional support, encouragement, and informational support. Excerpts from the phenomenological interviews are used to review and highlight key theoretical concepts from the research literatures on computer-mediated communication, social support, and the psychosocial needs of women with breast cancer. PMID:11010346

  16. A novel HLA-B*40 allele, B*40:01:40, identified in a Chinese individual.

    PubMed

    Pei, Y F; Huang, H N; Li, H C; Shen, W D

    2016-08-01

    A new allele, officially named B*40:01:40, was detected in a Chinese individual by sequence-based typing (SBT). The new allele differs from B*40:01:01 by a single nucleotide exchange at position 99 in codon 9, which results in synonymous substitution and seems not to compromise the HLA complex and T-cell receptor interaction. PMID:27302621

  17. Invasive Allele Spread under Preemptive Competition

    NASA Astrophysics Data System (ADS)

    Yasi, J. A.; Korniss, G.; Caraco, T.

    We study a discrete spatial model for invasive allele spread in which two alleles compete preemptively, initially only the "residents" (weaker competitors) being present. We find that the spread of the advantageous mutation is well described by homogeneous nucleation; in particular, in large systems the time-dependent global density of the resident allele is well approximated by Avrami's law.

  18. Reduced Height (Rht) Alleles Affect Wheat Grain Quality

    PubMed Central

    Casebow, Richard; Hadley, Caroline; Uppal, Rajneet; Addisu, Molla; Loddo, Stefano; Kowalski, Ania; Griffiths, Simon; Gooding, Mike

    2016-01-01

    The effects of dwarfing alleles (reduced height, Rht) in near isogenic lines on wheat grain quality are characterised in field experiments and related to effects on crop height, grain yield and GA-sensitivity. Alleles included those that conferred GA-insensitivity (Rht-B1b, Rht-B1c, Rht-D1b, Rht-D1c) as well as those that retained GA-sensitivity (rht(tall), Rht8, Rht8 + Ppd-D1a, Rht12). Full characterisation was facilitated by including factors with which the effects of Rht alleles are known to interact for grain yield (i.e. system, [conventional or organic]; tillage intensity [plough-based, minimum or zero]; nitrogen fertilizer level [0–450 kg N/ha]; and genetic backgrounds varying in height [cvs Maris Huntsman, Maris Widgeon, and Mercia]. Allele effects on mean grain weight and grain specific weight were positively associated with final crop height: dwarfing reduced these quality criteria irrespective of crop management or GA-sensitivity. In all but two experiments the effects of dwarfing alleles on grain nitrogen and sulphur concentrations were closely and negatively related to effects on grain yield, e.g. a quadratic relationship between grain yield and crop height manipulated by the GA-insensitive alleles was mirrored by quadratic relationships for nitrogen and sulphur concentrations: the highest yields and most dilute concentrations occurred around 80cm. In one of the two exceptional experiments the GA-insensitive Rht-B1b and Rht-B1c significantly (P<0.05) reduced grain nitrogen concentration in the absence of an effect on yield, and in the remaining experiment the GA-sensitive Rht8 significantly reduced both grain yield and grain nitrogen concentration simultaneously. When Rht alleles diluted grain nitrogen concentration, N:S ratios and SDS-sedimentation volumes were often improved. Hagberg falling number (HFN) was negatively related to crop height but benefits from dwarfing were only seen for GA-insensitive alleles. For HFN, therefore, there was the

  19. Reduced Height (Rht) Alleles Affect Wheat Grain Quality.

    PubMed

    Casebow, Richard; Hadley, Caroline; Uppal, Rajneet; Addisu, Molla; Loddo, Stefano; Kowalski, Ania; Griffiths, Simon; Gooding, Mike

    2016-01-01

    The effects of dwarfing alleles (reduced height, Rht) in near isogenic lines on wheat grain quality are characterised in field experiments and related to effects on crop height, grain yield and GA-sensitivity. Alleles included those that conferred GA-insensitivity (Rht-B1b, Rht-B1c, Rht-D1b, Rht-D1c) as well as those that retained GA-sensitivity (rht(tall), Rht8, Rht8 + Ppd-D1a, Rht12). Full characterisation was facilitated by including factors with which the effects of Rht alleles are known to interact for grain yield (i.e. system, [conventional or organic]; tillage intensity [plough-based, minimum or zero]; nitrogen fertilizer level [0-450 kg N/ha]; and genetic backgrounds varying in height [cvs Maris Huntsman, Maris Widgeon, and Mercia]. Allele effects on mean grain weight and grain specific weight were positively associated with final crop height: dwarfing reduced these quality criteria irrespective of crop management or GA-sensitivity. In all but two experiments the effects of dwarfing alleles on grain nitrogen and sulphur concentrations were closely and negatively related to effects on grain yield, e.g. a quadratic relationship between grain yield and crop height manipulated by the GA-insensitive alleles was mirrored by quadratic relationships for nitrogen and sulphur concentrations: the highest yields and most dilute concentrations occurred around 80cm. In one of the two exceptional experiments the GA-insensitive Rht-B1b and Rht-B1c significantly (P<0.05) reduced grain nitrogen concentration in the absence of an effect on yield, and in the remaining experiment the GA-sensitive Rht8 significantly reduced both grain yield and grain nitrogen concentration simultaneously. When Rht alleles diluted grain nitrogen concentration, N:S ratios and SDS-sedimentation volumes were often improved. Hagberg falling number (HFN) was negatively related to crop height but benefits from dwarfing were only seen for GA-insensitive alleles. For HFN, therefore, there was the

  20. Effective marker alleles associated with type 2 resistance to Fusarium head blight infection in fields

    PubMed Central

    Li, Tao; Luo, Meng; Zhang, Dadong; Wu, Di; Li, Lei; Bai, Guihua

    2016-01-01

    Molecular markers associated with known quantitative trait loci (QTLs) for type 2 resistance to Fusarium head blight (FHB) in bi-parental mapping population usually have more than two alleles in breeding populations. Therefore, understanding the association of each allele with FHB response is particularly important to marker-assisted enhancement of FHB resistance. In this paper, we evaluated FHB severities of 192 wheat accessions including landraces and commercial varieties in three field growing seasons, and genotyped this panel with 364 genome-wide informative molecular markers. Among them, 11 markers showed reproducible marker-trait association (p < 0.05) in at least two experiments using a mixed model. More than two alleles were identified per significant marker locus. These alleles were classified into favorable, unfavorable and neutral alleles according to the normalized genotypic values. The distributions of effective alleles at these loci in each wheat accession were characterized. Mean FHB severities increased with decreased number of favorable alleles at the reproducible loci. Chinese wheat landraces and Japanese accessions have more favorable alleles at the majority of the reproducible marker loci. FHB resistance levels of varieties can be greatly improved by introduction of these favorable alleles and removal of unfavorable alleles simultaneously at these QTL-linked marker loci. PMID:27436944

  1. A Computer Simulation Study of Vntr Population Genetics: Constrained Recombination Rules Out the Infinite Alleles Model

    PubMed Central

    Harding, R. M.; Boyce, A. J.; Martinson, J. J.; Flint, J.; Clegg, J. B.

    1993-01-01

    Extensive allelic diversity in variable numbers of tandem repeats (VNTRs) has been discovered in the human genome. For population genetic studies of VNTRs, such as forensic applications, it is important to know whether a neutral mutation-drift balance of VNTR polymorphism can be represented by the infinite alleles model. The assumption of the infinite alleles model that each new mutant is unique is very likely to be violated by unequal sister chromatid exchange (USCE), the primary process believed to generate VNTR mutants. We show that increasing both mutation rates and misalignment constraint for intrachromosomal recombination in a computer simulation model reduces simulated VNTR diversity below the expectations of the infinite alleles model. Maximal constraint, represented as slippage of single repeats, reduces simulated VNTR diversity to levels expected from the stepwise mutation model. Although misalignment rule is the more important variable, mutation rate also has an effect. At moderate rates of USCE, simulated VNTR diversity fluctuates around infinite alleles expectation. However, if rates of USCE are high, as for hypervariable VNTRs, simulated VNTR diversity is consistently lower than predicted by the infinite alleles model. This has been observed for many VNTRs and accounted for by technical problems in distinguishing alleles of neighboring size classes. We use sampling theory to confirm the intrinsically poor fit to the infinite alleles model of both simulated VNTR diversity and observed VNTR polymorphisms sampled from two Papua New Guinean populations. PMID:8293988

  2. Clostridium difficile Genome Editing Using pyrE Alleles.

    PubMed

    Ehsaan, Muhammad; Kuehne, Sarah A; Minton, Nigel P

    2016-01-01

    Precise manipulation (in-frame deletions and substitutions) of the Clostridium difficile genome is possible through a two-stage process of single-crossover integration and subsequent isolation of double-crossover excision events using replication-defective plasmids that carry a counterselection marker. Use of a codA (cytosine deaminase) or pyrE (orotate phosphoribosyltransferase) as counter selection markers appears equally effective, but there is considerable merit in using a pyrE mutant as the host as, through the use of allele-coupled exchange (ACE) vectors, mutants created (by whatever means) can be rapidly complemented concomitant with restoration of the pyrE allele. This avoids the phenotypic effects frequently observed with high-copy-number plasmids and dispenses with the need to add antibiotic to ensure plasmid retention. PMID:27507332

  3. Allele surfing promotes microbial adaptation from standing variation.

    PubMed

    Gralka, Matti; Stiewe, Fabian; Farrell, Fred; Möbius, Wolfram; Waclaw, Bartlomiej; Hallatschek, Oskar

    2016-08-01

    The coupling of ecology and evolution during range expansions enables mutations to establish at expanding range margins and reach high frequencies. This phenomenon, called allele surfing, is thought to have caused revolutions in the gene pool of many species, most evidently in microbial communities. It has remained unclear, however, under which conditions allele surfing promotes or hinders adaptation. Here, using microbial experiments and simulations, we show that, starting with standing adaptive variation, range expansions generate a larger increase in mean fitness than spatially uniform population expansions. The adaptation gain results from 'soft' selective sweeps emerging from surfing beneficial mutations. The rate of these surfing events is shown to sensitively depend on the strength of genetic drift, which varies among strains and environmental conditions. More generally, allele surfing promotes the rate of adaptation per biomass produced, which could help developing biofilms and other resource-limited populations to cope with environmental challenges. PMID:27307400

  4. Xe/sup +n/-Xe/sup +n/ charge-exchange experiment using a split-beam and beam-intersection technique

    SciTech Connect

    Mazarakis, M.G.; Berry, G.H.; Colton, E.P.

    1981-01-01

    We describe a design for colliding-beam charge-exchange experiments using the Xe beam that exits from the 1.5-MV Dynamitron of the Argonne National Laboratory Heavy-Ion-Fusion Facility. These experiments canb e performed at any Xe beam energy as it becomes available, from 1.5 MeV to 10 MeV, and at any charge state from Xe/sup +1/ to Xe/sup +8/.

  5. Reassessment of the garnet-clinopyroxene Fe-Mg exchange thermometer: I. Evaluation of the Pattison and Newton (1989) experiments

    NASA Astrophysics Data System (ADS)

    Aranovich, L. Y.; Pattison, D. R. M.

    1995-02-01

    This is Part I of a two-part study on the garnet(Grt)-clinopyroxene(Cpx) Fe-Mg exchange equilibrium widely used in geothermometry of amphibolites, granulites and eclogites. The experimental data set previously published by Pattison and Newton (PN) on this equilibrium comprises potentially the largest source of data used for extraction of thermody- namic properties for Grt and Cpx and for formulation of a new thermometer expression (Part 2 of this study). However, the experiments suggested unusual Grt and Cpx solution properties and resulted in a geothermometer expression that generally returns low temperatures for granulites. To verify the reliability of the experiments, and to test the experimental technique of Grt buffering used in the PN study, 69 of the 125 PN runs were reanalysed using wavelength dispersive spectroscopic analysis guided by backscattered electron images. Special attention was given to analysis of compositional changes in Grt in addition to Cpx. With minor exceptions, the reanalysis supports the analytical results of the original PN study. The mechanism of equilibration in the runs was a multicomponent solution-precipitation process involving dissolution of metastable Grt and Cpx starting materials and precipitation of newly formed Cpx and Grt, the latter assumed to represent equilibrium compositions. The experiments cannot be regarded either as reversed or as strictly bracketing. Nevertheless, Cpx compositional parameters, including Mg?, Na, Ca and Al, show the same smooth variations with temperature, pressure and composition as found by PN, suggestive of a close approach to equilibrium. Grt in run products retained the moderate heterogeneity of the starting Grt, although there are subtle compositional trends indicating small changes in Grt Mg? consistent with mass balance constraints. These results uphold the essential validity of the technique of Grt buffering used in the experiments. Nevertheless, it is possible that the final Grt

  6. Conformational dynamics of phenylene rings in poly(p-phenylene vinylene) as revealed by 13C magic-angle-spinning exchange nuclear magnetic resonance experiments

    NASA Astrophysics Data System (ADS)

    deAzevedo, E. R.; Franco, R. W. A.; Marletta, A.; Faria, R. M.; Bonagamba, T. J.

    2003-08-01

    Poly(p-phenylene vinylene) (PPV) has shown a great potential for electro-optical applications due to its electroluminescent and semiconducting properties. Such properties are directly related with the polymer chain conformation and dynamics. Then, it is important to understand in detail the local chain motions. In this work, three 13C solid-state magic-angle-spinning (MAS) exchange NMR techniques were used to study conformational dynamics of phenylene rings in PPV. The standard 2D MAS exchange experiment was used to identify exchange processes between equivalent and nonequivalent sites. Centerband-only detection of exchange (CODEX) experiments were applied to determine the amplitude of the phenylene ring flips and small-angle oscillations. Additionally, a new version of the CODEX technique, which allows for the selective observation of segments executing exchange between non-equivalent sites, is demonstrated and applied to determine the flipping fractions and the activation energies of the phenylene ring rotations. It was found that, at -15 °C, (26±3)% of the rings undergo 180° flips in the millisecond time scale, with average imprecision of (30±5)° and activation energies of (23±3) kJ/mol. Other (31±10)% of the rings perform only small-angle oscillations with an average amplitude of (9±2)°. These results corroborate previous experimental data and agree with recent ab initio calculations of potential energies barriers in phenylenevinylene oligomers.

  7. The tropical experiment of the stratosphere-troposphere exchange project (STEP): Science objectives, operations, and summary findings

    NASA Astrophysics Data System (ADS)

    Russell, P. B.; Pfister, L.; Selkirk, H. B.

    1993-05-01

    The Stratosphere-Troposphere Exchange Project Tropical Experiment (STEP Tropical) investigated stratosphere-troposphere exchange and dehydration processes in that region and season with the coldest average tropopause temperatures, the tropical western Pacific and northern Australia during the winter monsoon (January-February) of 1987. This is also a period of extensive convective activity and rainfall. In addition to this primary goal, STEP Tropical (1) extended stratospheric aircraft chemical tracer surveys to the southern hemisphere subtropics and mid-latitudes and (2) samples the anticyclone that dominates the circulation over Australia in the lower stratosphere during the winter monsoon. Advanced fast-response instruments on NASA's ER-2 aircraft measured meteorological variables, stratospheric and tropospheric tracers, particles, and radiative fluxes. ER-2 sorties included six ferry flight legs across the Pacific and eleven flights in the Australian region. The 1986-1987 monsoon was atypical in that (1) its data of onset, January 14, was 3 weeks later than normal and (2) it was unusually intense and sustained once it did arrive. As a consequence, almost all the flights were conducted under monsoon conditions, with only limited sampling of premonsoon and break-monsoon continental convection. Illustrations show flight paths for each sortie on satellite images and on 100 hPa synoptic flow charts as well as the timing of flights with respect to overall cloudiness in the Australian region. STEP Tropical results, reported in the accompanying set of papers, include (1) observational documentation of a convective scale cold trap that dries air of recent tropospheric origin to prevailing stratospheric minimum water vapor mixing ratios (3 ppmv or less); (2) indications that this drying mechanism can be effective not only in the anvils of the tallest clouds (which occur during ``break-monsoon'' conditions) but also in the anvils of tropical cyclones and monsoon mesoscale

  8. Experimental Determination of Thermodynamic Properties of Ion-Exchange in Heulandite: Binary Ion-Exchange Experiments at 55 and 85 oC Involving Ca2+, Sr2+, Na+, and K+

    SciTech Connect

    Fridriksson, T; Neuhoff, P S; Viani, B E; Bird, D K

    2004-04-26

    Heulandite is a common rock-forming zeolite that exhibits wide solid solution of extra framework cations, presumably due to ready ion exchange with aqueous solutions. In order to provide a quantitative basis for interpreting and predicting the distribution of aqueous species between heulandite and aqueous solutions, ion exchange equilibrium between heulandite and aqueous solutions with respect to the binary cation pairs Ca{sup 2+} - K{sup +}, Ca{sup 2+} - Na{sup +}, K{sup +} - Na{sup +}, K{sup +} - Sr{sup 2+}, Na{sup +} - Sr{sup 2+}, and Ca{sup 2+} - Sr{sup 2+} was investigated. Homoionic Ca-, K-, and Na-heulandites prepared from natural heulandite were equilibrated with 0.1 N Cl{sup -} solutions containing various proportions of the cations in a given binary pair at 55 and 85 C to define isotherms describing partitioning of the cations over a wide range of heulandite and solution composition with respect to the cations in each pair. In general, the experiments equilibrated rapidly, within 11-15 weeks at 55 C and 3-4 weeks at 85 C. The exception was the Ca{sup 2+} - Sr{sup 2+} binary exchange, which did not equilibrate even after 3 months at 55 C and 4 weeks at 85 C. Slow exchange of Sr{sup 2+} for Ca{sup 2+} also prohibited preparation of homoionic Sr-heulandite from the natural (Ca-rich) heulandite within 10 weeks in 2N SrCl{sub 2} solution at 90 C, although near homoionic Sr-heulandite was produced by exchange of K- and Na-heulandite. Experimentally determined isotherms were used to derive equilibrium constants for the ion exchange reactions and asymmetric Margules models describing the extent of non-ideality in extra framework solid solutions in heulandite. Regressed equilibrium constants for Ca{sup 2+}-Na{sup +}, Ca{sup 2+}-K{sup +}, and K{sup +}-Na{sup +} binary cation pairs at 55 C are internally consistent among each other (complying with the triangle rule), indicating good accuracy of these data. The maximum departure from internal Heulandite ion exchange

  9. Amide proton exchange rates of a bound pepsin inhibitor determined by isotope-edited proton NMR experiments

    SciTech Connect

    Fesik, S.W.; Luly, J.R.; Stein, H.H.; BaMaung, N.

    1987-09-30

    From a series of isotope-edited proton NMR spectra, amide proton exchange rates were measured at 20 C, 30 C, and 40/sup 0/C for a tightly bound /sup 15/N-labeled tripeptide inhibitor of porcine pepsin (IC50 = 1.7 X 10(-) M). Markedly different NH exchange rates were observed for the three amide protons of the bound inhibitor. The P1 NH exchanged much more slowly than the P2 NH and P3 NH. These results are discussed in terms of the relative solvent accessibility in the active site and the role of the NH protons of the inhibitor for hydrogen bonding to the enzyme. In this study a useful approach is demonstrated for obtaining NH exchange rates on ligands bound to biomacromolecules, the knowledge of which could be of potential utility in the design of therapeutically useful nonpeptide enzyme inhibitors from peptide leads.

  10. Ugrades of beam diagnostics in support of emittance-exchange experiments at the Fermilab A0 photoinjector

    SciTech Connect

    Lumpkin, A.H.; Johnson, A.S.; Ruan, J.; Santucci, J.; Sun, Y.-E.; Thurman-Keup, R.; Edwards, H.; /Fermilab

    2011-01-01

    The possibility of using electron beam phase space manipulations to support a free-electron laser accelerator design optimization has motivated our research. An ongoing program demonstrating the exchange of transverse horizontal and longitudinal emittances at the Fermilab A0 photoinjector has benefited recently from the upgrade of several of the key diagnostics stations. Accurate measurements of these properties upstream and downstream of the exchanger beamline are needed. Improvements in the screen resolution term and reduced impact of the optical system's depth-of-focus by using YAG:Ce single crystals normal to the beam direction will be described. The requirement to measure small energy spreads (<10 keV) in the spectrometer and the exchange process which resulted in bunch lengths less than 500 fs led to other diagnostics performance adjustments and upgrades as well. A longitudinal to transverse exchange example is also reported.

  11. Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Kazazic, Sasa; Zhang, Hui-Min; Schaub, Tanner M; Emmett, Mark R; Hendrickson, Christopher L; Blakney, Gregory T; Marshall, Alan G

    2010-04-01

    Mass analysis of proteolytic fragment peptides following hydrogen/deuterium exchange offers a general measure of solvent accessibility/hydrogen bonding (and thus conformation) of solution-phase proteins and their complexes. The primary problem in such mass analyses is reliable and rapid assignment of mass spectral peaks to the correct charge state and degree of deuteration of each fragment peptide, in the presence of substantial overlap between isotopic distributions of target peptides, autolysis products, and other interferant species. Here, we show that at sufficiently high mass resolving power (m/Delta m(50%) > or = 100,000), it becomes possible to resolve enough of those overlaps so that automated data reduction becomes possible, based on the actual elemental composition of each peptide without the need to deconvolve isotopic distributions. We demonstrate automated, rapid, reliable assignment of peptide masses from H/D exchange experiments, based on electrospray ionization FT-ICR mass spectra from H/D exchange of solution-phase myoglobin. Combined with previously demonstrated automated data acquisition for such experiments, the present data reduction algorithm enhances automation (and thus expands generality and applicability) for high-resolution mass spectrometry-based analysis of H/D exchange of solution-phase proteins. PMID:20116280

  12. Polymorphism of the HLA-B*15 group of alleles is generated following 5 lineages of evolution.

    PubMed

    Martínez-Laso, Jorge; Herraiz, Miguel Angel; Vidart, Jose Antonio; Peñaloza, Jorge; Barbolla, Maria Luz; Jurado, Maria Luisa; Cervera, Isabel

    2011-05-01

    Generation of the HLA-B*15 group of alleles has been analyzed using exon 1, intron 1, exon 2, intron 2, and exon 3 sequences from human and nonhuman primates. Results indicated that the 230 alleles analyzed could be grouped into 5 different lineages of evolution coming from nonhuman primate MHC-B* alleles sharing characteristic nucleotide sequences. The major evolutionary mechanism of evolution in this group of alleles is the gene conversion event with the exchange of genomic sequences present in other HLA-B*alleles. This evolutionary event reflects the importance of the exchanges between different genomic regions of distinct HLA-A*, -B*, or -C* alleles and only 1 group of HLA-B* alleles (B*15 in the present paper). These data also correlated with the geographic distribution of the lineages postulated and with the corresponding serologic specificities (B62, -63, -71, -72, -75, -76, and -77). In conclusion, the high degree of polymorphism of 1 group of alleles has a specific and simple pathway of evolution, which could result in new insight into the study of immune system functionality, disease association studies, and anthropological studies. PMID:21376098

  13. ELEVATED CO2 AND TEMPERATURE ALTER THE ECOSYSTEM C EXCHANGE IN A YOUNG DOUGLAS FIR MESOCOSM EXPERIMENT

    EPA Science Inventory

    We investigated the effects of elevated CO2 (EC) [ambient CO2 (AC) + 190 ppm] and elevated temperature (ET) [ambient temperature (AT) + 3.6 °C] on net ecosystem exchange (NEE) of seedling Douglas fir (Pseudotsuga menziesii) mesocosms. As the study utilized seedlings in reconstruc...

  14. Characterization of the treefrog null allele, 1991

    SciTech Connect

    Guttman, S.I.

    1992-04-01

    Spring peeper (Hyla crucifer) tadpoles collected from the waste storage area during the Biological and Ecological Site Characterization of the Feed Materials Production Center (FEMP) in 1986 and 1987 appeared to be unique. A null (inactive) allele was found at the glucose phosphate isomerase enzyme locus in significant frequencies (approximately 20%) each year; this allele did not appear to occur in the offsite sample collected approximately 15km from the FEMP. Null alleles at this locus have not been reported in other amphibian populations; when they have been found in other organisms they have invariably been lethal in the homozygous condition.

  15. Characterization of the treefrog null allele

    SciTech Connect

    Guttman, S.I. . Dept. of Zoology)

    1990-12-01

    As part of the authors intensive year-long baseline ecological study, they characterized the degree of genetic polymorphism and heterozygosity in selected Feed Materials Production Center (FMPC) populations using electrophoretic techniques. These data are being used as an indicator of stress by comparing populations on and off the FMPC site. The current study was initiated to determine whether this GPI null allele is lethal, when homozygous, in spring peepers. Also, a sampling protocol was implemented to determine whether a linear effect occurs relative to the frequency of the null allele offsite and to determine the origination site of the null allele. 18 refs., 2 figs., 4 tabs.

  16. Pyrosequencing for Accurate Imprinted Allele Expression Analysis

    PubMed Central

    Yang, Bing; Damaschke, Nathan; Yao, Tianyu; McCormick, Johnathon; Wagner, Jennifer; Jarrard, David

    2016-01-01

    Genomic imprinting is an epigenetic mechanism that restricts gene expression to one inherited allele. Improper maintenance of imprinting has been implicated in a number of human diseases and developmental syndromes. Assays are needed that can quantify the contribution of each paternal allele to a gene expression profile. We have developed a rapid, sensitive quantitative assay for the measurement of individual allelic ratios termed Pyrosequencing for Imprinted Expression (PIE). Advantages of PIE over other approaches include shorter experimental time, decreased labor, avoiding the need for restriction endonuclease enzymes at polymorphic sites, and prevent heteroduplex formation which is problematic in quantitative PCR-based methods. We demonstrate the improved sensitivity of PIE including the ability to detect differences in allelic expression down to 1%. The assay is capable of measuring genomic heterozygosity as well as imprinting in a single run. PIE is applied to determine the status of Insulin-like Growth Factor-2 (IGF2) imprinting in human and mouse tissues. PMID:25581900

  17. UREA/ammonium ion removal system for the orbiting frog otolith experiment. [ion exchange resins for water treatment during space missions

    NASA Technical Reports Server (NTRS)

    Schulz, J. R.; Anselmi, R. T.

    1976-01-01

    The feasibility of using free urease enzyme and ANGC-101 ion exchange resin to remove urea and ammonium ion for space system waste water applications was studied. Specifically examined is the prevention of urea and ammonia toxicity in a 30-day Orbiting Frog Otolith (OFO) flight experiment. It is shown that free urease enzyme used in conjunction with ANGC-101 ion-exchange resin and pH control can control urea and amonium ion concentration in unbuffered recirculating water. In addition, the resin does not adversely effect the bullfrogs by lowering the concentration of cations below critical minimum levels. Further investigations on bioburden control, frog waste excretion on an OFO diet, a trade-off analysis of methods of automating the urea/ammonium ion removal system and fabrication and test of a semiautomated breadboard were recommended as continuing efforts. Photographs of test equipment and test animals are shown.

  18. Variation in soil moisture and N availability modulates carbon and water exchange in a California grassland experiment

    SciTech Connect

    St. Clair, S.B.; Sudderth, E.; Fischer, M.L.; Torn, M.S.; Stuart, S.; Salve, R.; Eggett, D.; Ackerly, D.

    2009-03-15

    Variability in the magnitude and timing of precipitation is predicted to change under future climate scenarios. The primary objective of this study was to understand how variation in precipitation patterns consisting of soil moisture pulses mixed with intermittent dry down events influence ecosystem gas fluxes. We characterized the effects of precipitation amount and timing, N availability, and plant community composition on whole ecosystem and leaf gas exchange in a California annual grassland mesocosm study system that allowed precise control of soil moisture conditions. Ecosystem CO2 and fluxes increased significantly with greater precipitation and were positively correlated with soil moisture. A repeated 10 day dry down period following 11 days of variable precipitation inputs strongly depressed net ecosystem CO2 exchange (NEE) across a range of season precipitation totals, and plant community types. Ecosystem respiration (Re), evapotranspiration (ET) and leaf level photosynthesis (Amax) showed greatest sensitivity to dry down periods in low precipitation plots. Nitrogen additions significantly increased NEE, Re and Amax, particularly as water availability was increased. These results demonstrate that N availability and intermittent periods of soil moisture deficit (across a wide range of cumulative season precipitation totals) strongly modulate ecosystem gas exchange.

  19. Testing Hardy-Weinberg equilibrium on allelic data from VNTR loci

    SciTech Connect

    Geisser, S. ); Johnson, W. )

    1992-11-01

    Several methods for testing independence of pairs of alleles in a population that are obtained from a VNTR locus are presented. The authors assume an exchangeable quasi-continuous distribution of the fragment lengths used to measure the allelic pairs. Bivariate-estimated quantiles computed from the quantiles of the entire data set are then utilized for testing independence. These methods have the advantage of being minimally susceptible to the criticism of (a) the inability of a technology to measure to a few small-sized or rather large-sized fragments and (b) inadequate estimation of the homozygotic proportion. 6 refs., 3 tabs.

  20. Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression.

    PubMed

    Soderlund, Carol A; Nelson, William M; Goff, Stephen A

    2014-01-01

    Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor), where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense), and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available from https://code.google.com/p/allele

  1. Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression

    PubMed Central

    Soderlund, Carol A.; Nelson, William M.; Goff, Stephen A.

    2014-01-01

    Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor), where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense), and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available from https://code.google.com/p/allele

  2. Applying reactive models to column experiments to assess the hydrogeochemistry of seawater intrusion: Optimising ACUAINTRUSION and selecting cation exchange coefficients with PHREEQC

    NASA Astrophysics Data System (ADS)

    Boluda-Botella, N.; Valdes-Abellan, J.; Pedraza, R.

    2014-03-01

    Three sets of laboratory column experimental results concerning the hydrogeochemistry of seawater intrusion have been modelled using two codes: ACUAINTRUSION (Chemical Engineering Department, University of Alicante) and PHREEQC (U.S.G.S.). These reactive models utilise the hydrodynamic parameters determined using the ACUAINTRUSION TRANSPORT software and fit the chloride breakthrough curves perfectly. The ACUAINTRUSION code was improved, and the instabilities were studied relative to the discretisation. The relative square errors were obtained using different combinations of the spatial and temporal steps: the global error for the total experimental data and the partial error for each element. Good simulations for the three experiments were obtained using the ACUAINTRUSION software with slight variations in the selectivity coefficients for both sediments determined in batch experiments with fresh water. The cation exchange parameters included in ACUAINTRUSION are those reported by the Gapon convention with modified exponents for the Ca/Mg exchange. PHREEQC simulations performed using the Gains-Thomas convention were unsatisfactory, with the exchange coefficients from the database of PHREEQC (or range), but those determined with fresh water - natural sediment allowed only an approximation to be obtained. For the treated sediment, the adjusted exchange coefficients were determined to improve the simulation and are vastly different from those from the database of PHREEQC or batch experiment values; however, these values fall in an order similar to the others determined under dynamic conditions. Different cation concentrations were simulated using two different software packages; this disparity could be attributed to the defined selectivity coefficients that affect the gypsum equilibrium. Consequently, different calculated sulphate concentrations are obtained using each type of software; a smaller mismatch was predicted using ACUAINTRUSION. In general, the presented

  3. No oxygen isotope exchange between water and APS-sulfate at surface temperature: Evidence from quantum chemical modeling and triple-oxygen isotope experiments

    NASA Astrophysics Data System (ADS)

    Kohl, Issaku E.; Asatryan, Rubik; Bao, Huiming

    2012-10-01

    In both laboratory experiments and natural environments where microbial dissimilatory sulfate reduction (MDSR) occurs in a closed system, the δ34S ((34S/32S)sample/(34S/32S)standard - 1) for dissolved SO42- has been found to follow a typical Rayleigh-Distillation path. In contrast, the corresponding δ18O ((18O/16O)sample/(18O/16O)standard) - 1) is seen to plateau with an apparent enrichment of between 23‰ and 29‰ relative to that of ambient water under surface conditions. This apparent steady-state in the observed difference between δ18O and δ18OO can be attributed to any of these three steps: (1) the formation of adenosine-5'-phosphosulfate (APS) from ATP and SO42-, (2) oxygen exchange between sulfite (or other downstream sulfoxy-anions) and water later in the MDSR reaction chain and its back reaction to APS and sulfate, and (3) the re-oxidation of produced H2S or precursor sulfoxy-anions to sulfate in environments containing Fe(III) or O2. This study examines the first step as a potential pathway for water oxygen incorporation into sulfate. We examined the structures and process of APS formation using B3LYP/6-31G(d,p) hybrid density functional theory, implemented in the Gaussian-03 program suite, to predict the potential for oxygen exchange. We conducted a set of in vitro, enzyme-catalyzed, APS formation experiments (with no further reduction to sulfite) to determine the degree of oxygen isotope exchange between the APS-sulfate and water. Triple-oxygen-isotope labeled water was used in the reactor solutions to monitor oxygen isotope exchange between water and APS sulfate. The formation and hydrolysis of APS were identified as potential steps for oxygen exchange with water to occur. Quantum chemical modeling indicates that the combination of sulfate with ATP has effects on bond strength and symmetry of the sulfate. However, these small effects impart little influence on the integrity of the SO42- tetrahedron due to the high activation energy required for

  4. Geographically Distinct and Domain-Specific Sequence Variations in the Alleles of Rice Blast Resistance Gene Pib

    PubMed Central

    Vasudevan, Kumar; Vera Cruz, Casiana M.; Gruissem, Wilhelm; Bhullar, Navreet K.

    2016-01-01

    Rice blast is caused by Magnaporthe oryzae, which is the most destructive fungal pathogen affecting rice growing regions worldwide. The rice blast resistance gene Pib confers broad-spectrum resistance against Southeast Asian M. oryzae races. We investigated the allelic diversity of Pib in rice germplasm originating from 12 major rice growing countries. Twenty-five new Pib alleles were identified that have unique single nucleotide polymorphisms (SNPs), insertions and/or deletions, in addition to the polymorphic nucleotides that are shared between the different alleles. These partially or completely shared polymorphic nucleotides indicate frequent sequence exchange events between the Pib alleles. In some of the new Pib alleles, nucleotide diversity is high in the LRR domain, whereas, in others it is distributed among the NB-ARC and LRR domains. Most of the polymorphic amino acids in LRR and NB-ARC2 domains are predicted as solvent-exposed. Several of the alleles and the unique SNPs are country specific, suggesting a diversifying selection of alleles in various geographical locations in response to the locally prevalent M. oryzae population. Together, the new Pib alleles are an important genetic resource for rice blast resistance breeding programs and provide new information on rice-M. oryzae interactions at the molecular level. PMID:27446145

  5. Adsorption of CO2, N2, and CH4 in Cs-exchanged chabazite: A combination of van der Waals density functional theory calculations and experiment study

    NASA Astrophysics Data System (ADS)

    Shang, Jin; Li, Gang; Singh, Ranjeet; Xiao, Penny; Danaci, David; Liu, Jefferson Z.; Webley, Paul A.

    2014-02-01

    The crucial role of dispersion force in correctly describing the adsorption of some typical small-size gas molecules (e.g., CO2, N2, and CH4) in ion-exchanged chabazites has been investigated at different levels of theory, including the standard density functional theory calculation using the Perdew, Burke, and Ernzerhof (PBE) exchange-correlation functional and van der Waals density functional theory (vdWDFT) calculations using different exchange-correlation models - vdW_DF2, optB86b, optB88, and optPBE. Our results show that the usage of different vdWDFT functionals does not significantly change the adsorption configuration or the profile of static charge rearrangement of the gas-chabazite complexes, in comparison with the results obtained using the PBE. The calculated values of adsorption enthalpy using different functionals are compared with our experimental results. We conclude that the incorporation of dispersion interaction is imperative to correctly predict the trend of adsorption enthalpy values, in terms of different gas molecules and Cs+ cation densities in the adsorbents, even though the absolute values of adsorption enthalpy are overestimated by approximate 10 kJ/mol compared with experiments.

  6. Neoclassical Simulations of Fusion Alpha Particles in Pellet Charge Exchange Experiments on the Tokamak Fusion Test Reactor

    SciTech Connect

    Batha, S.H.; Budny, R.V.; Darrow, D.S.; Levinton, F.M.; Redi, M.H.; et al

    1999-02-01

    Neoclassical simulations of alpha particle density profiles in high fusion power plasmas on the Tokamak Fusion Test Reactor (TFTR) [Phys. Plasmas 5 (1998) 1577] are found to be in good agreement with measurements of the alpha distribution function made with a sensitive active neutral particle diagnostic. The calculations are carried out in Hamiltonian magnetic coordinates with a fast, particle-following Monte Carlo code which includes the neoclassical transport processes, a recent first-principles model for stochastic ripple loss and collisional effects. New global loss and confinement domain calculations allow an estimate of the actual alpha particle densities measured with the pellet charge exchange diagnostic.

  7. Multiscale study of bacterial growth: Experiments and model to understand the impact of gas exchange on global growth

    NASA Astrophysics Data System (ADS)

    Lalanne-Aulet, David; Piacentini, Adalberto; Guillot, Pierre; Marchal, Philippe; Moreau, Gilles; Colin, Annie

    2015-11-01

    Using a millifluidics and macroscale setup, we study quantitatively the impact of gas exchange on bacterial growth. In millifluidic environments, the permeability of the incubator materials allows an unlimited oxygen supply by diffusion. Moreover, the efficiency of diffusion at small scales makes the supply instantaneous in comparison with the cell division time. In hermetic closed vials, the amount of available oxygen is low. The growth curve has the same trend but is quantitatively different from the millifluidic situation. The analysis of all the data allows us to write a quantitative modeling enabling us to capture the entire growth process.

  8. Radioactive Spent Ion-Exchange Resins Conditioning by the Hot Supercompaction Process at Tihange NPP - Early Experience - 12200

    SciTech Connect

    Braet, Johan; Charpentier, David; Centner, Baudouin; Vanderperre, Serge

    2012-07-01

    Spent ion-exchange resins are considered to be problematic waste that, in many cases, requires special approaches and precautions during their conditioning to meet the acceptance criteria for disposal. In Belgium, for economical reasons, the Volume Reduction Factor is a key criterion. After Tractebel Engineering performed a technical and economical comparison of the industrially available systems, Tihange NPP decided to install a spent ion-exchange resins hot supercompaction unit with Tractebel Engineering in the role of architect-engineer. The treatment and conditioning unit processes the spent ion-exchange resins through the following steps: dewatering of the resins, drying the resins under deep vacuum, discharging the dried resins into compactable drums, super-compacting the drums to generate pellets, grouting the pellets into standard 400 litres waste drums (overpacks) licensed for final disposal in the near-surface repository in Belgium. Several developments were required to adapt the reference process and equipment to PWR spent ion-exchange bead resins and Belgian radioactive waste acceptance criteria. In order to avoid cracks on the compacted drum, and external surface contamination from resin leaks, some improvements were achieved to minimize spring-back as well as the risk of cracking the drum wall. Placing the compactable drum inside a second, slightly larger drum, guarantees clean and reproducible pellets. Currently the commissioning phase is on-going. Numerous process validation tests have been completed. An acceptance file was transmitted to the Belgian Waste Management Authority recently. This will be followed by demonstration tests necessary to obtain their final acceptance of the installation. More than 3 800 drums of mixed powdered and bead resins have been processed by the reference Hot Compaction process, achieving a Volume Reduction Factor (VRF) of 2.5. The equipment has been proven to be a reliable technology with low operation and maintenance

  9. Handicapping Social Exchange Theory.

    ERIC Educational Resources Information Center

    Mishler, Barbara

    The economic theory of social exchange has some serious shortcomings when applied to minorities--especially the disabled. First, it assumes dyads comprise the basic unit where exchange occurs and that rewards and costs must occur at that level. Second, the model standardizes the experience of white, Western European and American males. The model…

  10. Neoclassical simulations of fusion alpha particles in pellet charge exchange experiments on the Tokamak Fusion Test Reactor

    SciTech Connect

    Redi, M.H.; Batha, S.H.; Budny, R.V.; Darrow, D.S.; Levinton, F.M.; McCune, D.C.; Medley, S.S.; Petrov, M.P.; von Goeler, S.; White, R.B.; Zarnstorff, M.C.; Zweben, S.J.; TFTR Team

    1999-07-01

    Neoclassical simulations of alpha particle density profiles in high fusion power plasmas on the Tokamak Fusion Test Reactor [Phys. Plasmas {bold 5}, 1577 (1998)] are found to be in good agreement with measurements of the alpha distribution function made with a sensitive active neutral particle diagnostic. The calculations are carried out in Hamiltonian magnetic coordinates with a fast, particle-following Monte Carlo code which includes the neoclassical transport processes, a recent first-principles model for stochastic ripple loss and collisional effects. New calculations show that monotonic shear alpha particles are virtually unaffected by toroidal field ripple. The calculations show that in reversed shear the confinement domain is not empty for trapped alphas at birth and allow an estimate of the actual alpha particle densities measured with the pellet charge exchange diagnostic. {copyright} {ital 1999 American Institute of Physics.}

  11. Spin-exchange optically pumped polarized 3He target for low-energy charged particle scattering experiments

    NASA Astrophysics Data System (ADS)

    Katabuchi, T.; Buscemi, S.; Cesaratto, J. M.; Clegg, T. B.; Daniels, T. V.; Fassler, M.; Neufeld, R. B.; Kadlecek, S.

    2005-03-01

    We have constructed, tested, and calibrated a polarized He3 target system which facilitates p-He3 elastic scattering at proton energies as low as 2MeV. This system consists of a target cell placed in a uniform B field inside a scattering chamber and an external optical pumping station utilizing Rb spin exchange. Computer-controlled valves allow polarized He3 gas to be transferred quickly between the optical pumping station and the spherical Pyrex target cell, which has Kapton film covering apertures for the passing beam and the scattering particles. The magnetic field required to maintain He3 polarization in the target cell is created with a compact, shielded sine-theta coil. Target gas polarimetry is accomplished using nuclear magnetic resonance and calibrated using the known analyzing power of α-He3 scattering.

  12. Three allele combinations associated with Multiple Sclerosis

    PubMed Central

    Favorova, Olga O; Favorov, Alexander V; Boiko, Alexey N; Andreewski, Timofey V; Sudomoina, Marina A; Alekseenkov, Alexey D; Kulakova, Olga G; Gusev, Eugenyi I; Parmigiani, Giovanni; Ochs, Michael F

    2006-01-01

    Background Multiple sclerosis (MS) is an immune-mediated disease of polygenic etiology. Dissection of its genetic background is a complex problem, because of the combinatorial possibilities of gene-gene interactions. As genotyping methods improve throughput, approaches that can explore multigene interactions appropriately should lead to improved understanding of MS. Methods 286 unrelated patients with definite MS and 362 unrelated healthy controls of Russian descent were genotyped at polymorphic loci (including SNPs, repeat polymorphisms, and an insertion/deletion) of the DRB1, TNF, LT, TGFβ1, CCR5 and CTLA4 genes and TNFa and TNFb microsatellites. Each allele carriership in patients and controls was compared by Fisher's exact test, and disease-associated combinations of alleles in the data set were sought using a Bayesian Markov chain Monte Carlo-based method recently developed by our group. Results We identified two previously unknown MS-associated tri-allelic combinations: -509TGFβ1*C, DRB1*18(3), CTLA4*G and -238TNF*B1,-308TNF*A2, CTLA4*G, which perfectly separate MS cases from controls, at least in the present sample. The previously described DRB1*15(2) allele, the microsatellite TNFa9 allele and the biallelic combination CCR5Δ32, DRB1*04 were also reidentified as MS-associated. Conclusion These results represent an independent validation of MS association with DRB1*15(2) and TNFa9 in Russians and are the first to find the interplay of three loci in conferring susceptibility to MS. They demonstrate the efficacy of our approach for the identification of complex-disease-associated combinations of alleles. PMID:16872485

  13. Switching of a Mating-Type a Mutant Allele in Budding Yeast SACCHAROMYCES CEREVISIAE

    PubMed Central

    Klar, Amar J. S.; Fogel, Seymour; Radin, David N.

    1979-01-01

    Aimed at investigating the recovery of a specific mutant allele of the mating type locus (MAT) by switching a defective MAT allele, these experiments provide information bearing on several models proposed for MAT interconversion in bakers yeast, Saccharomyces cerevisiae. Hybrids between heterothallic (ho) cells carrying a mutant MATa allele, designated mata-2, and MATα ho strains show a high capacity for mating with MATa strains. The MATα/mata-2 diploids do not sporulate. However, zygotic clones obtained by mating MATα homothallic (HO) cells with mata-2 ho cells are unable to mate and can sporulate. Tetrad analysis of such clones revealed two diploid (MATα/MATa):two haploid segregants. Therefore, MAT switches occur in MATα/mata-2 HO/ho cells to produce MATα/MATa cells capable of sporulation. In heterothallic strains, the mata-2 allele can be switched to a functional MATα and subsequently to a functional MATa. Among 32 MATα to MATa switches tested, where the MATα was previously derived from the mata-2 mutant, only one mata-2 like isolate was observed. However, the recovered allele, unlike the parental allele, conplements the matα ste1–5 mutant, suggesting that these alleles are not identical and that the recovered allele presumably arose as a mutation of the MATα locus. No mata-2 was recovered by HO-mediated switching of MATα (previously obtained from mata-2 by HO) in 217 switches analyzed. We conclude that in homothallic and heterothallic strains, the mata-2 allele can be readily switched to a functional MATα and subsequently to a functional MATa locus. Overall, the results are in accord with the cassette model (Hicks, Strathern and Herskowitz 1977b) proposed to explain MAT interconversions. PMID:395020

  14. Tetrasomic Segregation for Multiple Alleles in Alfalfa

    PubMed Central

    Quiros, Carlos F.

    1982-01-01

    Evidence of tetrasomic inheritance in alfalfa, Medicago sativa L. and M. falcata L., for multiple codominant alleles at three isozymic loci is reported in this study. The locus Prx-1 governing anodal peroxidase and the loci Lap-1 and Lap-2 governing anodal leucine-aminopeptidase were studied by starch gel electrophoresis in seedling root tissue or seeds. The progenies from several di-, tri- or tetra-allelic plants belong to the species M. sativa and M. falcata and their hybrids were studied for the segregation of the three genes. In all cases, tetrasomic inheritance of chromosomal-type segregation was observed. In another progeny resulting from the crossing of two plants involving four different alleles at locus Lap-2, tetrasomic segregation with the possible occurrence of double reduction was observed. This study presents direct evidence of autotetraploidy and the existence of tetra-allelic loci in alfalfa. It also supports the concept that the species M. sativa and M. falcata are genetically close enough to be considered biotypes of a common species. PMID:17246077

  15. Experience of Treatments of Amanita phalloides-Induced Fulminant Liver Failure with Molecular Adsorbent Recirculating System and Therapeutic Plasma Exchange.

    PubMed

    Zhang, Jicheng; Zhang, Ying; Peng, Zhiyong; Maberry, Donald; Feng, Xueqiang; Bian, Pengfei; Ma, Wenjuan; Wang, Chunting; Qin, Chengyong

    2014-01-01

    Ingestion of the mushroom containing Amanita phalloides can induce fulminant liver failure and death. There are no specific antidotes. Blood purifications, such as molecular adsorbent recirculating system (MARS) and therapeutic plasma exchange (TPE), are potential therapies. However, the extent to which these technologies avert the deleterious effects of amatoxins remains controversial; the optimal intensity, duration, and initiation criteria have not been determined yet. This study aimed to retrospectively observe the effects of MARS and TPE on nine patients with A. phalloides-induced fulminant liver failure. The survival rate for the nine patients was 66.7%. Both TPE and MARS might remove toxins and improve liver functions. However, a single session of TPE produced immediately greater improvements in alanine aminotransferase (-60% vs. -16.3%), aspartate aminotransferase (-47.6% vs. -15.4%), and total bilirubin (-37.3% vs. -17.1%) (compared with the values of pretreatment, all p < 0.05) than MARS compared with MARS. Early intervention may be more effective than delayed therapy. Additionally, the presence of severe liver failure and renal failure indicated worse outcome. Although these findings are promising, additional case-controlled, randomized studies are required to confirm our results. PMID:24727538

  16. Exchange Transfusion in the Treatment of Neonatal Septic Shock: A Ten-Year Experience in a Neonatal Intensive Care Unit

    PubMed Central

    Pugni, Lorenza; Ronchi, Andrea; Bizzarri, Bianca; Consonni, Dario; Pietrasanta, Carlo; Ghirardi, Beatrice; Fumagalli, Monica; Ghirardello, Stefano; Mosca, Fabio

    2016-01-01

    Septic shock, occurring in about 1% of neonates hospitalized in neonatal intensive care unit (NICU), is a major cause of death in the neonatal period. In the 1980s and 90s, exchange transfusion (ET) was reported by some authors to be effective in the treatment of neonatal sepsis and septic shock. The main aim of this retrospective study was to compare the mortality rate of neonates with septic shock treated only with standard care therapy (ScT group) with the mortality rate of those treated with ScT and ET (ET group). All neonates with septic shock admitted to our NICU from 2005 to 2015 were included in the study. Overall, 101/9030 (1.1%) neonates had septic shock. Fifty neonates out of 101 (49.5%) received one or more ETs. The mortality rate was 36% in the ET group and 51% in the ScT group (p = 0.16). At multivariate logistic regression analysis, controlling for potentially confounding factors significantly associated with death (gestational age, serum lactate, inotropic drugs, oligoanuria), ET showed a marked protective effect (Odds Ratio 0.21, 95% Confidence Interval: 0.06–0.71; p = 0.01). The lack of observed adverse events should encourage the use of this procedure in the treatment of neonates with septic shock. PMID:27171076

  17. Life After the Ban: An Assessment of US Syringe Exchange Programs’ Attitudes About and Early Experiences With Federal Funding

    PubMed Central

    Martin, Erika G.; Bowman, Sarah E.; Mann, Marita R.; Beletsky, Leo

    2012-01-01

    Objectives. We aimed to determine whether syringe exchange programs (SEPs) currently receive or anticipate pursuing federal funding and barriers to funding applications following the recent removal of the long-standing ban on using federal funds for SEPs. Methods. We conducted a telephone-administered cross-sectional survey of US SEPs. Descriptive statistics summarized responses; bivariate analyses examined differences in pursuing funding and experiencing barriers by program characteristics. Results. Of the 187 SEPs (92.1%) that responded, 90.9% were legally authorized. Three received federal funds and 116 intended to pursue federal funding. Perceived federal funding barriers were common and included availability and accessibility of funds, legal requirements such as written police support, resource capacity to apply and comply with funding regulations, local political and structural organization, and concern around altering program culture. Programs without legal authorization, health department affiliation, large distribution, or comprehensive planning reported more federal funding barriers. Conclusions. Policy implementation gaps appear to render federal support primarily symbolic. In practice, funding opportunities may not be available to all SEPs. Increased technical assistance and legal reform could improve access to federal funds, especially for SEPs with smaller capacity and tenuous local support. PMID:22420810

  18. Practice experiences of running UK DonorLink, a voluntary information exchange register for adults related through donor conception.

    PubMed

    Crawshaw, Marilyn; Marshall, Lyndsey

    2008-12-01

    Previous practices of withholding information from those conceived through donor conception are changing. However, little is known about the service needs of those affected. In response to this, the UK Government-funded pilot voluntary information exchange and contact register, UK DonorLink, was launched in 2004, covering conceptions prior to August 1991. It is the only register worldwide that relies primarily on DNA testing to establish genetic connectedness in the absence of written records. Approximately 150 adults came forward to register in the first three years of operation, drawn from all interested parties. Matches between half-siblings have been made, but none yet between donor and offspring. Employing staff with expertise in post-adoption work has proved effective, as long as additional training and support specific to donor issues is provided. The infrastructure required to promote and deliver the service reflects the complex mix of skills and tasks required, and confirms that a service provided through independent counsellors alone would be inappropriate. Having a geographically and socially widespread potential registrant group, together with a limited budget, has limited the effectiveness of advertising and promotion campaigns. Ethical and emotional complexities arising through the direct service are highlighted, including those presented by DNA use. PMID:19085259

  19. Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments.

    PubMed

    Patel, Dhilon S; Pendrill, Robert; Mallajosyula, Sairam S; Widmalm, Göran; MacKerell, Alexander D

    2014-03-20

    Conformational sampling for a set of 10 α- or β-(1→6)-linked oligosaccharides has been studied using explicit solvent Hamiltonian replica exchange (HREX) simulations and NMR spectroscopy techniques. Validation of the force field and simulation methodology is done by comparing calculated transglycosidic J coupling constants and proton-proton distances with the corresponding NMR data. Initial calculations showed poor agreement, for example, with >3 Hz deviation of the calculated (3)J(H5,H6R) values from the experimental data, prompting optimization of the ω torsion angle parameters associated with (1→6)-linkages. The resulting force field is in overall good agreement (i.e., within ∼0.5 Hz deviation) from experimental (3)J(H5,H6R) values, although some small limitations are evident. Detailed hydrogen bonding analysis indicates that most of the compounds lack direct intramolecular H-bonds between the two monosaccharides; however, minor sampling of the O6···HO2' hydrogen bond is present in three compounds. The results verify the role of the gauche effect between O5 and O6 atoms in gluco- and manno-configured pyranosides causing the ω torsion angle to sample an equilibrium between the gt and gg rotamers. Conversely, galacto-configured pyranosides sample a population distribution in equilibrium between gt and tg rotamers, while the gg rotamer populations are minor. Water radial distribution functions suggest decreased accessibility to the O6 atom in the (1→6)-linkage as compared to the O6' atom in the nonreducing sugar. The role of bridging water molecules between two sugar moieties on the distributions of ω torsion angles in oligosaccharides is also explored. PMID:24552401

  20. Conformational Properties of α- or β-(1→6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments

    PubMed Central

    2015-01-01

    Conformational sampling for a set of 10 α- or β-(1→6)-linked oligosaccharides has been studied using explicit solvent Hamiltonian replica exchange (HREX) simulations and NMR spectroscopy techniques. Validation of the force field and simulation methodology is done by comparing calculated transglycosidic J coupling constants and proton–proton distances with the corresponding NMR data. Initial calculations showed poor agreement, for example, with >3 Hz deviation of the calculated 3J(H5,H6R) values from the experimental data, prompting optimization of the ω torsion angle parameters associated with (1→6)-linkages. The resulting force field is in overall good agreement (i.e., within ∼0.5 Hz deviation) from experimental 3J(H5,H6R) values, although some small limitations are evident. Detailed hydrogen bonding analysis indicates that most of the compounds lack direct intramolecular H-bonds between the two monosaccharides; however, minor sampling of the O6···HO2′ hydrogen bond is present in three compounds. The results verify the role of the gauche effect between O5 and O6 atoms in gluco- and manno-configured pyranosides causing the ω torsion angle to sample an equilibrium between the gt and gg rotamers. Conversely, galacto-configured pyranosides sample a population distribution in equilibrium between gt and tg rotamers, while the gg rotamer populations are minor. Water radial distribution functions suggest decreased accessibility to the O6 atom in the (1→6)-linkage as compared to the O6′ atom in the nonreducing sugar. The role of bridging water molecules between two sugar moieties on the distributions of ω torsion angles in oligosaccharides is also explored. PMID:24552401

  1. The tropical experiment of the Stratosphere-Troposphere Exchange Project (STEP) - Science objectives, operations, and summary findings

    NASA Technical Reports Server (NTRS)

    Russell, P. B.; Pfister, L.; Selkirk, H. B.

    1993-01-01

    An overview is presented of the tropical component of STEP. The STEP cooperative experiments are described and summaries are presented of the STEP tropical ER-2 aircraft flights. STEP tropical results on dehydration and transfer and the mechanisms of upward transfer are summarized. Illustrations show flight paths for each sortie on satellite images and on 100 hPa synoptic flow charts, as well as the timing of flights with respect to overall cloudiness in the Australian region.

  2. HLA-B alleles of the Cayapa of Ecuador: New B39 and B15 alleles

    SciTech Connect

    Garber, T.L.; Butler, L.M.; Watkins, D.I.

    1995-05-01

    Recent data suggest that HLA-B locus alleles can evolve quickly in native South American populations. To investigate further this phenomenon of new HLA-B variants among Amerindians, we studied samples from another South American tribe, the Cayapa from Ecuador. We selected individuals for HLA-B molecular typing based upon their HLA class II typing results. Three new variants of HLA-B39 and one new variant of HLA-B15 were found in the Cayapa: HLA-B*3905, HLA-B*3906, HLA-B*3907, and HLA-B*1522. A total of thirteen new HLA-B alleles have now been found in the four South American tribes studied. Each of these four tribes studied, including the Cayapa, had novel alleles that were not found in any of the other tribes, suggesting that many of these new HLA-B alleles may have evolved since the Paleo-Indians originally populated South America. Each of these 13 new alleles contained predicted amino acid replacements that were located in the peptide binding site. These amino acid replacements may affect the sequence motif of the bound peptides, suggesting that these new alleles have been maintained by selection. New allelic variants have been found for all common HLA-B locus antigenic groups present in South American tribes with the exception of B48. In spite of its high frequency in South American tribes, no evidence for variants of B48 has been found in all the Amerindians studied, suggesting that B48 may have unique characteristics among the B locus alleles. 70 refs., 2 figs., 2 tabs.

  3. Multiple and independent origins of short seeded alleles of GS3 in rice

    PubMed Central

    Takano-Kai, Noriko; Jiang, Hui; Powell, Adrian; McCouch, Susan; Takamure, Itsuro; Furuya, Naruto; Doi, Kazuyuki; Yoshimura, Atsushi

    2013-01-01

    GRAIN SIZE 3 (GS3) is a cloned gene that is related to seed length. Here we report the discovery of new deletion alleles at the GS3 locus, each of which confer short seed. We selected ten short seeded cultivars from a collection of 282 diverse cultivars. Sequence analysis across the GS3 gene in these ten cultivars identified three novel alleles and a known allele that contain several independent deletion(s) in the fifth exon of GS. These independent deletion variants each resulted in a frameshift mutation that caused a premature stop codon, and they were functionally similar to one another. Each coded for a truncated gene product that behaved as an incomplete dominant allele and conferred a short seeded phenotype. Haplotype analysis of these sequence variants indicated that two of the variants were of japonica origin, and two were from indica. Transformation experiments demonstrated that one of the deletion alleles of GS3 decrease the cell number in the upper epidermis of the glume, resulting in a significant reduction in seed length. The multiple and independent origins of these short seeded alleles indicate that farmers and early breeders imposed artificial selection favoring short seeds. PMID:23641184

  4. Optimization of Heat Exchangers

    SciTech Connect

    Ivan Catton

    2010-10-01

    The objective of this research is to develop tools to design and optimize heat exchangers (HE) and compact heat exchangers (CHE) for intermediate loop heat transport systems found in the very high temperature reator (VHTR) and other Generation IV designs by addressing heat transfer surface augmentation and conjugate modeling. To optimize heat exchanger, a fast running model must be created that will allow for multiple designs to be compared quickly. To model a heat exchanger, volume averaging theory, VAT, is used. VAT allows for the conservation of mass, momentum and energy to be solved for point by point in a 3 dimensional computer model of a heat exchanger. The end product of this project is a computer code that can predict an optimal configuration for a heat exchanger given only a few constraints (input fluids, size, cost, etc.). As VAT computer code can be used to model characteristics )pumping power, temperatures, and cost) of heat exchangers more quickly than traditional CFD or experiment, optimization of every geometric parameter simultaneously can be made. Using design of experiment, DOE and genetric algorithms, GE, to optimize the results of the computer code will improve heat exchanger disign.

  5. Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size.

    PubMed

    Garza, J C; Slatkin, M; Freimer, N B

    1995-07-01

    The distributions of allele sizes at eight simple-sequence repeat (SSR) or microsatellite loci in chimpanzees are found and compared with the distributions previously obtained from several human populations. At several loci, the differences in average allele size between chimpanzees and humans are sufficiently small that there might be a constraint on the evolution of average allele size. Furthermore, a model that allows for a bias in the mutation process shows that for some loci a weak bias can account for the observations. Several alleles at one of the loci (Mfd 59) were sequenced. Differences between alleles of different lengths were found to be more complex than previously assumed. An 8-base-pair deletion was present in the nonvariable region of the chimpanzee locus. This locus contains a previously unrecognized repeated region, which is imperfect in humans and perfect in chimpanzees. The apparently greater opportunity for mutation conferred by the two perfect repeat regions in chimpanzees is reflected in the higher variance in repeat number at Mfd 59 in chimpanzees than in humans. These data indicate that interspecific differences in allele length are not always attributable to simple changes in the number of repeats. PMID:7659015

  6. Allele-specific expression assays using Solexa

    PubMed Central

    Main, Bradley J; Bickel, Ryan D; McIntyre, Lauren M; Graze, Rita M; Calabrese, Peter P; Nuzhdin, Sergey V

    2009-01-01

    Background Allele-specific expression (ASE) assays can be used to identify cis, trans, and cis-by-trans regulatory variation. Understanding the source of expression variation has important implications for disease susceptibility, phenotypic diversity, and adaptation. While ASE is commonly measured via relative fluorescence at a SNP, next generation sequencing provides an opportunity to measure ASE in an accurate and high-throughput manner using read counts. Results We introduce a Solexa-based method to perform large numbers of ASE assays using only a single lane of a Solexa flowcell. In brief, transcripts of interest, which contain a known SNP, are PCR enriched and barcoded to enable multiplexing. Then high-throughput sequencing is used to estimate allele-specific expression using sequencing counts. To validate this method, we measured the allelic bias in a dilution series and found high correlations between measured and expected values (r>0.9, p < 0.001). We applied this method to a set of 5 genes in a Drosophila simulans parental mix, F1 and introgression and found that for these genes the majority of expression divergence can be explained by cis-regulatory variation. Conclusion We present a new method with the capacity to measure ASE for large numbers of assays using as little as one lane of a Solexa flowcell. This will be a valuable technique for molecular and population genetic studies, as well as for verification of genome-wide data sets. PMID:19740431

  7. Allelic variation contributes to bacterial host specificity

    SciTech Connect

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; Zhao, Shaohua; McDermott, Patrick F.; Weill, François-Xavier; Mainil, Jacques G.; Arze, Cesar; Fricke, W. Florian; Edwards, Robert A.; Brisson, Dustin; Zhang, Nancy R.; Rankin, Shelley C.; Schifferli, Dieter M.

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

  8. Allelic variation contributes to bacterial host specificity

    DOE PAGESBeta

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; et al

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population andmore » functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.« less

  9. Allelic variation contributes to bacterial host specificity

    PubMed Central

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; Zhao, Shaohua; McDermott, Patrick F.; Weill, François-Xavier; Mainil, Jacques G.; Arze, Cesar; Fricke, W. Florian; Edwards, Robert A.; Brisson, Dustin; Zhang, Nancy R.; Rankin, Shelley C.; Schifferli, Dieter M.

    2015-01-01

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts. PMID:26515720

  10. Reconstructing the prior probabilities of allelic phylogenies.

    PubMed Central

    Golding, G Brian

    2002-01-01

    In general when a phylogeny is reconstructed from DNA or protein sequence data, it makes use only of the probabilities of obtaining some phylogeny given a collection of data. It is also possible to determine the prior probabilities of different phylogenies. This information can be of use in analyzing the biological causes for the observed divergence of sampled taxa. Unusually "rare" topologies for a given data set may be indicative of different biological forces acting. A recursive algorithm is presented that calculates the prior probabilities of a phylogeny for different allelic samples and for different phylogenies. This method is a straightforward extension of Ewens' sample distribution. The probability of obtaining each possible sample according to Ewens' distribution is further subdivided into each of the possible phylogenetic topologies. These probabilities depend not only on the identity of the alleles and on 4N(mu) (four times the effective population size times the neutral mutation rate) but also on the phylogenetic relationships among the alleles. Illustrations of the algorithm are given to demonstrate how different phylogenies are favored under different conditions. PMID:12072482

  11. Allelic variation contributes to bacterial host specificity.

    PubMed

    Yue, Min; Han, Xiangan; De Masi, Leon; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S; Fraser, George P; Zhao, Shaohua; McDermott, Patrick F; Weill, François-Xavier; Mainil, Jacques G; Arze, Cesar; Fricke, W Florian; Edwards, Robert A; Brisson, Dustin; Zhang, Nancy R; Rankin, Shelley C; Schifferli, Dieter M

    2015-01-01

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts. PMID:26515720

  12. Oxygen isotope fractionation between chlorite and water from 170 to 350 C: A preliminary assessment based on partial exchange and fluid/rock experiments

    SciTech Connect

    Cole, D.R.; Ripley, E.M.

    1999-02-01

    Oxygen isotope fractionations in laboratory systems have been determined between chlorite and water at 170--350 C. In one series of experiments, the Northrop-Clayton partial exchange method was used where three (sometimes four) isotopically different waters were reacted with chlorite. The percents of exchange determined for the four times from shortest to longest are 4.4, 6.5, 8.0, and 11.9. The fractionations calculated from the Northrop and Clayton method are in modest agreement for the four run durations: 0.13, 0.26, {minus}0.46, and {minus}0.55 per mil. Errors associated with each of these fractionations are quite large (e.g. {+-}1.2 per mil for the longest run). The value determined for the longest run of {approximately}20 weeks is the most reliable of the group and compares very closely with a value of {approximately}{minus}0.7 per mil estimated by Wenner and Taylor based on natural chlorides. Good agreement is also observed with the estimates, {minus}1.2 and {minus}1.3% calculated at 350 C for chlorite compositions with [({Sigma}Fe)/{Sigma}Fe + Mg] = 0.313 and 0.444, respectively, from equations given by Savin and Lee based on their empirical bond-type method. Additional fractionation data have been estimated from hydrothermal granite-fluid experiments where chlorite formed from biotite. Detailed thin section, scanning electron microscope (SEM), x-ray diffraction (XRD), and electron microprobe analyses demonstrate that biotite is altered exclusively to chlorite in 13 granite-fluid experiments conducted at the following conditions: T = 170--300 C, P = vapor saturation - 200 b, salinity = H{sub 2}O, 0.1 and 1 m NaCl, fluid/biotite mass ratios = 3--44, run durations = 122--772 h. The amount of chlorite, quantified through point counting and XRD, increased with increasing temperature, salinity, and time. The isotope compositions of chlorite were calculated from mass balance and compared to the final measured {delta}{sup 18}O of the fluids. The 10{sup 3}ln {alpha

  13. Increasing long term response by selecting for favorable minor alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Long-term response of genomic selection can be improved by considering allele frequencies of selected markers or quantitative trait loci (QTLs). A previous formula to weight allele frequency of favorable minor alleles was tested, and 2 new formulas were developed. The previous formula used nonlinear...

  14. Mutant maize variety containing the glt1-1 allele

    DOEpatents

    Nelson, O.E.; Pan, D.

    1994-07-19

    A maize plant has in its genome a non-mutable form of a mutant allele designated vitX-8132. The allele is located at a locus designated as glt which conditions kernels having an altered starch characteristic. Maize plants including such a mutant allele produce a starch that does not increase in viscosity on cooling, after heating. 2 figs.

  15. Mutant maize variety containing the glt1-1 allele

    DOEpatents

    Nelson, Oliver E.; Pan, David

    1994-01-01

    A maize plant has in its genome a non-mutable form of a mutant allele designated vitX-8132. The allele is located at a locus designated as glt which conditions kernels having an altered starch characteristic. Maize plants including such a mutant allele produce a starch that does not increase in viscosity on cooling, after heating.

  16. Kinetics of Sr and Nd exchange in silicate liquids: Theory, experiments, and applications to uphill diffusion, isotopic equilibration, and irreversible mixing of magmas

    SciTech Connect

    Lesher, C.E.

    1994-05-10

    Diffusion coefficients that govern chemical and isotopic exchange of Sr and Nd were determined from compositional profiles developed between juxtaposed anhydrous basaltic and rhyolitic liquids. Analysis of simple diffusion couples involving isotopically enriched and normal tholeiitic basalt and metaluminous rhyolite recover Sr and Nd self-diffusion coefficients (D{sup *}) in the end-member compositions of contrasting polymerization. Self-diffusion of Sr is 7 times faster in basaltic melt than rhyolitic melt at 1255{degrees}C and 1 GPa, while self-diffusion of Nd is more than 1 order of magnitude greater in basalt than rhyolite. Also, at these conditions, D{sub Sr}{sup *} is a factor of 3 greater than D{sub Nd}{sup *} in basalt and an order of magnitude greater than D{sub Nd}{sup *} in rhyolite. The results of a Botlzmann-Matano analysis of {sup 87}Sr/{Sigma}Sr and {sup 144}Nd/{Sigma}Nd profiles of complex diffusion couples composed of isotopically normal basalt and enriched rhyolite yield diffusion coefficients for intermediate bulk compositions in agreement with interpolated values given by the relationships above. An important feature of the interdiffusion of basaltic and rhyolitic liquids is the equilibration of isotopic composition in advance of chemical homogenization. This behavior is best displayed by Sr in the present experiments and predicted for Nd. These results are considered in a magmatic context, where intimate blending of magmas during mixing is frustrated by large rheological contrasts and/or insufficient exposure time. Time-dependent diffusional exchange between mingling magmas leads to covariations in chemical and isotopic compositions that differ markedly from the expectations of bulk mixing. Examples presented offer alternative interpretations for the compositional relationships found among magmatic rocks of hybrid origin. 63 refs., 14 figs., 4 tabs.

  17. A novel HLA-B allele, HLA-B*35:279, identified by sequencing-based typing in a Czech patient.

    PubMed

    Mrazek, F; Onderkova, J; Königova, N; Siffnerova, V; Vrana, M; Ambruzova, Z; Skoumalova, I; Petrek, M; Raida, L

    2016-08-01

    The identification of a novel HLA-B*35:279 allele in a Czech patient is described. This allele is identical to the B*35:03:01 variant except the G/A nucleotide exchange at position 652 of the HLA-B gene that corresponds to the amino acid substitution from valine to isoleucine in alpha 3 domain of the HLA-B antigen. PMID:27273911

  18. Interprofessional Global Health Education at Oregon Health and Science University: The Interprofessional Community Health and Education Exchange (iCHEE) Experience

    PubMed Central

    Palmer, Valerie S.; Mazumder, Rajarshi; Spencer, Peter S.

    2015-01-01

    Problem The rapidly diversifying population of North America has disparate health needs that are addressed by creative community-based training of health science students. Approach The authors report 5 years (2008–2012) of experience implementing a novel interprofessional Community Health and Education Exchange (iCHEE) elective course for dental, medical, nursing, nutrition, pharmacy, physician assistant, and public health students of Oregon Health & Science University (OHSU). This pioneering interprofessional course was created by the OHSU Global Health Center and is offered in fall, winter, and spring quarters. Students interact with individual clients drawn from community centers supporting refugees, recent immigrants, and other underserved people. In addition to health concerns, clients are encouraged to share backgrounds and experiences with student teams. Clients receive guidance on nutrition, exercise, pharmaceuticals, and accessible health services. Student teams perform a non-invasive health check on clients with the assistance of faculty mentors who, upon finding a physical or mental health issue, refer the client from the educational setting to an appropriate health care facility. Outcomes In addition to supporting health promotion and early intervention for medically underserved people, students reported gaining valuable cross-cultural knowledge, understanding, and experience from clients. Students also appreciated the value of diverse skills and knowledge available in their multidisciplinary teams. Through the end of 2012, over 300 health-professions students worked with approximately 1,200 clients to complete the iCHEE course. Next Steps The iCHEE model should prove helpful in preparing health-professions students at other institutions to understand and serve diverse populations. PMID:24918760

  19. Borrowed alleles and convergence in serpentine adaptation.

    PubMed

    Arnold, Brian J; Lahner, Brett; DaCosta, Jeffrey M; Weisman, Caroline M; Hollister, Jesse D; Salt, David E; Bomblies, Kirsten; Yant, Levi

    2016-07-19

    Serpentine barrens represent extreme hazards for plant colonists. These sites are characterized by high porosity leading to drought, lack of essential mineral nutrients, and phytotoxic levels of metals. Nevertheless, nature forged populations adapted to these challenges. Here, we use a population-based evolutionary genomic approach coupled with elemental profiling to assess how autotetraploid Arabidopsis arenosa adapted to a multichallenge serpentine habitat in the Austrian Alps. We first demonstrate that serpentine-adapted plants exhibit dramatically altered elemental accumulation levels in common conditions, and then resequence 24 autotetraploid individuals from three populations to perform a genome scan. We find evidence for highly localized selective sweeps that point to a polygenic, multitrait basis for serpentine adaptation. Comparing our results to a previous study of independent serpentine colonizations in the closely related diploid Arabidopsis lyrata in the United Kingdom and United States, we find the highest levels of differentiation in 11 of the same loci, providing candidate alleles for mediating convergent evolution. This overlap between independent colonizations in different species suggests that a limited number of evolutionary strategies are suited to overcome the multiple challenges of serpentine adaptation. Interestingly, we detect footprints of selection in A. arenosa in the context of substantial gene flow from nearby off-serpentine populations of A. arenosa, as well as from A. lyrata In several cases, quantitative tests of introgression indicate that some alleles exhibiting strong selective sweep signatures appear to have been introgressed from A. lyrata This finding suggests that migrant alleles may have facilitated adaptation of A. arenosa to this multihazard environment. PMID:27357660

  20. Borrowed alleles and convergence in serpentine adaptation

    PubMed Central

    Arnold, Brian J.; Lahner, Brett; DaCosta, Jeffrey M.; Weisman, Caroline M.; Hollister, Jesse D.; Salt, David E.; Bomblies, Kirsten; Yant, Levi

    2016-01-01

    Serpentine barrens represent extreme hazards for plant colonists. These sites are characterized by high porosity leading to drought, lack of essential mineral nutrients, and phytotoxic levels of metals. Nevertheless, nature forged populations adapted to these challenges. Here, we use a population-based evolutionary genomic approach coupled with elemental profiling to assess how autotetraploid Arabidopsis arenosa adapted to a multichallenge serpentine habitat in the Austrian Alps. We first demonstrate that serpentine-adapted plants exhibit dramatically altered elemental accumulation levels in common conditions, and then resequence 24 autotetraploid individuals from three populations to perform a genome scan. We find evidence for highly localized selective sweeps that point to a polygenic, multitrait basis for serpentine adaptation. Comparing our results to a previous study of independent serpentine colonizations in the closely related diploid Arabidopsis lyrata in the United Kingdom and United States, we find the highest levels of differentiation in 11 of the same loci, providing candidate alleles for mediating convergent evolution. This overlap between independent colonizations in different species suggests that a limited number of evolutionary strategies are suited to overcome the multiple challenges of serpentine adaptation. Interestingly, we detect footprints of selection in A. arenosa in the context of substantial gene flow from nearby off-serpentine populations of A. arenosa, as well as from A. lyrata. In several cases, quantitative tests of introgression indicate that some alleles exhibiting strong selective sweep signatures appear to have been introgressed from A. lyrata. This finding suggests that migrant alleles may have facilitated adaptation of A. arenosa to this multihazard environment. PMID:27357660

  1. Allelic genealogies in sporophytic self-incompatibility systems in plants.

    PubMed Central

    Schierup, M H; Vekemans, X; Christiansen, F B

    1998-01-01

    Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed. PMID:9799270

  2. Direct Fluorescence Detection of Allele-Specific PCR Products Using Novel Energy-Transfer Labeled Primers.

    PubMed

    Winn-Deen

    1998-12-01

    Background: Currently analysis of point mutations can be done by allele-specific polymerase chain reaction (PCR) followed by gel analysis or by gene-specific PCR followed by hybridization with an allele-specific probe. Both of these mutation detection methods require post-PCR laboratory time and run the risk of contaminating subsequent experiments with the PCR product liberated during the detection step. The author has combined the PCR amplification and detection steps into a single procedure suitable for closed-tube analysis. Methods and Results: Allele-specific PCR primers were designed as Sunrise energy-transfer primers and contained a 3' terminal mismatch to distinguish between normal and mutant DNA. Cloned normal (W64) and mutant (R64) templates of the beta3-adrenergic receptor gene were tested to verify amplification specificity and yield. A no-target negative control was also run with each reaction. After PCR, each reaction was tested for fluorescence yield by measuring fluorescence on a spectrofluorimeter or fluorescent microtitreplate reader. The cloned controls and 24 patient samples were tested for the W64R mutation by two methods. The direct fluorescence results with the Sunrise allele-specific PCR method gave comparable genotypes to those obtained with the PCR/ restriction digest/gel electrophoresis control method. No PCR artifacts were observed in the negative controls or in the PCR reactions run with the mismatched target. Conclusions: The results of this pilot study indicate good PCR product and fluorescence yield from allele-specific energy-transfer labeled primers, and the capability of distinguishing between normal and mutant alleles based on fluorescence alone, without the need for restriction digestion, gel electrophoresis, or hybridization with an allele-specific probe. PMID:10089280

  3. Ion-exchange reactions on clay minerals coupled with advection/dispersion processes. Application to Na+/Ca2+ exchange on vermiculite: Reactive-transport modeling, batch and stirred flow-through reactor experiments

    NASA Astrophysics Data System (ADS)

    Tertre, E.; Hubert, F.; Bruzac, S.; Pacreau, M.; Ferrage, E.; Prêt, D.

    2013-07-01

    The present study aims at testing the validity of using an Na+/Ca2+ ion-exchange model, derived from batch data to interpret experimental Ca2+-for-Na+ exchange breakthrough curves obtained on vermiculite (a common swelling clay mineral in surface environments). The ion-exchange model was constructed considering the multi-site nature of the vermiculite surface as well as the exchange of all aqueous species (Mg2+ derived from the dissolution of the solid and H+). The proposed ion-exchange model was then coupled with a transport model, and the predicted breakthrough curves were compared with the experimental ones obtained using a well stirred flow-through reactor. For a given solute residence time in the reactor (typically 50 min), our thermodynamic model based on instantaneous equilibrium was found to accurately reproduce several of the experimental breakthrough curves, depending on the Na+ and Ca2+ concentrations of the influents pumped through the reactor. However the model failed to reproduce experimental breakthrough curves obtained at high flow rates and low chemical gradient between the exchanger phase and the solution. An alternative model based on a hybrid equilibrium/kinetic approach was thus used and allowed predicting experimental data. Based on these results, we show that a simple parameter can be used to differentiate between thermodynamic and kinetic control of the exchange reaction with water flow. The results of this study are relevant for natural systems where two aquatic environments having contrasted chemistries interact. Indeed, the question regarding the attainment of a full equilibrium in such a system during the contact time of the aqueous phase with the particle/colloid remains most often open. In this context, we show that when a river (a flow of fresh water) encounters marine colloids, a systematic full equilibrium can be assumed (i.e., the absence of kinetic effects) when the residence time of the solute in 1 m3 of the system is ⩾6200 h.

  4. Emittance and Phase Space Exchange

    SciTech Connect

    Xiang, Dao; Chao, Alex; /SLAC

    2011-08-19

    Alternative chicane-type beam lines are proposed for exact emittance exchange between horizontal phase space (x; x{prime}) and longitudinal phase space (z; {delta}). Methods to achieve exact phase space exchanges, i.e. mapping x to z, x{prime} to {delta}, z to x and {delta} to x{prime} are suggested. Methods to mitigate the thick-lens effect of the transverse cavity on emittance exchange are discussed. Some applications of the phase space exchanger and the feasibility of an emittance exchange experiment with the proposed chicane-type beam line at SLAC are discussed.

  5. Exquisite allele discrimination by toehold hairpin primers

    PubMed Central

    Byrom, Michelle; Bhadra, Sanchita; Jiang, Yu Sherry; Ellington, Andrew D.

    2014-01-01

    The ability to detect and monitor single nucleotide polymorphisms (SNPs) in biological samples is an enabling research and clinical tool. We have developed a surprising, inexpensive primer design method that provides exquisite discrimination between SNPs. The field of DNA computation is largely reliant on using so-called toeholds to initiate strand displacement reactions, leading to the execution of kinetically trapped circuits. We have now similarly found that the short toehold sequence to a target of interest can initiate both strand displacement within the hairpin and extension of the primer by a polymerase, both of which will further stabilize the primer:template complex. However, if the short toehold does not bind, neither of these events can readily occur and thus amplification should not occur. Toehold hairpin primers were used to detect drug resistance alleles in two genes, rpoB and katG, in the Mycobacterium tuberculosis genome, and ten alleles in the Escherichia coli genome. During real-time PCR, the primers discriminate between mismatched templates with Cq delays that are frequently so large that the presence or absence of mismatches is essentially a ‘yes/no’ answer. PMID:24990378

  6. Allelic disequilibrium and allele frequency distribution as a function of social and demographic history.

    PubMed Central

    Thompson, E A; Neel, J V

    1997-01-01

    Allelic disequilibrium between closely linked genes is a common observation in human populations and often gives rise to speculation concerning the role of selective forces. In a previous treatment, we have developed a population model of the expected distribution of rare variants (including private polymorphisms) in Amerindians and have argued that, because of the great expansion of Amerindian numbers with the advent of agriculture, most of these rare variants are of relatively recent origin. Many other populations have similar histories of striking recent expansions. In this treatment, we demonstrate that, in consequence of this fact, a high degree of linkage disequilibrium between two nonhomologous alleles <0.5 cM apart is the "normal" expectation, even in the absence of selection. This expectation is enhanced by the previous subdivision of human populations into relatively isolated tribes characterized by a high level of endogamy and inbreeding. We also demonstrate that the alleles associated with a recessive disease phenotype are expected to exist in a population in very variable frequencies: there is no need to postulate positive selection with respect to the more common disease-associated alleles for such entities as phenylketonuria or cystic fibrosis. PMID:8981963

  7. Schizophrenia susceptibility alleles are enriched for alleles that affect gene expression in adult human brain

    PubMed Central

    Richards, Alexander L; Jones, Lesley; Moskvina, Valentina; Kirov, George; Gejman, Pablo V; Levinson, Douglas F; Sanders, Alan R; Purcell, Shaun; Visscher, Peter M; Craddock, Nick; Owen, Michael J; Holmans, Peter; O’Donovan, Michael C

    2016-01-01

    It is widely thought that alleles that influence susceptibility to common diseases, including schizophrenia, will frequently do so through effects on gene expression. Since only a small proportion of the genetic variance for schizophrenia has been attributed to specific loci, this remains an unproven hypothesis. The International Schizophrenia Consortium (ISC) recently reported a substantial polygenic contribution to that disorder, and that schizophrenia risk alleles are enriched among SNPs selected for marginal evidence for association (p<0.5) from genome wide association studies (GWAS). It follows that if schizophrenia susceptibility alleles are enriched for those that affect gene expression, those marginally associated SNPs which are also eQTLs should carry more true association signals compared with SNPs which are not. To test this, we identified marginally associated (p<0.5) SNPs from two of the largest available schizophrenia GWAS datasets. We assigned eQTL status to those SNPs based upon an eQTL dataset derived from adult human brain. Using the polygenic score method of analysis reported by the ISC, we observed and replicated the observation that higher probability cis-eQTLs predicted schizophrenia better than those with a lower probability for being a cis-eQTL. Our data support the hypothesis that alleles conferring risk of schizophrenia are enriched among those that affect gene expression. Moreover, our data show that notwithstanding the likely developmental origin of schizophrenia, studies of adult brain tissue can in principle allow relevant susceptibility eQTLs to be identified. PMID:21339752

  8. Identification of Allelic Variants of Pendrin (SLC26A4) with Loss and Gain of Function

    PubMed Central

    Dossena, Silvia; Bizhanova, Aigerim; Nofziger, Charity; Bernardinelli, Emanuele; Ramsauer, Josef; Kopp, Peter; Paulmichl, Markus

    2011-01-01

    Background Pendrin is a multifunctional anion transporter that exchanges chloride and iodide in the thyroid, as well as chloride and bicarbonate in the inner ear, kidney and airways. Loss or reduction in the function of pendrin results in both syndromic (Pendred syndrome) and non-syndromic (non-syndromic enlarged vestibular aqueduct (ns-EVA)) hearing loss. Factors inducing an up-regulation of pendrin in the kidney and the lung may have an impact on the pathogenesis of hypertension, chronic obstructive pulmonary disease (COPD) and asthma. Here we characterize the ion transport activity of wild-type (WT) pendrin and seven of its allelic variants selected among those reported in the single nucleotide polymorphisms data base (dbSNPs), some of which were previously identified in a cohort of individuals with normal hearing or deaf patients belonging to the Spanish population. Methods WT and mutated pendrin allelic variants were functionally characterized in a heterologous over-expression system by means of fluorometric methods evaluating the I−/Cl− and Cl−/OH− exchange and an assay evaluating the efflux of radiolabeled iodide. Results The transport activity of pendrin P70L, P301L and F667C is completely abolished; pendrin V609G and D687Y allelic variants are functionally impaired but retain significant transport. Pendrin F354S activity is indistinguishable from WT, while pendrin V88I and G740S exhibit a gain of function. Conclusion Amino acid substitutions involving a proline always result in a severe loss of function of pendrin. Two hyperfunctional allelic variants (V88I, G740S) have been identified, and they may have a contributing role in the pathogenesis of hypertension, COPD and asthma. PMID:22116359

  9. Allele-specific disparity in breast cancer

    PubMed Central

    2011-01-01

    Background In a cancer cell the number of copies of a locus may vary due to amplification and deletion and these variations are denoted as copy number alterations (CNAs). We focus on the disparity of CNAs in tumour samples, which were compared to those in blood in order to identify the directional loss of heterozygosity. Methods We propose a numerical algorithm and apply it to data from the Illumina 109K-SNP array on 112 samples from breast cancer patients. B-allele frequency (BAF) and log R ratio (LRR) of Illumina were used to estimate Euclidian distances. For each locus, we compared genotypes in blood and tumour for subset of samples being heterozygous in blood. We identified loci showing preferential disparity from heterozygous toward either the A/B-allele homozygous (allelic disparity). The chi-squared and Cochran-Armitage trend tests were used to examine whether there is an association between high levels of disparity in single nucleotide polymorphisms (SNPs) and molecular, clinical and tumour-related parameters. To identify pathways and network functions over-represented within the resulting gene sets, we used Ingenuity Pathway Analysis (IPA). Results To identify loci with a high level of disparity, we selected SNPs 1) with a substantial degree of disparity and 2) with substantial frequency (at least 50% of the samples heterozygous for the respective locus). We report the overall difference in disparity in high-grade tumours compared to low-grade tumours (p-value < 0.001) and significant associations between disparity in multiple single loci and clinical parameters. The most significantly associated network functions within the genes represented in the loci of disparity were identified, including lipid metabolism, small-molecule biochemistry, and nervous system development and function. No evidence for over-representation of directional disparity in a list of stem cell genes was obtained, however genes appeared to be more often altered by deletion than by

  10. Allele Specific p53 Mutant Reactivation

    PubMed Central

    Yu, Xin; Vazquez, Alexei; Levine, Arnold J.; Carpizo, Darren R.

    2012-01-01

    Summary Rescuing the function of mutant p53 protein is an attractive cancer therapeutic strategy. Using the NCI anticancer drug screen data, we identified two compounds from the thiosemicarbazone family that manifest increased growth inhibitory activity in mutant p53 cells, particularly for the p53R175 mutant. Mechanistic studies reveal that NSC319726 restores WT structure and function to the p53R175 mutant. This compound kills p53R172H knock-in mice with extensive apoptosis and inhibits xenograft tumor growth in a 175-allele specific mutant p53 dependent manner. This activity depends upon the zinc ion chelating properties of the compound as well as redox changes. These data identify NSC319726 as a p53R175 mutant reactivator and as a lead compound for p53 targeted drug development. PMID:22624712

  11. HEAT EXCHANGER

    DOEpatents

    Fox, T.H. III; Richey, T. Jr.; Winders, G.R.

    1962-10-23

    A heat exchanger is designed for use in the transfer of heat between a radioactive fiuid and a non-radioactive fiuid. The exchanger employs a removable section containing the non-hazardous fluid extending into the section designed to contain the radioactive fluid. The removable section is provided with a construction to cancel out thermal stresses. The stationary section is pressurized to prevent leakage of the radioactive fiuid and to maintain a safe, desirable level for this fiuid. (AEC)

  12. Kinetics of Sr and Nd exchange in silicate liquids: Theory, experiments, and applications to uphill diffusion, isotopic equilibration, and irreversible mixing of magmas

    NASA Astrophysics Data System (ADS)

    Lesher, C. E.

    1994-05-01

    Diffusion coefficents that govern chemical isotopic exchange of Sr and Nd were determined from compositional profiles developed between juxtaposed anhydous basaltic and rhyolitic liquids. Analysis of simple diffusion couples involving isotopically enriched and normal tholeiitic basalt and metaluminous rhyolite recover Sr and Nd self-diffusion coefficients (D(sup *)) in the end-member compositions of contrasting polymerization. Self-diffusion of Sr is 7 times faster in basaltic melt than rhyolitic melt at 1255 C and 1 GPa, while self-diffusion of Nd is more than 1 order of magnitude greater in basalt than rhyolite. Also, at these conditions, D(sup *)(sub Sr) is a factor of 3 greater than D(sup asterisk)(sub Nd) in basalt and an order of magnitude greater than D(sup asterisk)(sub Nd) in rhyolite. Variations in D(sup *)(sub Sr) and D(sup asterisk)(sub Nd) with bulk composition and temperature between 1255-1465 C are described by ln D(sup *)(sub Sr) = -16.25 - (16348/T) + 8.02(0.73 - X(sub SiO2)) and ln D(sup asterisk)(sub Nd) = 13.73 - (23875/T) + 14.43(0.73 - X(sub SiO2)), where the units of D(sup *) are square meters per second, T is temperature in kelvins, and X(sub SiO2) is weight fraction silica. The results of a Boltzmann-Matano analysis of Sr-87/sigma Sr and Nd-144/sigma Nd profiles of complex diffusion couples composed of isotopically normal basalt and enriched rhyolite yield diffusion coefficients for intermediate bulk compositions in agreement with interpolated values given by the relationships above. An important feature of the interdiffusion of basaltic and rhyolitic liquids is the equilibration of isotopic composition in advance of chemical homogenization. This behavior is best displayed by Sr in the present experiments and predicted for Nd. In addition, Sr, Nd, and Al show initial periods of uphill diffusion, while other melt components diffuse down their respective concentration gradients leading to chemical homogenization. Despite uphill diffusive

  13. RHCE variant allele: RHCE*ce254G,733G.

    PubMed

    Keller, Jessica A; Horn, Trina; Chiappa, Colleen; Melland, Camilla; Vietz, Christine; Castilho, Lilian; Keller, Margaret A

    2014-01-01

    A novel RHCE allele was identified in a 53-year-old African American female blood donor with an Rh phenotype of D+ CE-c+ e+ and a negative antibody screen. The donor's cells typed e+ with all antisera tested. By gel-based genotyping and Edna analysis, the two RHCE alleles in this donor were characterized.One allele was found to be the known allele RHCE*Ol.20.01(RHCE*ce733G) and the second was novel: RHCE*Ol.06.02(RHCE*ce254G,733G). PMID:25695437

  14. Nomenclature for human CYP2D6 alleles.

    PubMed

    Daly, A K; Brockmöller, J; Broly, F; Eichelbaum, M; Evans, W E; Gonzalez, F J; Huang, J D; Idle, J R; Ingelman-Sundberg, M; Ishizaki, T; Jacqz-Aigrain, E; Meyer, U A; Nebert, D W; Steen, V M; Wolf, C R; Zanger, U M

    1996-06-01

    To standardize CYP2D6 allele nomenclature, and to conform with international human gene nomenclature guidelines, an alternative to the current arbitrary system is described. Based on recommendations for human genome nomenclature, we propose that alleles be designated by CYP2D6 followed by an asterisk and a combination of roman letters and arabic numerals distinct for each allele with the number specifying the key mutation and, where appropriate, a letter specifying additional mutations. Criteria for classification as a separate allele and protein nomenclature are also presented. PMID:8807658

  15. The effect of deleterious alleles on adaptation in asexual populations.

    PubMed Central

    Johnson, Toby; Barton, Nick H

    2002-01-01

    We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles. PMID:12242249

  16. Mutated tumor alleles are expressed according to their DNA frequency

    PubMed Central

    Castle, John C.; Loewer, Martin; Boegel, Sebastian; Tadmor, Arbel D.; Boisguerin, Valesca; de Graaf, Jos; Paret, Claudia; Diken, Mustafa; Kreiter, Sebastian; Türeci, Özlem; Sahin, Ugur

    2014-01-01

    The transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number, and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. In conclusion, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency. PMID:24752137

  17. Mutated tumor alleles are expressed according to their DNA frequency.

    PubMed

    Castle, John C; Loewer, Martin; Boegel, Sebastian; Tadmor, Arbel D; Boisguerin, Valesca; de Graaf, Jos; Paret, Claudia; Diken, Mustafa; Kreiter, Sebastian; Türeci, Özlem; Sahin, Ugur

    2014-01-01

    The transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number, and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. In conclusion, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency. PMID:24752137

  18. A single nucleotide polymorphism in an exon dictates allele dependent differential splicing of episialin mRNA.

    PubMed Central

    Ligtenberg, M J; Gennissen, A M; Vos, H L; Hilkens, J

    1991-01-01

    The episialin gene (MUC1) encodes an epithelial mucin containing a variable number of repeats with a length of twenty amino acids, resulting in many different alleles that can be subdivided into two size classes. The episialin pre-mRNA uses either one of two neighbouring splice acceptor sites for exon 2, which mainly encodes the repeats. Using the genetic polymorphism of the episialin gene to identify different alleles, we show here that the splice site recognition is allele dependent and is based on a single A/G nucleotide difference in exon 2 eight nucleotides downstream of the second splice acceptor site. Transfection experiments confirm that this polymorphic nucleotide regulates the splice site selection. The identity of this nucleotide is in most cases correlated with one of the size classes of the alleles, indicating that mutations altering the number of repeats seldom arise by unequal cross-over between the repeat regions. Images PMID:2014168

  19. Higher Education Exchange, 2014

    ERIC Educational Resources Information Center

    Brown, David W., Ed.; Witte, Deborah, Ed.

    2014-01-01

    Research shows that not only does higher education not see the public; when the public, in turn, looks at higher education, it sees mostly malaise, inefficiencies, expense, and unfulfilled promises. Yet, the contributors to this issue of the "Higher Education Exchange" tell of bright spots in higher education where experiments in working…

  20. Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles.

    SciTech Connect

    Sieker, Florian; Springer, Sebastian; Zacharias, Martin W.

    2007-02-01

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. MHC class I molecules load antigenic peptides in the endoplasmic reticulum and present them at the cell surface. Efficiency of peptide loading depends on the class I allele and can involve interaction with tapasin and other proteins of the loading complex. Allele HLA-B*4402 (Asp at position 116) depends on tapasin for efficient peptide loading, whereas HLA-B*4405 (identical to B*4402 except for Tyr116) can efficiently load peptides in the absence of tapasin. Both alleles adopt very similar structures in the presence of the same peptide. Comparative unrestrained molecular dynamics simulations on the 1/2 peptide binding domains performed in the presence of bound peptides resulted in structures in close agreement with experiments for both alleles. In the absence of peptides, allele-specific conformational changes occurred in the first segment of the 2-helix that flanks the peptide C-terminal binding region (F-pocket) and contacts residue 116. This segment is also close to the proposed tapasin contact region. For B*4402, a shift toward an altered F-pocket structure deviating significantly from the bound form was observed. Subsequent free energy simulations on induced F-pocket opening in B*4402 confirmed a conformation that deviated significantly from the bound structure. For B*4405, a free energy minimum close to the bound structure was found. The simulations suggest that B*4405 has a greater tendency to adopt a peptide receptive conformation in the absence of peptide, allowing tapasin-independent peptide loading. A possible role of tapasin could be the stabilization of a peptide-receptive class I conformation for HLA-B*4402 and other tapasin-dependent alleles.

  1. Detection of new HLA-DPB1 alleles generated by interallelic gene conversion using PCR amplification of DPB1 second exon sequences from sperm

    SciTech Connect

    Erlich, H.; Zangenberg, G.; Bugawan, T.

    1994-09-01

    The rate at which allelic diversity at the HLA class I and class II loci evolves has been the subject of considerable controversy as have the mechanisms which generate new alleles. The patchwork pattern of polymorphism, particularly within the second exon of the HLA-DPB1 locus where the polymorphic sequence motifs are localized to 6 discrete regions, is consistent with the hypothesis that much of the allelic sequence variation may have been generated by segmental exchange (gene conversion). To measure the rate of new DPB1 variant generation, we have developed a strategy in which DPB1 second exon sequences are amplified from pools of FACS-sorted sperm (n=50) from a heterozygous sperm donor. Pools of sperm from these heterozygous individuals are amplified with an allele-specific primer for one allele and analyzed with sequence-specific oligonucleotide probes (SSOP) complementary to the other allele. This screening procedure, which is capable of detecting a single variant molecule in a pool of parental alleles, allows the identification of new variants that have been generated by recombination and/or gene conversion between the two parental alleles. To control for potential PCR artifacts, the same screening procedure was carried out with mixtures of sperm from DPB1 *0301/*0301 and DPB1 *0401/ 0401 individuals. Pools containing putative new variants DPB1 alleles were analyzed further by cloning into M13 and sequencing the M13 clones. Our current estimate is that about 1/10,000 sperm from these heterozygous individuals represents a new DPB1 allele generated by micro-gene conversion within the second exon.

  2. Identification of the third/extra allele for forensic application in cases with TPOX tri-allelic pattern.

    PubMed

    Picanço, Juliane Bentes; Raimann, Paulo Eduardo; da Motta, Carlos Henrique Ares Silveira; Rodenbusch, Rodrigo; Gusmão, Leonor; Alho, Clarice Sampaio

    2015-05-01

    Genotyping of polymorphic short tandem repeats (STRs) loci is widely used in forensic DNA analysis. STR loci eventually present tri-allelic pattern as a genotyping irregularity and, in that situation, the doubt about the tri-allele locus frequency calculation can reduce the analysis strength. In the TPOX human STR locus, tri-allelic genotypes have been reported with a widely varied frequency among human populations. We investigate whether there is a single extra allele (the third allele) in the TPOX tri-allelic pattern, what it is, and where it is, aiming to understand its genomic anatomy and to propose the knowledge of this TPOX extra allele from genetic profile, thus preserving the two standard TPOX alleles in forensic analyses. We looked for TPOX tri-allelic subjects in 75,113 Brazilian families. Considering only the parental generation (mother+father) we had 150,226 unrelated subjects evaluated. From this total, we found 88 unrelated subjects with tri-allelic pattern in the TPOX locus (0.06%; 88/150,226). Seventy three of these 88 subjects (73/88; 83%) had the Clayton's original Type 2 tri-allelic pattern (three peaks of even intensity). The remaining 17% (15/88) show a new Type 2 derived category with heterozygote peak imbalance (one double dose peak plus one regular sized peak). In this paper we present detailed data from 66 trios (mother+father+child) with true biological relationships. In 39 of these families (39/66; 59%) the extra TPOX allele was transmitted either from the mother or from the father to the child. Evidences indicated the allele 10 as the extra TPOX allele, and it is on the X chromosome. The present data, which support the previous Lane hypothesis, improve the knowledge about tri-allelic pattern of TPOX CODIS' locus allowing the use of TPOX profile in forensic analyses even when with tri-allelic pattern. This evaluation is now available for different forensic applications. PMID:25549886

  3. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots.

    PubMed

    Baker, Christopher L; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M; Paigen, Kenneth

    2015-09-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape. PMID:26368021

  4. Science exchanges

    NASA Astrophysics Data System (ADS)

    Richman, Barbara T.

    Dwindling scientific and technical exchange between the United States and the Soviet Union and prospects for enhancing such exchanges were discussed at an August 2 hearing by the Foreign Affairs Committee of the U.S. House of Representatives. The committee also heard overviews on the United States' approach to international exchange of science and technology. The hearing was the first in a series on current and future international science and technology programs.Four of eight science and technology agreements with the USSR that have expired in the last 15 months, including one on space, have not been renewed. The remaining four agreements have been extended into 1987 and 1988. Two others, including one on oceanography, are scheduled to run out in 1984.

  5. Genetic Variability and Distribution of Mating Type Alleles in Field Populations of Leptosphaeria maculans from France

    PubMed Central

    Gout, Lilian; Eckert, Maria; Rouxel, Thierry; Balesdent, Marie-Hélène

    2006-01-01

    Leptosphaeria maculans is the most ubiquitous fungal pathogen of Brassica crops and causes the devastating stem canker disease of oilseed rape worldwide. We used minisatellite markers to determine the genetic structure of L. maculans in four field populations from France. Isolates were collected at three different spatial scales (leaf, 2-m2 field plot, and field) enabling the evaluation of spatial distribution of the mating type alleles and of genetic variability within and among field populations. Within each field population, no gametic disequilibrium between the minisatellite loci was detected and the mating type alleles were present at equal frequencies. Both sexual and asexual reproduction occur in the field, but the genetic structure of these populations is consistent with annual cycles of randomly mating sexual reproduction. All L. maculans field populations had a high level of gene diversity (H = 0.68 to 0.75) and genotypic diversity. Within each field population, the number of genotypes often was very close to the number of isolates. Analysis of molecular variance indicated that >99.5% of the total genetic variability was distributed at a small spatial scale, i.e., within 2-m2 field plots. Population differentiation among the four field populations was low (GST < 0.02), suggesting a high degree of gene exchange between these populations. The high gene flow evidenced here in French populations of L. maculans suggests a rapid countrywide diffusion of novel virulence alleles whenever novel resistance sources are used. PMID:16391041

  6. Genetic variability and distribution of mating type alleles in field populations of Leptosphaeria maculans from France.

    PubMed

    Gout, Lilian; Eckert, Maria; Rouxel, Thierry; Balesdent, Marie-Hélène

    2006-01-01

    Leptosphaeria maculans is the most ubiquitous fungal pathogen of Brassica crops and causes the devastating stem canker disease of oilseed rape worldwide. We used minisatellite markers to determine the genetic structure of L. maculans in four field populations from France. Isolates were collected at three different spatial scales (leaf, 2-m2 field plot, and field) enabling the evaluation of spatial distribution of the mating type alleles and of genetic variability within and among field populations. Within each field population, no gametic disequilibrium between the minisatellite loci was detected and the mating type alleles were present at equal frequencies. Both sexual and asexual reproduction occur in the field, but the genetic structure of these populations is consistent with annual cycles of randomly mating sexual reproduction. All L. maculans field populations had a high level of gene diversity (H = 0.68 to 0.75) and genotypic diversity. Within each field population, the number of genotypes often was very close to the number of isolates. Analysis of molecular variance indicated that >99.5% of the total genetic variability was distributed at a small spatial scale, i.e., within 2-m2 field plots. Population differentiation among the four field populations was low (GST < 0.02), suggesting a high degree of gene exchange between these populations. The high gene flow evidenced here in French populations of L. maculans suggests a rapid countrywide diffusion of novel virulence alleles whenever novel resistance sources are used. PMID:16391041

  7. Heat exchanger

    SciTech Connect

    Drury, C.R.

    1988-02-02

    A heat exchanger having primary and secondary conduits in heat-exchanging relationship is described comprising: at least one serpentine tube having parallel sections connected by reverse bends, the serpentine tube constituting one of the conduits; a group of open-ended tubes disposed adjacent to the parallel sections, the open-ended tubes constituting the other of the conduits, and forming a continuous mass of contacting tubes extending between and surrounding the serpentine tube sections; and means securing the mass of tubes together to form a predetermined cross-section of the entirety of the mass of open-ended tubes and tube sections.

  8. Biased Allelic Expression in Human Primary Fibroblast Single Cells

    PubMed Central

    Borel, Christelle; Ferreira, Pedro G.; Santoni, Federico; Delaneau, Olivier; Fort, Alexandre; Popadin, Konstantin Y.; Garieri, Marco; Falconnet, Emilie; Ribaux, Pascale; Guipponi, Michel; Padioleau, Ismael; Carninci, Piero; Dermitzakis, Emmanouil T.; Antonarakis, Stylianos E.

    2015-01-01

    The study of gene expression in mammalian single cells via genomic technologies now provides the possibility to investigate the patterns of allelic gene expression. We used single-cell RNA sequencing to detect the allele-specific mRNA level in 203 single human primary fibroblasts over 133,633 unique heterozygous single-nucleotide variants (hetSNVs). We observed that at the snapshot of analyses, each cell contained mostly transcripts from one allele from the majority of genes; indeed, 76.4% of the hetSNVs displayed stochastic monoallelic expression in single cells. Remarkably, adjacent hetSNVs exhibited a haplotype-consistent allelic ratio; in contrast, distant sites located in two different genes were independent of the haplotype structure. Moreover, the allele-specific expression in single cells correlated with the abundance of the cellular transcript. We observed that genes expressing both alleles in the majority of the single cells at a given time point were rare and enriched with highly expressed genes. The relative abundance of each allele in a cell was controlled by some regulatory mechanisms given that we observed related single-cell allelic profiles according to genes. Overall, these results have direct implications in cellular phenotypic variability. PMID:25557783

  9. A gene feature enumeration approach for describing HLA allele polymorphism.

    PubMed

    Mack, Steven J

    2015-12-01

    HLA genotyping via next generation sequencing (NGS) poses challenges for the use of HLA allele names to analyze and discuss sequence polymorphism. NGS will identify many new synonymous and non-coding HLA sequence variants. Allele names identify the types of nucleotide polymorphism that define an allele (non-synonymous, synonymous and non-coding changes), but do not describe how polymorphism is distributed among the individual features (the flanking untranslated regions, exons and introns) of a gene. Further, HLA alleles cannot be named in the absence of antigen-recognition domain (ARD) encoding exons. Here, a system for describing HLA polymorphism in terms of HLA gene features (GFs) is proposed. This system enumerates the unique nucleotide sequences for each GF in an HLA gene, and records these in a GF enumeration notation that allows both more granular dissection of allele-level HLA polymorphism and the discussion and analysis of GFs in the absence of ARD-encoding exon sequences. PMID:26416087

  10. The frequency of HLA alleles in the Romanian population.

    PubMed

    Constantinescu, Ileana; Boșcaiu, Voicu; Cianga, Petru; Dinu, Andrei-Antoniu; Gai, Elena; Melinte, Mihaela; Moise, Ana

    2016-03-01

    Knowledge of human leukocyte antigen (HLA) allele frequencies is essential for bone marrow and kidney donor searches. The Romanian Caucasian population is heterogeneous and information on HLA polymorphism has not been well studied. We characterized the HLA genetic profile and allele frequencies of regional populations in Romania. HLA-A, B and DRB1 alleles were examined in 8252 individuals, belonging to the four main regions of Romania. The most common alleles found in the Romanian population are the following: HLA-A*01, A*02, A*03, A*11, A*24; HLA-B*18, B*35, B*44, B*51 and HLA-DRB1*01, DRB1*03, DRB1*07, DRB1*11, DRB1*13, DRB1*15, DRB1*16. More than half of the alleles are non-homogeneously spread in Romania. These results provide a starting point for future analyses of genetic heterogeneity in Romania. PMID:26711124

  11. Veterans Health Administration Experience with Data Quality Surveillance of Continuity of Care Documents: Interoperability Challenges for eHealth Exchange Participants

    PubMed Central

    Lyle, Jay; Bouhaddou, Omar; Botts, Nathan; Swall, Marie; Pan, Eric; Cullen, Terry; Donahue, Margaret; Hsing, Nelson

    2015-01-01

    As part of ongoing data quality efforts authors monitored health information retrieved through the United States Department of Veterans Affairs’ (VA) Virtual Lifetime Electronic Record (VLER) Health operation. Health data exchanged through the eHealth Exchange (managed by Healtheway, Inc.) between VA and external care providers was evaluated in order to test methods of data quality surveillance and to identify key quality concerns. Testing evaluated transition of care data from 20 VLER Health partners. Findings indicated operational monitoring discovers issues not addressed during onboarding testing, that many issues result from specification ambiguity, and that many issues require human review. We make recommendations to address these issues, specifically to embed automated testing tools within information exchange transactions and to continuously monitor and improve data quality, which will facilitate adoption and use. PMID:26958223

  12. Heat exchanger

    DOEpatents

    Daman, Ernest L.; McCallister, Robert A.

    1979-01-01

    A heat exchanger is provided having first and second fluid chambers for passing primary and secondary fluids. The chambers are spaced apart and have heat pipes extending from inside one chamber to inside the other chamber. A third chamber is provided for passing a purge fluid, and the heat pipe portion between the first and second chambers lies within the third chamber.

  13. Allelic association of the D2 dopamine receptor gene with receptor-binding characteristics in alcoholism

    SciTech Connect

    Noble, E.P.; Blum, K.; Ritchie, T.; Montgomery, A.; Sheridan, P.J. )

    1991-07-01

    The allelic association of the human D2 dopamine receptor gene with the binding characteristics of the D2 dopamine receptor was determined in 66 brains of alcoholic and non-alcoholic subjects. In a blinded experiment, DNA from the cerebral cortex was treated with the restriction endonuclease Taql and probed with a 1.5-kilobase (kb) digest of a clone (lambda hD2G1) of the human D2 dopamine receptor gene. The binding characteristics (Kd (binding affinity) and Bmax (number of binding sites)) of the D2 dopamine receptor were determined in the caudate nuclei of these brains using tritiated spiperone as the ligand. The adjusted Kd was significantly lower in alcoholic than in nonalcoholic subjects. In subjects with the A1 allele, in whom a high association with alcoholism was found, the Bmax was significantly reduced compared with the Bmax of subjects with the A2 allele. Moreover, a progressively reduced Bmax was found in subjects with A2/A2, A1/A2, and A1/A1 alleles, with subjects with A2/A2 having the highest mean values, and subjects with A1/A1, the lowest. The polymorphic pattern of the D2 dopamine receptor gene and its differential expression of receptors suggests the involvement of the dopaminergic system in conferring susceptibility to at least one subtype of severe alcoholism.

  14. Dynamics of Neutral and Selected Alleles When the Offspring Distribution Is Skewed

    PubMed Central

    Der, Ricky; Epstein, Charles; Plotkin, Joshua B.

    2012-01-01

    We analyze the dynamics of two alternative alleles in a simple model of a population that allows for large family sizes in the distribution of offspring number. This population model was first introduced by Eldon and Wakeley, who described the backward-time genealogical relationships among sampled individuals, assuming neutrality. We study the corresponding forward-time dynamics of allele frequencies, with or without selection. We derive a continuum approximation, analogous to Kimura’s diffusion approximation, and we describe three distinct regimes of behavior that correspond to distinct regimes in the coalescent processes of Eldon and Wakeley. We demonstrate that the effect of selection is strongly amplified in the Eldon–Wakeley model, compared to the Wright–Fisher model with the same variance effective population size. Remarkably, an advantageous allele can even be guaranteed to fix in the Eldon–Wakeley model, despite the presence of genetic drift. We compute the selection coefficient required for such behavior in populations of Pacific oysters, based on estimates of their family sizes. Our analysis underscores that populations with the same effective population size may nevertheless experience radically different forms of genetic drift, depending on the reproductive mechanism, with significant consequences for the resulting allele dynamics. PMID:22661323

  15. Natural allelic variations of xenobiotic-metabolizing enzymes affect sexual dimorphism in Oryzias latipes

    PubMed Central

    Katsumura, Takafumi; Oda, Shoji; Nakagome, Shigeki; Hanihara, Tsunehiko; Kataoka, Hiroshi; Mitani, Hiroshi; Kawamura, Shoji; Oota, Hiroki

    2014-01-01

    Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection. Interestingly, sexually selected traits show geographical variations within species despite strong directional selective pressures. This paradox has eluded many evolutionary biologists for some time, and several models have been proposed (e.g. ‘indicator model’ and ‘trade-off model’). However, disentangling which of these theories explains empirical patterns remains difficult, because genetic polymorphisms that cause variation in sexual differences are still unknown. In this study, we show that polymorphisms in cytochrome P450 (CYP) 1B1, which encodes a xenobiotic-metabolizing enzyme, are associated with geographical differences in sexual dimorphism in the anal fin morphology of medaka fish (Oryzias latipes). Biochemical assays and genetic cross experiments show that high- and low-activity CYP1B1 alleles enhanced and declined sex differences in anal fin shapes, respectively. Behavioural and phylogenetic analyses suggest maintenance of the high-activity allele by sexual selection, whereas the low-activity allele possibly has experienced positive selection due to by-product effects of CYP1B1 in inferred ancestral populations. The present data can elucidate evolutionary mechanisms behind genetic variations in sexual dimorphism and indicate trade-off interactions between two distinct mechanisms acting on the two alleles with pleiotropic effects of xenobiotic-metabolizing enzymes. PMID:25377463

  16. Population Dynamics of Sex-Determining Alleles in Honey Bees and Self-Incompatibility Alleles in Plants

    PubMed Central

    Yokoyama, Shozo; Nei, Masatoshi

    1979-01-01

    Mathematical theories of the population dynamics of sex-determining alleles in honey bees are developed. It is shown that in an infinitely large population the equilibrium frequency of a sex allele is 1/n, where n is the number of alleles in the population, and the asymptotic rate of approach to this equilibrium is 2/(3n) per generation. Formulae for the distribution of allele frequencies and the effective and actual numbers of alleles that can be maintained in a finite population are derived by taking into account the population size and mutation rate. It is shown that the allele frequencies in a finite population may deviate considerably from 1/n. Using these results, available data on the number of sex alleles in honey bee populations are discussed. It is also shown that the number of self-incompatibility alleles in plants can be studied in a much simpler way by the method used in this paper. A brief discussion about general overdominant selection is presented. PMID:17248901

  17. QTL mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower

    PubMed Central

    Whitney, Kenneth D.; Broman, Karl W.; Kane, Nolan C.; Hovick, Stephen M.; Randell, Rebecca A.; Rieseberg, Loren H.

    2014-01-01

    The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 SNP markers, and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological, and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favored in the wild. QTL for a number of other ecophysiological, phenological, and architectural traits co-localized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence. PMID:25522096

  18. Downhole heat exchangers

    SciTech Connect

    Culver, G.; Lund, J.W.

    1999-09-01

    The downhole heat exchanger (DHE) eliminates the problem of disposal of geothermal fluid, since only heat is taken from the well. The exchanger consists of a system of pipes or tubes suspended in the well through which clean secondary water is pumped or allowed to circulate by natural convection. These systems offer substantial economic savings over surface heat exchangers where a single-well system is adequate (typically less than 0.8 MWt, with well depths up to about 500 ft) and may be economical under certain conditions at well depths to 1500 ft. Several designs have proven successful; but, the most popular are a simple hairpin loop or multiple loops of iron pipe (similar to the tubes in a U-tube and shell exchanger) extending to near the well bottom. An experimental design consisting of multiple small tubes with headers at each end suspended just below the water surface appears to offer economic and heating capacity advantages. The paper describes design and construction details and New Zealand`s experience with downhole heat exchangers.

  19. Mini-Column Ion-Exchange Separation and Atomic Absorption Quantitation of Nickel, Cobalt, and Iron: An Undergraduate Quantitative Analysis Experiment.

    ERIC Educational Resources Information Center

    Anderson, James L.; And Others

    1980-01-01

    Presents an undergraduate quantitative analysis experiment, describing an atomic absorption quantitation scheme that is fast, sensitive and comparatively simple relative to other titration experiments. (CS)

  20. Kinetics of P/sub i/-P/sub i/ exchange in rat liver mitochondria. Rapid filtration experiments in the millisecond time range

    SciTech Connect

    Ligeti, E.; Brandolin, G.; Dupont, Y.; Vignais, P.V.

    1985-07-30

    Phosphate-phosphate exchange through the inorganic phosphate (P/sub i/) carrier of rat liver mitochondria was investigated by a new rapid filtration technique, which does not require the use of transport inhibitors to stop the reaction and offers high time resolution (starting from 10 ms), thus allowing kinetic measurements on a fine time scale even at room temperature. At approximately 22 degrees C, isotopic equilibrium of (TSP)P/sub i/ is achieved within 0.8-2.5 s--depending on the P/sub i/ concentration--and an initial linear phase, lasting for 400-500 ms, is observed. Complete inhibition of P/sub i/ exchange by an excess of mersalyl, a well-known organomercurial inhibitor, required 200 ms, pointing to the insufficiency of this reagent for effective inhibitor stop. On the other hand, investigation of the effect of mersalyl on the initial rate of P/sub i/ exchange supports earlier observations on the protective effect of this inhibitor. In nonrespiring mitochondria, at pH 7.3, P/sub i/ exchange exhibited a K/sub m/ of 1.6 mM and a V/sub max/ of 3.0 mumol min-1 (mg of mitochondrial protein)-1. The maximal velocity of P/sub i/ transport is significantly higher than the maximal velocity of all the other components of oxidative phosphorylation at comparable temperatures. The possible physiological significance of this excess capacity is discussed.

  1. Allele frequencies at microsatellite loci: The stepwise mutation model revisited

    SciTech Connect

    Valdes, A.M.; Slatkin, M. ); Freimer, N.B. )

    1993-03-01

    The authors summarize available data on the frequencies of alleles at microsatellite loci in human populations and compare observed distributions of allele frequencies to those generated by a simulation of the stepwise mutation model. They show that observed frequency distributions at 108 loci are consistent with the results of the model under the assumption that mutations cause an increase or decrease in repeat number by one and under the condition that the product Nu, where N is the effective population size and u is the mutation rate, is larger than one. It is also shown that the variance of the distribution of allele sizes is a useful estimator of Nu and performs much better than previously suggested estimators for the stepwise mutation model. In the data, there is no correlation between the mean and variance in allele size at a locus or between the number of alleles and mean allele size, which suggests that the mutation rate at these loci is independent of allele size. 39 refs., 6 figs., 4 tabs.

  2. Common alleles contribute to schizophrenia in CNV carriers

    PubMed Central

    Tansey, K E; Rees, E; Linden, D E; Ripke, S; Chambert, K D; Moran, J L; McCarroll, S A; Holmans, P; Kirov, G; Walters, J; Owen, M J; O'Donovan, M C

    2016-01-01

    The genetic architecture of schizophrenia is complex, involving risk alleles ranging from common alleles of weak effect to rare alleles of large effect, the best exemplar of the latter being large copy number variants (CNVs). It is currently unknown whether pathophysiology in those with defined rare mutations overlaps with that in other individuals with the disorder who do not share the same rare mutation. Under an extreme heterogeneity model, carriers of specific high-penetrance mutations form distinct subgroups. In contrast, under a polygenic threshold model, high-penetrance rare allele carriers possess many risk factors, of which the rare allele is the only one, albeit an important, factor. Under the latter model, cases with rare mutations can be expected to share some common risk alleles, and therefore pathophysiological mechanisms, with cases without the same mutation. Here we show that, compared with controls, individuals with schizophrenia who have known pathogenic CNVs carry an excess burden of common risk alleles (P=2.25 × 10−17) defined from a genome-wide association study largely based on individuals without known CNVs. Our finding is not consistent with an extreme heterogeneity model for CNV carriers, but does offer support for the polygenic threshold model of schizophrenia. That this is so provides support for the notion that studies aiming to model the effects of rare variation may uncover pathophysiological mechanisms of relevance to those with the disorder more widely. PMID:26390827

  3. Common alleles contribute to schizophrenia in CNV carriers.

    PubMed

    Tansey, K E; Rees, E; Linden, D E; Ripke, S; Chambert, K D; Moran, J L; McCarroll, S A; Holmans, P; Kirov, G; Walters, J; Owen, M J; O'Donovan, M C

    2016-08-01

    The genetic architecture of schizophrenia is complex, involving risk alleles ranging from common alleles of weak effect to rare alleles of large effect, the best exemplar of the latter being large copy number variants (CNVs). It is currently unknown whether pathophysiology in those with defined rare mutations overlaps with that in other individuals with the disorder who do not share the same rare mutation. Under an extreme heterogeneity model, carriers of specific high-penetrance mutations form distinct subgroups. In contrast, under a polygenic threshold model, high-penetrance rare allele carriers possess many risk factors, of which the rare allele is the only one, albeit an important, factor. Under the latter model, cases with rare mutations can be expected to share some common risk alleles, and therefore pathophysiological mechanisms, with cases without the same mutation. Here we show that, compared with controls, individuals with schizophrenia who have known pathogenic CNVs carry an excess burden of common risk alleles (P=2.25 × 10(-17)) defined from a genome-wide association study largely based on individuals without known CNVs. Our finding is not consistent with an extreme heterogeneity model for CNV carriers, but does offer support for the polygenic threshold model of schizophrenia. That this is so provides support for the notion that studies aiming to model the effects of rare variation may uncover pathophysiological mechanisms of relevance to those with the disorder more widely. PMID:26390827

  4. Bayesian Inference of Natural Selection from Allele Frequency Time Series.

    PubMed

    Schraiber, Joshua G; Evans, Steven N; Slatkin, Montgomery

    2016-05-01

    The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such direct observations of allele frequency dynamics are expected to be more powerful than inferences made using patterns of linked neutral variation obtained from modern individuals. We developed a Bayesian method to make use of allele frequency time series data and infer the parameters of general diploid selection, along with allele age, in nonequilibrium populations. We introduce a novel path augmentation approach, in which we use Markov chain Monte Carlo to integrate over the space of allele frequency trajectories consistent with the observed data. Using simulations, we show that this approach has good power to estimate selection coefficients and allele age. Moreover, when applying our approach to data on horse coat color, we find that ignoring a relevant demographic history can significantly bias the results of inference. Our approach is made available in a C++ software package. PMID:27010022

  5. A pseudodeficiency allele (D152N) of the human {beta}-glucuronidase gene

    SciTech Connect

    Vervoort, R.; Liebaers, I.; Lissens, W.

    1995-10-01

    We present evidence that a 480G{r_arrow}A transition in the coding region of the {Beta}glucuronidase gene, which results in an aspartic-acid-to-asparagine substitution at amino acid position 152 (D152N), produces a pseudodeficiency allele (GUSBp) that leads to greatly reduced levels of {Beta}-glucuronidase activity without apparent deleterious consequences. The 48OG{r_arrow}A mutation was found initially in the pseudodeficient mother of a child with mucopolysaccharidosis VII (MPSVII), but it was not on her disease-causing allele, which carried the L176F mutation. The 480G{r_arrow}A change was also present in an unrelated individual with another MPSVII allele who had unusually low {Beta}-glucuronidase activity, but whose clinical symptoms were probably unrelated to {Beta}-glucuronidase deficiency. This individual also had an R357X mutation, probably on his second allele. We screened 100 unrelated normal individuals for the 480G{r_arrow}A mutation with a PCR method and detected one carrier. Reduced {Beta}-glucuronidase activity following transfection of COS cells with the D152N cDNA supported the causal relationship between the D152N allele and pseudodeficiency. The mutation reduced the fraction of expressed enzyme that was secreted. Pulse-chase experiments indicated that the reduced activity in COS cells was due to accelerated intracellular turnover of the D152N enzyme. They also suggested that a potential glycosylation site created by the mutation is utilized in {approximately}50% of the enzyme expressed. 25 refs., 3 figs., 3 tabs.

  6. Frequency of alleles conferring resistance to the Bt toxins Cry1Ac and Cry2Ab in Australian populations of Helicoverpa armigera (Lepidoptera: Noctuidae).

    PubMed

    Mahon, R J; Olsen, K M; Downes, S; Addison, S

    2007-12-01

    Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) is an important lepidopteran pest of cotton (Gossypium spp.) in Australia and the Old World. From 2002, F2 screens were used to examine the frequency of resistance alleles in Australian populations of H. armigera to Bacillus thuringiensis (Bt) CrylAc and Cry2Ab, the two insecticidal proteins present in the transgenic cotton Bollgard II. At that time, Ingard (expressing Cry1Ac) cotton had been grown in Australia for seven seasons, and Bollgard II was about to be commercially released. The principal objective of our study was to determine whether sustained exposure caused an elevated frequency of alleles conferring resistance to Cry1Ac in a species with a track record of evolving resistance to conventional insecticides. No major alleles conferring resistance to Cry1Ac were found. The frequency of resistance alleles for Cry1Ac was <0.0003, with a 95% credibility interval between 0 and 0.0009. In contrast, alleles conferring resistance to Cry2Ab were found at a frequency of 0.0033 (0.0017, 0.0055). The first isolation of this allele was found before the widespread deployment of Bollgard II. For both toxins the experiment-wise detection probability was 94.4%. Our results suggest that alleles conferring resistance to Cry1Ac are rare and that a relatively high baseline frequency of alleles conferring resistance to Cry2Ab existed before the introduction of Bt cotton containing this toxin. PMID:18232402

  7. A loss-of-function allele of OsHMA3 associated with high cadmium accumulation in shoots and grain of Japonica rice cultivars.

    PubMed

    Yan, Jiali; Wang, Peitong; Wang, Peng; Yang, Meng; Lian, Xingming; Tang, Zhong; Huang, Chao-Feng; Salt, David E; Zhao, Fang Jie

    2016-09-01

    Excessive cadmium (Cd) accumulation in rice poses a risk to food safety. OsHMA3 plays an important role in restricting Cd translocation from roots to shoots. A non-functional allele of OsHMA3 has been reported in some Indica rice cultivars with high Cd accumulation, but it is not known if OsHMA3 allelic variation is associated with Cd accumulation in Japonica cultivars. In this study, we identified a Japonica cultivar with consistently high Cd accumulation in shoots and grain in both field and greenhouse experiments. The cultivar possesses an OsHMA3 allele with a predicted amino acid mutation at the 380(th) position from Ser to Arg. The haplotype had no Cd transport activity when the gene was expressed in yeast, and the allele did not complement a known nonfunctional allele of OsHMA3 in F1 test. The allele is present only in temperate Japonica cultivars among diversity panels of 1483 rice cultivars. Different cultivars possessing this allele showed greatly increased root-to-shoot Cd translocation and a shift in root Cd speciation from Cd-S to Cd-O bonding determined by synchrotron X-ray absorption spectroscopy. Our study has identified a new loss-of-function allele of OsHMA3 in Japonica rice cultivars leading to high Cd accumulation in shoots and grain. PMID:27038090

  8. Field experience with a new installation for countercurrent ion-exchange treatment of low-mineralized natural water with high content of organic impurities

    NASA Astrophysics Data System (ADS)

    Larin, B. M.; Larin, A. B.; Oparin, M. Yu.; Vinogradov, V. N.

    2009-06-01

    Results obtained from examination of the working characteristics of filters are presented together with the filtering material analysis data that were obtained on a new high-output plant for ion-exchange treatment of natural water with high content of organic impurities. Stable operation of the plant is pointed out, and difficulties are indicated that arise from the fact that the water treatment system does not contain a unit for coagulation in a clarifier.

  9. A New Electrophoresis Technique to Seperate Microsatellite Alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Traditional agarose and polyacrylamide gel electrophoresis have been used commonly for microsatellite (simple sequence repeats, SSRs) analysis, but they are labor- intensive and not always able to provide accurate sizes for different alleles. Capillary sequencers provide automated analysis and accur...

  10. Differential and limited expression of mutant alleles in multiple myeloma

    PubMed Central

    Rashid, Naim U.; Sperling, Adam S.; Bolli, Niccolo; Wedge, David C.; Van Loo, Peter; Tai, Yu-Tzu; Shammas, Masood A.; Fulciniti, Mariateresa; Samur, Mehmet K.; Richardson, Paul G.; Magrangeas, Florence; Minvielle, Stephane; Futreal, P. Andrew; Anderson, Kenneth C.; Avet-Loiseau, Herve; Parmigiani, Giovanni

    2014-01-01

    Recent work has delineated mutational profiles in multiple myeloma and reported a median of 52 mutations per patient, as well as a set of commonly mutated genes across multiple patients. In this study, we have used deep sequencing of RNA from a subset of these patients to evaluate the proportion of expressed mutations. We find that the majority of previously identified mutations occur within genes with very low or no detectable expression. On average, 27% (range, 11% to 47%) of mutated alleles are found to be expressed, and among mutated genes that are expressed, there often is allele-specific expression where either the mutant or wild-type allele is suppressed. Even in the absence of an overall change in gene expression, the presence of differential allelic expression within malignant cells highlights the important contribution of RNA-sequencing in identifying clinically significant mutational changes relevant to our understanding of myeloma biology and also for therapeutic applications. PMID:25237203

  11. Differential and limited expression of mutant alleles in multiple myeloma.

    PubMed

    Rashid, Naim U; Sperling, Adam S; Bolli, Niccolo; Wedge, David C; Van Loo, Peter; Tai, Yu-Tzu; Shammas, Masood A; Fulciniti, Mariateresa; Samur, Mehmet K; Richardson, Paul G; Magrangeas, Florence; Minvielle, Stephane; Futreal, P Andrew; Anderson, Kenneth C; Avet-Loiseau, Herve; Campbell, Peter J; Parmigiani, Giovanni; Munshi, Nikhil C

    2014-11-13

    Recent work has delineated mutational profiles in multiple myeloma and reported a median of 52 mutations per patient, as well as a set of commonly mutated genes across multiple patients. In this study, we have used deep sequencing of RNA from a subset of these patients to evaluate the proportion of expressed mutations. We find that the majority of previously identified mutations occur within genes with very low or no detectable expression. On average, 27% (range, 11% to 47%) of mutated alleles are found to be expressed, and among mutated genes that are expressed, there often is allele-specific expression where either the mutant or wild-type allele is suppressed. Even in the absence of an overall change in gene expression, the presence of differential allelic expression within malignant cells highlights the important contribution of RNA-sequencing in identifying clinically significant mutational changes relevant to our understanding of myeloma biology and also for therapeutic applications. PMID:25237203

  12. Understanding the Adsorption of PFOA on MIL-101(Cr)-Based Anionic-Exchange Metal-Organic Frameworks: Comparing DFT Calculations with Aqueous Sorption Experiments.

    PubMed

    Liu, Kai; Zhang, Siyu; Hu, Xiyue; Zhang, Kunyang; Roy, Ajay; Yu, Gang

    2015-07-21

    To examine the effects of different functionalization methods on adsorption behavior, anionic-exchange MIL-101(Cr) metal-organic frameworks (MOFs) were synthesized using preassembled modification (PAM) and postsynthetic modification (PSM) methods. Perfluorooctanoic acid (PFOA) adsorption results indicated that the maximum PFOA adsorption capacity was 1.19 and 1.89 mmol g(-1) for anionic-exchange MIL-101(Cr) prepared by PAM and PSM, respectively. The sorption equilibrium was rapidly reached within 60 min. Our results indicated that PSM is a better modification technique for introducing functional groups onto MOFs for adsorptive removal because PAM places functional groups onto the aperture of the nanopore, which hinders the entrance of organic contaminants. Our experimental results and the results of complementary density functional theory calculations revealed that in addition to the anion-exchange mechanism, the major PFOA adsorption mechanism is a combination of Lewis acid/base complexation between PFOA and Cr(III) and electrostatic interaction between PFOA and the protonated carboxyl groups of the bdc (terephthalic acid) linker. PMID:26066631

  13. DRD4 dopamine receptor allelic diversity in various primate species

    SciTech Connect

    Adamson, M.; Higley, D.; O`Brien, S.

    1994-09-01

    The DRD4 dopamine receptor is uniquely characterized by a 48 bp repeating segment within the coding region, located in exon III. Different DRD4 alleles are produced by the presence of additional 48 bp repeats, each of which adds 16 amino acids to the length of the 3rd intracytoplasmic loop of the receptor. The DRD4 receptor is therefore an intriguing candidate gene for behaviors which are influenced by dopamine function. In several human populations, DRD4 alleles with 2-8 and 10 repeats have previously been identified, and the 4 and 7 repeat alleles are the most abundant. We have determined DRD4 genotypes in the following nonhuman primate species: chimpanzee N=2, pygmy chimpanzee N=2, gorilla N=4, siamang N=2, Gelada baboon N=1, gibbon N=1, orangutan (Bornean and Sumatran) N=62, spider monkey N=4, owl monkey N=1, Colobus monkey N=1, Patas monkey N=1, ruffed lemur N=1, rhesus macaque N=8, and vervet monkey N=28. The degree of DRD4 polymorphism and which DRD4 alleles were present both showed considerable variation across primate species. In contrast to the human, rhesus macaque monkeys were monomorphic. The 4 and 7 repeat allels, highly abundant in the human, may not be present in certain other primates. For example, the four spider monkeys we studied showed the 7, 8 and 9 repeat length alleles and the only gibbon we analyzed was homozygous for the 9 repeat allele (thus far not observed in the human). Genotyping of other primate species and sequencing of the individual DRD4 repeat alleles in different species may help us determine the ancestral DRD4 repeat length and identify connections between DRD4 genotype and phenotype.

  14. Heat exchanger

    DOEpatents

    Brackenbury, Phillip J.

    1986-04-01

    A heat exchanger comparising a shell attached at its open end to one side of a tube sheet and a detachable head connected to the other side of said tube sheet. The head is divided into a first and second chamber in fluid communication with a nozzle inlet and nozzle outlet, respectively, formed in said tube sheet. A tube bundle is mounted within said shell and is provided with inlets and outlets formed in said tube sheet in communication with said first and second chambers, respectively.

  15. Allele-specific MMP-3 transcription under in vivo conditions

    SciTech Connect

    Zhu Chaoyong; Odeberg, Jacob; Hamsten, Anders; Eriksson, Per . E-mail: Per.Eriksson@ki.se

    2006-09-29

    A common matrix metalloproteinases-3 (MMP-3) -1612 5A/6A promoter polymorphism is associated with risk for cardiovascular disease, rheumatoid arthritis, and other diseases. Here we used the haplotype chromatin immunoprecipitation method to study allele-specific MMP-3 expression under in vivo conditions in heterozygous THP-1 cells. Pyrosequencing was used to analyse the ratio of 5A-allele to 6A-allele after chromatin immunoprecipitation using an antibody against phosphorylated active RNA polymerase II. There was no allele-specific difference in transcriptional activity during basal conditions, i.e., in unstimulated monocytic THP-1 cells. However, after stimulation of MMP-3 expression by monocyte differentiation or incubation with IL-1{beta}, the haplotype containing the 5A-allele was associated with higher transcriptional activity compared with the 6A-containing haplotype. Electromobility shift assay demonstrated increased binding of nuclear proteins to the 5A-allele after monocyte differentiation. In conclusion, the common MMP-3 5A/6A promoter polymorphism appears to be functional only during specific environmental conditions involving inflammation.

  16. Allelic association of human dopamine D sub 2 receptor gene in alcoholism

    SciTech Connect

    Blum, K.; Sheridan, P.J.; Montgomery, A.; Jagadeeswaran, P.; Nogami, H.; Briggs, A.H. ); Noble, E.P.; Ritchie, T.; Cohn, J.B. )

    1990-04-18

    In a blinded experiment, the authors report the first allelic association of the dopamine D{sub 2} receptor gene in alcoholism. From 70 brain samples of alcoholics and nonalcoholics, DNA was digested with restriction endonucleases and probed with a clone that contained the entire 3{prime} coding exon, the polyadenylation signal, and approximately 16.4 kilobases of noncoding 3{prime} sequence of the human dopamine D{sub 2} receptor gene ({lambda}hD2G1). In the present samples, the presence of A1 allele of the dopamine D{sub 2} receptor gene correctly classified 77% of alcoholics, and its absence classified 72% of nonalcoholics. The polymorphic pattern of this receptor gene suggests that a gene that confers susceptibility to at least one form of alcoholism is located on the q22-q23 region of chromosome 11.

  17. Peer-to-Peer Consultations: Ancillary Services Peer Exchange with India: Experience from South Africa, Europe & the United States (Fact Sheet)

    SciTech Connect

    Not Available

    2014-05-01

    In support of national and subnational decision makers, the 21st Century Power Partnership regularly works with country partners to organize peer-to-peer consultations on critical issues. In March 2014, 21CPP collaborated with the Regulatory Assistance Project - India to host two peer-to-peer exchanges among experts from India, South Africa, Europe, and the United States to discuss the provision of ancillary services, particularly in the context of added variability and uncertainty from renewable energy. This factsheet provides a high level summary of the peer-to-peer consultation.

  18. Modeling and experiment reveal an unexpected stereoelectronic effect on conformation and scalar couplings of alpha-aminoorganostannanes, with possible relevance to the tin-lithium exchange reaction.

    PubMed

    Santiago, Marcelina; Low, Eddy; Chambournier, Gilles; Gawley, Robert E

    2003-10-31

    The solution conformation of N-methyl-2-(tributylstannyl)piperidines has been determined through the use of vicinal 119Sn-13C coupling constants, revealing a conformational distortion caused by an unexpected stereoelectronic effect in some cases. Specifically, the "equatorial" conformer is distorted into a half-chair, in which the nitrogen lone pair eclipses the C-Sn bond. This distortion, which "costs" approximately 1 kcal/mol, correlates with a conformational dependence of geminal 119Sn-15N couplings and a possible correlation with reactivity in the tin-lithium exchange reaction. PMID:14575474

  19. A limit to the divergent allele advantage model supported by variable pathogen recognition across HLA-DRB1 allele lineages.

    PubMed

    Lau, Q; Yasukochi, Y; Satta, Y

    2015-11-01

    Genetic diversity in human leukocyte antigen (HLA) molecules is thought to have arisen from the co-evolution between host and pathogen and maintained by balancing selection. Heterozygote advantage is a common proposed scenario for maintaining high levels of diversity in HLA genes, and extending from this, the divergent allele advantage (DAA) model suggests that individuals with more divergent HLA alleles bind and recognize a wider array of antigens. While the DAA model seems biologically suitable for driving HLA diversity, there is likely an upper threshold to the amount of sequence divergence. We used peptide-binding and pathogen-recognition capacity of DRB1 alleles as a model to further explore the DAA model; within the DRB1 locus, we examined binding predictions based on two distinct phylogenetic groups (denoted group A and B) previously identified based on non-peptide-binding region (PBR) nucleotide sequences. Predictions in this study support that group A allele and group B allele lineages have contrasting binding/recognition capacity, with only the latter supporting the DAA model. Furthermore, computer simulations revealed an inconsistency in the DAA model alone with observed extent of polymorphisms, supporting that the DAA model could only work effectively in combination with other mechanisms. Overall, we support that the mechanisms driving HLA diversity are non-exclusive. By investigating the relationships among HLA alleles, and pathogens recognized, we can provide further insights into the mechanisms on how humans have adapted to infectious diseases over time. PMID:26392055

  20. Impriniting of human H19: Allele-specific CpG methylation, loss of the active allele in Wilms tumor, and potential for somatic allele switching

    SciTech Connect

    Zhang, Y.; Shields, T.; Crenshaw, T.; Hao, Y.; Moulton, T.; Tycko, B. )

    1993-07-01

    Genomic imprinting and monoallelic gene expression appear to play a role in human genetic disease and tumorigenesis. The human H19 gene, at chromosome 11p15, has previously been shown to be monoallelically expressed. Since CpG methylation has been implicated in imprinting, the authors analyzed methylation of H19 DNA. In fetal and adult organs the transcriptionally silent H19 allele was extensively hypermethylated through the entire gene and its promoter, and, consistent with a functional role for DNA methylation, expression of an H19 promoter-reporter construct was inhibited by in vitro methylation. Gynogenetic ovarian teratomas were found to contain only hypomethylated H19 DNA, suggesting that the expressed H19 allele might be maternal. This was confirmed by analysis of 11p15 polymorphisms in a patient with Wilms tumor. The tumor had lost the maternal 11p15, and H19 expression in the normal kidney was exclusively from this allele. Imprinting of human H19 appears to be susceptible to tissue-specific modulation in somatic development; in one individual, cerebellar cells were found to express only the otherwise silent allele. Implications of these findings for the role of DNA methylation in imprinting and for H19 as a candidate imprinted tumor-suppressor gene are discussed. 57 refs., 7 figs.

  1. The Lethal(1)tw-6(cs) Mutation of Drosophila Melanogaster Is a Dominant Antimorphic Allele of Nod and Is Associated with a Single Base Change in the Putative Atp-Binding Domain

    PubMed Central

    Rasooly, R. S.; New, C. M.; Zhang, P.; Hawley, R. S.; Baker, B. S.

    1991-01-01

    The l(1)TW-6(cs) mutation is a cold-sensitive recessive lethal mutation in Drosophila melanogaster, that affects both meiotic and mitotic chromosome segregation. We report the isolation of three revertants of this mutation. All three revert both the meiotic and mitotic effects as well as the cold sensitivity, demonstrating that all three phenotypes are due to a single lesion. We further show that these revertants fail to complement an amorphic allele of the nod (no distributive disjunction) locus, which encodes a kinesin-like protein. These experiments demonstrate that l(1)TW-6(cs) is an antimorphic allele of nod, and we rename it nod(DTW). Sequencing of the nod locus on a nod(DTW)-bearing chromosome reveals a single base change in the putative ATP-binding region of the motor domain of nod. Recessive, loss-of-function mutations at the nod locus specifically disrupt the segregation of nonexchange chromosomes in female meiosis. We demonstrate that, at 23.5°, the meiotic defects in nod(DTW)/+ females are similar to those observed in nod/nod females; that is, the segregation of nonexchange chromosomes is abnormal. However, in nod(DTW)/nod(DTW) females, or in nod(DTW)/+ females at 18°, we observe a more severe meiotic defect that apparently affects the segregation of both exchange and nonexchange chromosomes. In addition, nod(DTW) homozygotes and hemizygous males have previously been shown to exhibit mitotic defects including somatic chromosome breakage and loss. We propose that the defective protein encoded by the nod(DTW) allele interferes with proper chromosome movement during both meiosis and mitosis, perhaps by binding irreversibly to microtubules. PMID:1743485

  2. How the Number of Alleles Influences Gene Expression

    NASA Astrophysics Data System (ADS)

    Hat, Beata; Paszek, Pawel; Kimmel, Marek; Piechor, Kazimierz; Lipniacki, Tomasz

    2007-07-01

    The higher organisms, eukaryotes, are diploid and most of their genes have two homological copies (alleles). However, the number of alleles in a cell is not constant. In the S phase of the cell cycle all the genome is duplicated and then in the G2 phase and mitosis, which together last for several hours, most of the genes have four copies instead of two. Cancer development is, in many cases, associated with a change in allele number. Several genetic diseases are caused by haploinsufficiency: Lack of one of the alleles or its improper functioning. In the paper we consider the stochastic expression of a gene having a variable number of copies. We applied our previously developed method in which the reaction channels are split into slow (connected with change of gene state) and fast (connected with mRNA/protein synthesis/decay), the later being approximated by deterministic reaction rate equations. As a result we represent gene expression as a piecewise deterministic time-continuous Markov process, which is further related with a system of partial differential hyperbolic equations for probability density functions (pdfs) of protein distribution. The stationary pdfs are calculated analytically for haploidal gene or numerically for diploidal and tetraploidal ones. We distinguished nine classes of simultaneous activation of haploid, diploid and tetraploid genes. This allows for analysis of potential consequences of gene duplication or allele loss. We show that when gene activity is autoregulated by a positive feedback, the change in number of gene alleles may have dramatic consequences for its regulation and may not be compensated by the change of efficiency of mRNA synthesis per allele.

  3. Raman signatures of strong Kitaev exchange correlations in (Na1‑xLix)2IrO3: Experiments and theory

    NASA Astrophysics Data System (ADS)

    Nath Gupta, Satyendra; Sriluckshmy, P. V.; Mehlawat, Kavita; Balodhi, Ashiwini; Mishra, Dileep K.; Hassan, S. R.; Ramakrishnan, T. V.; Muthu, D. V. S.; Singh, Yogesh; Sood, A. K.

    2016-05-01

    Inelastic light scattering studies on single crystals of (Na1‑x Li x )2IrO3 (x = 0, 0.05 and 0.15) show a polarization-independent broad band at ∼ 2750 cm‑1 with a large band-width ∼ 1800 \\text{cm}-1 . For Na2IrO3 the broad band is seen for temperatures ≤ 200 \\text{K} and persists inside the magnetically ordered state. For Li samples, the intensity of this mode increases, shifts to lower wave numbers, and persists to higher temperatures. Such a mode has recently been predicted (by Knolle et al.) as a signature of the Kitaev spin liquid. We assign the observation of the broad band to be a signature of strong Kitaev exchange correlations. The fact that the broad band persists even inside the magnetically ordered state suggests that dynamically fluctuating moments survive even below T N . This is further supported by our mean-field calculations. The Raman response calculated in mean-field theory shows that the broad band predicted for the SL state survives in the magnetically ordered state near the zigzag-spin liquid phase boundary. A comparison with the theoretical model gives an estimate of the Kitaev exchange interaction parameter to be J_K≈ 57 \\text{meV} .

  4. Experience Industry

    ERIC Educational Resources Information Center

    Laslett, R. L.

    1978-01-01

    The author, a tertiary chemistry teacher, spent a period of six weeks in a research project with an industrial firm. Describes his experience, the benefits and insight he gained from such an exchange. (GA)

  5. Lab mice in the field: unorthodox daily activity and effects of a dysfunctional circadian clock allele.

    PubMed

    Daan, Serge; Spoelstra, Kamiel; Albrecht, Urs; Schmutz, Isabelle; Daan, Moritz; Daan, Berte; Rienks, Froukje; Poletaeva, Inga; Dell'Omo, Giacomo; Vyssotski, Alexei; Lipp, Hans-Peter

    2011-04-01

    experiments on fitness consequences in the natural environment. It also demonstrates that the activity of mice, while strictly nocturnal in the laboratory, may be partially or completely diurnal in the field. The new method allows assessment of natural selection on specific alleles on a day-today basis. PMID:21454292

  6. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

    PubMed Central

    2012-01-01

    Background High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases. Results We designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third, preliminary experiment we attempted to sequence novel amplicons for other class II loci with mixed success. Conclusions The presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons. PMID:22866951

  7. Segmented heat exchanger

    DOEpatents

    Baldwin, Darryl Dean; Willi, Martin Leo; Fiveland, Scott Byron; Timmons, Kristine Ann

    2010-12-14

    A segmented heat exchanger system for transferring heat energy from an exhaust fluid to a working fluid. The heat exchanger system may include a first heat exchanger for receiving incoming working fluid and the exhaust fluid. The working fluid and exhaust fluid may travel through at least a portion of the first heat exchanger in a parallel flow configuration. In addition, the heat exchanger system may include a second heat exchanger for receiving working fluid from the first heat exchanger and exhaust fluid from a third heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the second heat exchanger in a counter flow configuration. Furthermore, the heat exchanger system may include a third heat exchanger for receiving working fluid from the second heat exchanger and exhaust fluid from the first heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the third heat exchanger in a parallel flow configuration.

  8. Systematic Detection of Epistatic Interactions Based on Allele Pair Frequencies

    PubMed Central

    Ackermann, Marit; Beyer, Andreas

    2012-01-01

    Epistatic genetic interactions are key for understanding the genetic contribution to complex traits. Epistasis is always defined with respect to some trait such as growth rate or fitness. Whereas most existing epistasis screens explicitly test for a trait, it is also possible to implicitly test for fitness traits by searching for the over- or under-representation of allele pairs in a given population. Such analysis of imbalanced allele pair frequencies of distant loci has not been exploited yet on a genome-wide scale, mostly due to statistical difficulties such as the multiple testing problem. We propose a new approach called Imbalanced Allele Pair frequencies (ImAP) for inferring epistatic interactions that is exclusively based on DNA sequence information. Our approach is based on genome-wide SNP data sampled from a population with known family structure. We make use of genotype information of parent-child trios and inspect 3×3 contingency tables for detecting pairs of alleles from different genomic positions that are over- or under-represented in the population. We also developed a simulation setup which mimics the pedigree structure by simultaneously assuming independence of the markers. When applied to mouse SNP data, our method detected 168 imbalanced allele pairs, which is substantially more than in simulations assuming no interactions. We could validate a significant number of the interactions with external data, and we found that interacting loci are enriched for genes involved in developmental processes. PMID:22346757

  9. Rare allelic forms of PRDM9 associated with childhood leukemogenesis

    PubMed Central

    Hussin, Julie; Sinnett, Daniel; Casals, Ferran; Idaghdour, Youssef; Bruat, Vanessa; Saillour, Virginie; Healy, Jasmine; Grenier, Jean-Christophe; de Malliard, Thibault; Busche, Stephan; Spinella, Jean-François; Larivière, Mathieu; Gibson, Greg; Andersson, Anna; Holmfeldt, Linda; Ma, Jing; Wei, Lei; Zhang, Jinghui; Andelfinger, Gregor; Downing, James R.; Mullighan, Charles G.; Awadalla, Philip

    2013-01-01

    One of the most rapidly evolving genes in humans, PRDM9, is a key determinant of the distribution of meiotic recombination events. Mutations in this meiotic-specific gene have previously been associated with male infertility in humans and recent studies suggest that PRDM9 may be involved in pathological genomic rearrangements. In studying genomes from families with children affected by B-cell precursor acute lymphoblastic leukemia (B-ALL), we characterized meiotic recombination patterns within a family with two siblings having hyperdiploid childhood B-ALL and observed unusual localization of maternal recombination events. The mother of the family carries a rare PRDM9 allele, potentially explaining the unusual patterns found. From exomes sequenced in 44 additional parents of children affected with B-ALL, we discovered a substantial and significant excess of rare allelic forms of PRDM9. The rare PRDM9 alleles are transmitted to the affected children in half the cases; nonetheless there remains a significant excess of rare alleles among patients relative to controls. We successfully replicated this latter observation in an independent cohort of 50 children with B-ALL, where we found an excess of rare PRDM9 alleles in aneuploid and infant B-ALL patients. PRDM9 variability in humans is thought to influence genomic instability, and these data support a potential role for PRDM9 variation in risk of acquiring aneuploidies or genomic rearrangements associated with childhood leukemogenesis. PMID:23222848

  10. Estimating allelic diversity generated by excision of different transposon types.

    PubMed

    Nordborg, M; Walbot, V

    1995-05-01

    Methods are presented for calculating the number and type of different DNA sequences generated by base excision and insertion events at a given site in a known DNA sequence. We calculate, for example, that excision of the Mu1 transposon from the bz1::Mu1 allele of maize should generate more than 500,000 unique alleles given the extent of base deletion (up to 34 bases removed) and base insertion (0-5 bases) observed thus far in sequenced excision alleles. Analysis of this universe of potential alleles can, for example, be used to predict the frequency of creation of stop codons or repair-generated duplications. In general, knowledge of the distribution of alleles can be used to evaluate models of both excision and repair by determining whether particular events occur more frequently than expected. Such quantitative analysis complements the qualitative description provided by the DNA sequence of individual events. Similar methods can be used to evaluate the outcome of other cases of DNA breakage and repair such as programmed V(D)J recombination in immunoglobin genes. PMID:24172918

  11. STR allele sequence variation: Current knowledge and future issues.

    PubMed

    Gettings, Katherine Butler; Aponte, Rachel A; Vallone, Peter M; Butler, John M

    2015-09-01

    This article reviews what is currently known about short tandem repeat (STR) allelic sequence variation in and around the twenty-four loci most commonly used throughout the world to perform forensic DNA investigations. These STR loci include D1S1656, TPOX, D2S441, D2S1338, D3S1358, FGA, CSF1PO, D5S818, SE33, D6S1043, D7S820, D8S1179, D10S1248, TH01, vWA, D12S391, D13S317, Penta E, D16S539, D18S51, D19S433, D21S11, Penta D, and D22S1045. All known reported variant alleles are compiled along with genomic information available from GenBank, dbSNP, and the 1000 Genomes Project. Supplementary files are included which provide annotated reference sequences for each STR locus, characterize genomic variation around the STR repeat region, and compare alleles present in currently available STR kit allelic ladders. Looking to the future, STR allele nomenclature options are discussed as they relate to next generation sequencing efforts underway. PMID:26197946

  12. Association of smoking behavior with an odorant receptor allele telomeric to the human major histocompatibility complex.

    PubMed

    Santos, Pablo Sandro Carvalho; Füst, George; Prohászka, Zoltán; Volz, Armin; Horton, Roger; Miretti, Marcos; Yu, Chack-Yung; Beck, Stephan; Uchanska-Ziegler, Barbara; Ziegler, Andreas

    2008-12-01

    Smoking behavior has been associated in two independent European cohorts with the most common Caucasian human leukocyte antigen (HLA) haplotype (A1-B8-DR3). We aimed to test whether polymorphic members of the two odorant receptor (OR) clusters within the extended HLA complex might be responsible for the observed association, by genotyping a cohort of Hungarian women in which the mentioned association had been found. One hundred and eighty HLA haplotypes from Centre d'Etude du Polymorphisme Humain families were analyzed in silico to identify single-nucleotide polymorphisms (SNPs) within OR genes that are in linkage disequilibrium with the A1-B8-DR3 haplotype, as well as with two other haplotypes indirectly linked to smoking behavior. A nonsynonymous SNP within the OR12D3 gene (rs3749971(T)) was found to be linked to the A1-B8-DR3 haplotype. This polymorphism leads to a (97)Thr --> Ile exchange that affects a putative ligand binding region of the OR12D3 protein. Smoking was found to be associated in the Hungarian cohort with the rs3749971(T) allele (p = 1.05 x 10(-2)), with higher significance than with A1-B8-DR3 (p = 2.38 x 10(-2)). Our results link smoking to a distinct OR allele, and demonstrate that the rs3749971(T) polymorphism is associated with the HLA haplotype-dependent differential recognition of cigarette smoke components, at least among Caucasian women. PMID:18939942

  13. Seed fates in crop–wild hybrid sunflower: crop allele and maternal effects

    PubMed Central

    Pace, Brian A; Alexander, Helen M; Emry, Jason D; Mercer, Kristin L

    2015-01-01

    Domestication has resulted in selection upon seed traits found in wild populations, yet crop-wild hybrids retain some aspects of both parental phenotypes. Seed fates of germination, dormancy, and mortality can influence the success of crop allele introgression in crop-wild hybrid zones, especially if crop alleles or crop-imparted seed coverings result in out-of-season germination. We performed a seed burial experiment using crop, wild, and diverse hybrid sunflower (Helianthus annuus) cross types to test how a cross type's maternal parent and nuclear genetic composition might affect its fate under field conditions. We observed higher maladaptive fall germination in the crop- and F1- produced seeds than wild-produced seeds and, due to an interaction with percent crop alleles, fall germination was higher for cross types with more crop-like nuclear genetics. By spring, crop-produced cross types had the highest overwintering mortality, primarily due to higher fall germination. Early spring germination was identical across maternal types, but germination continued for F1-produced seeds. In conclusion, the more wild-like the maternal parent or the less proportion of the cross type's genome contributed by the crop, the greater likelihood a seed will remain ungerminated than die. Wild-like dormancy may facilitate introgression through future recruitment from the soil seed bank. PMID:25685189

  14. Seed fates in crop-wild hybrid sunflower: crop allele and maternal effects.

    PubMed

    Pace, Brian A; Alexander, Helen M; Emry, Jason D; Mercer, Kristin L

    2015-02-01

    Domestication has resulted in selection upon seed traits found in wild populations, yet crop-wild hybrids retain some aspects of both parental phenotypes. Seed fates of germination, dormancy, and mortality can influence the success of crop allele introgression in crop-wild hybrid zones, especially if crop alleles or crop-imparted seed coverings result in out-of-season germination. We performed a seed burial experiment using crop, wild, and diverse hybrid sunflower (Helianthus annuus) cross types to test how a cross type's maternal parent and nuclear genetic composition might affect its fate under field conditions. We observed higher maladaptive fall germination in the crop- and F1- produced seeds than wild-produced seeds and, due to an interaction with percent crop alleles, fall germination was higher for cross types with more crop-like nuclear genetics. By spring, crop-produced cross types had the highest overwintering mortality, primarily due to higher fall germination. Early spring germination was identical across maternal types, but germination continued for F1-produced seeds. In conclusion, the more wild-like the maternal parent or the less proportion of the cross type's genome contributed by the crop, the greater likelihood a seed will remain ungerminated than die. Wild-like dormancy may facilitate introgression through future recruitment from the soil seed bank. PMID:25685189

  15. Changes in allelic imbalances in locally advanced breast cancers after chemotherapy

    PubMed Central

    Varna, M; Soliman, H; Feugeas, J-P; Turpin, E; Chapelin, D; Legrès, L; Plassa, L-F; de Roquancourt, A; Espié, M; Misset, J-L; Janin, A; de Thé, H; Bertheau, P

    2007-01-01

    In advanced breast cancers, TP53 mutation is highly predictive of complete response to high-dose epirubicin/cyclophosphamide chemotherapy. In these tumours with an altered control of genomic stability, accumulation of chemotherapy-induced genetic alterations may contribute to cell death and account for complete response. To explore the effects of chemotherapy on stability of the tumour genome, allelic profiles were obtained from microdissected tumour samples before and after chemotherapy in 29 unresponsive breast cancers (9 with TP53 mutation). Ninety-four per cent allelic profiles remained unchanged after treatment. Interestingly, 11 profiles (6%) showed important changes after treatment; allelic imbalances significantly increased (four cases) or decreased (seven cases) after chemotherapy in three distinct experiments, two of which using laser microdissected tumour cells. These genetic changes were not linked to the TP53 status, but one tumour showed complete disappearance of TP53-mutated cells in the residual tumour after treatment. Altogether, these observations carry important implications for the clonal evolution of breast cancers treated with DNA-damaging agents, as they point both to the importance of tumour heterogeneity and chemotherapy-driven selection of subclones. PMID:17876337

  16. Feasibility of referring drug users from a needle exchange program into an addiction treatment program: experience with a mobile treatment van and LAAM maintenance.

    PubMed

    Kuo, Irene; Brady, Joseph; Butler, Carol; Schwartz, Robert; Brooner, Robert; Vlahov, David; Strathdee, Steffanie A

    2003-01-01

    We evaluated program entry, retention, and early treatment response of needle exchange program (NEP) attenders referred to a drug treatment program using levomethadyl acetate hydrochloride (LAAM). Of 163 referrals, 114 (70%) entered the program, and 84% were retained for at least 90 days. Comparing baseline and follow-up visits after 1 month, there were significant reductions in the Addiction Severity Index subscale scores for drug and alcohol use and legal situation. We observed a 31% and 22% reduction in heroin- and cocaine-positive urine tests, respectively (p < .0001). Although LAAM is no longer considered a first line treatment for heroin addiction, these results demonstrate the feasibility of utilizing long-acting agonist therapies such as LAAM to treat opioid dependence among NEP attenders. PMID:12646332

  17. Elevated frequency of sister chromatid exchanges in lymphocytes of victims of the Tokyo sarin disaster and in experiments exposing lymphocytes to by-products of sarin synthesis.

    PubMed

    Li, Q; Minami, M; Clement, J G; Boulet, C A

    1998-09-01

    More than 5000 passengers of Tokyo subway trains were injured with toxic chemicals including the nerve gas sarin. Most of the victims examined had marked miosis and decreased serum cholinesterase activity. To monitor the genetic aftereffects of sarin exposure, we measured sister chromatid exchanges (SCEs) of the victims using peripheral blood lymphocytes. The frequency of SCEs was significantly higher in the victims than in the control group. Analyzing results using samples of urine from the victims suggested that the victims were exposed to not only sarin per se, but by-products of sarin synthesis, i.e. diisopropyl methylphosphonate (DIMP), diethyl methylphosphonate (DEMP) and ethyl isopropyl methylphosphonate (EIMP). Thus, the in vitro SCE-inducing effect of DIMP, DEMP and EIMP was examined using human lymphocytes and we obtained positive results. PMID:9776566

  18. Fault-Tolerant Heat Exchanger

    NASA Technical Reports Server (NTRS)

    Izenson, Michael G.; Crowley, Christopher J.

    2005-01-01

    A compact, lightweight heat exchanger has been designed to be fault-tolerant in the sense that a single-point leak would not cause mixing of heat-transfer fluids. This particular heat exchanger is intended to be part of the temperature-regulation system for habitable modules of the International Space Station and to function with water and ammonia as the heat-transfer fluids. The basic fault-tolerant design is adaptable to other heat-transfer fluids and heat exchangers for applications in which mixing of heat-transfer fluids would pose toxic, explosive, or other hazards: Examples could include fuel/air heat exchangers for thermal management on aircraft, process heat exchangers in the cryogenic industry, and heat exchangers used in chemical processing. The reason this heat exchanger can tolerate a single-point leak is that the heat-transfer fluids are everywhere separated by a vented volume and at least two seals. The combination of fault tolerance, compactness, and light weight is implemented in a unique heat-exchanger core configuration: Each fluid passage is entirely surrounded by a vented region bridged by solid structures through which heat is conducted between the fluids. Precise, proprietary fabrication techniques make it possible to manufacture the vented regions and heat-conducting structures with very small dimensions to obtain a very large coefficient of heat transfer between the two fluids. A large heat-transfer coefficient favors compact design by making it possible to use a relatively small core for a given heat-transfer rate. Calculations and experiments have shown that in most respects, the fault-tolerant heat exchanger can be expected to equal or exceed the performance of the non-fault-tolerant heat exchanger that it is intended to supplant (see table). The only significant disadvantages are a slight weight penalty and a small decrease in the mass-specific heat transfer.

  19. Puroindoline allelic diversity in Indian wheat germplasm and identification of new allelic variants

    PubMed Central

    Kumar, Rohit; Arora, Shaweta; Singh, Kashmir; Garg, Monika

    2015-01-01

    Grain hardness is an important quality trait that influences product development in wheat. This trait is governed by variation in puroindoline proteins (PINA and PINB). Our study evaluated 551 Indian wheat germplasm lines for diversity in Pina and Pinb genes. Eighty-two lines were shortlisted for full length sequencing and grain hardness studies. Sequencing studies identified six unknown alleles: two for the Pina gene and four for the Pinb gene. Five of them were novel with non-synonymous changes in the corresponding amino acid sequences. Identified mutations in the deduced mature proteins and their pre- and pro-peptides influenced the hardness characteristics of the grain. We classified these 82 varieties into different hardness categories with reference to international and Indian systems of classification. The majority of Indian wheat varieties were categorized as hard. This study revealed that unexplored Indian wheat germplasm can be a good source of genetic variability for both Pina and Pinb genes, helping in marker-assisted breeding and in obtaining wheat with different textural properties. PMID:26366114

  20. Molecular genetic mechanisms of allelic specific regulation of murine Comt expression.

    PubMed

    Segall, Samantha K; Shabalina, Svetlana A; Meloto, Carolina B; Wen, Xia; Cunningham, Danielle; Tarantino, Lisa M; Wiltshire, Tim; Gauthier, Josée; Tohyama, Sarasa; Martin, Loren J; Mogil, Jeffrey S; Diatchenko, Luda

    2015-10-01

    A functional allele of the mouse catechol-O-methyltransferase (Comt) gene is defined by the insertion of a B2 short interspersed repeat element in its 3'-untranslated region (UTR). This allele has been associated with a number of phenotypes, such as pain and anxiety. In comparison with mice carrying the ancestral allele (Comt+), Comt B2i mice show higher Comt mRNA and enzymatic activity levels. Here, we investigated the molecular genetic mechanisms underlying this allelic specific regulation of Comt expression. Insertion of the B2 element introduces an early polyadenylation signal generating a shorter Comt transcript, in addition to the longer ancestral mRNA. Comparative analysis and in silico prediction of Comt mRNA potential targets within the transcript 3' to the B2 element was performed and allowed choosing microRNA (miRNA) candidates for experimental screening: mmu-miR-3470a, mmu-miR-3470b, and mmu-miR-667. Cell transfection with each miRNA downregulated the expression of the ancestral transcript and COMT enzymatic activity. Our in vivo experiments showed that mmu-miR-667-3p is strongly correlated with decreasing amounts of Comt mRNA in the brain, and lentiviral injections of mmu-miR-3470a, mmu-miR-3470b, and mmu-miR-667 increase hypersensitivity in the mouse formalin model, consistent with reduced COMT activity. In summary, our data demonstrate that the Comt+ transcript contains regulatory miRNA signals in its 3'-untranslated region leading to mRNA degradation; these signals, however, are absent in the shorter transcript, resulting in higher mRNA expression and activity levels. PMID:26067582

  1. Generation of Mice with a Conditional Allele for Ift172

    PubMed Central

    Howard, Paul W.; Howard, Tiffani L.; Maurer, Richard A.

    2009-01-01

    Ift172 encodes a gene product that is part of a complex that mediates intraflagellar transport (IFT), a process necessary for the genesis and maintenance of cilia. Genetic studies in mice have offered evidence that Ift172 also plays a role in hedgehog signaling. Disruption of Ift172 in mice is associated with lethality at about embryonic day 11, limiting studies to understand the role for Ift172 in later development and the adult. To further our understanding of the later roles of Ift172, we have generated mice with a conditional allele for Ift172. We have confirmed the phenotype of the disrupted allele by using CRE expression directed by the prx1 enhancer to disrupt the conditional Ift172 allele in the developing limb. PMID:19521792

  2. Apolipoprotein E alleles in women with severe pre-eclampsia.

    PubMed Central

    Nagy, B; Rigó, J; Fintor, L; Karádi, I; Tóth, T

    1998-01-01

    This study investigated the frequency of apolipoprotein E (apoE) alleles among women with severe pre-eclampsia. The presence of the three most common apoE alleles (epsilon 2, epsilon 3, epsilon 4) was determined by polymerase chain reaction-restriction fragment length polymorphism in three groups of white women: non-pregnant healthy (n = 101), pregnant healthy (n = 52), and pregnant with a diagnosis of severe pre-eclampsia (n = 54). The frequency of apo epsilon 2 was highest among women with severe pre-eclampsia (16.6%) followed by non-pregnant women (12.9%), and those experiencing a healthy pregnancy (10.6%). The higher frequency of the apo epsilon 2 allele detected among women with severe pre-eclampsia suggests that apoE may play a role in the development of pre-eclampsia. PMID:9659248

  3. Extensive HLA class I allele promiscuity among viral CTL epitopes

    PubMed Central

    Frahm, Nicole; Yusim, Karina; Suscovich, Todd J.; Adams, Sharon; Sidney, John; Hraber, Peter; Hewitt, Hannah S.; Linde, Caitlyn H.; Kavanagh, Daniel G.; Woodberry, Tonia; Henry, Leah M.; Faircloth, Kellie; Listgarten, Jennifer; Kadie, Carl; Jojic, Nebojsa; Sango, Kaori; Brown, Nancy V.; Pae, Eunice; Zaman, M. Tauheed; Bihl, Florian; Khatri, Ashok; John, Mina; Mallal, Simon; Marincola, Francesco M.; Walker, Bruce D.; Sette, Alessandro; Heckerman, David; Korber, Bette T.; Brander, Christian

    2008-01-01

    Summary Promiscuous binding of T helper epitopes to MHC class II molecules has been well established, but few examples of promiscuous class I restricted epitopes exist. To address the extent of promiscuity of HLA class I peptides, responses to 242 well-defined viral epitopes were tested in 100 subjects regardless of the individuals’ HLA type. Surprisingly, half of all detected responses were seen in the absence of the originally reported restricting HLA class I allele, and only 3% of epitopes were recognized exclusively in the presence of their original allele. Functional assays confirmed the frequent recognition of HLA class I-restricted T cell epitopes on several alternative alleles across HLA class I supertypes and encoded on different class I loci. These data have significant implications for the understanding of MHC class I restricted antigen presentation and vaccine development. PMID:17705138

  4. Distribution of a pseudodeficiency allele among Tay-Sachs carriers

    SciTech Connect

    Tomczak, J.; Grebner, E.E. ); Boogen, C. )

    1993-08-01

    Recently Triggs-Raine et al. (1992) identified a new mutation in the gene coding for the [alpha]-subunit of [beta]-hexosaminidase A (hex A), the enzyme whose deficiency causes Tay-Sachs disease. This mutation, a C[sub 739]-to-T transition in exon 7, results in an altered enzyme that is active (albeit at reduced levels) in cells but that has essentially no activity in serum. This so-called pseudodeficient allele was first detected in compound heterozygotes who also carried a Tay-Sachs disease allele and therefore had no detectable hex A in their serum but who were in good health. Carriers of this apparently benign mutation are generally indistinguishable from carriers of a lethal mutation by means of routine enzyme-based screening tests, because the product of the pseudodeficient allele is not detectable in serum and has decreased activity in cells. This suggests that some individuals who have been classified as Tay-Sachs carriers are actually carriers of the pseudodeficient allele and are not at risk to have a child affected with Tay-Sachs disease. The pseudodeficient allele may also be responsible for some inconclusive diagnoses, where leukocyte values fall below the normal range but are still above the carrier range. The fact that there are now two mutant alleles (the psuedodeficient and the adult) that are indistinguishable from the lethal infantile mutations by means of enzyme assay yet that are phenotypically very different and that together may account for as much as 12% of enzyme-defined carriers on the basis of the data here suggests that DNA analysis should be part of a comprehensive screening program. It will be particularly useful to identify the mutations in couples at risk, before they undergo prenatal diagnosis. DNA analysis will also resolve some inconclusive diagnoses.

  5. Allele-specific DNA methylation reinforces PEAR1 enhancer activity.

    PubMed

    Izzi, Benedetta; Pistoni, Mariaelena; Cludts, Katrien; Akkor, Pinar; Lambrechts, Diether; Verfaillie, Catherine; Verhamme, Peter; Freson, Kathleen; Hoylaerts, Marc F

    2016-08-18

    Genetic variation in the PEAR1 locus is linked to platelet reactivity and cardiovascular disease. The major G allele of rs12041331, an intronic cytosine guanine dinucleotide-single-nucleotide polymorphism (CpG-SNP), is associated with higher PEAR1 expression in platelets and endothelial cells than the minor A allele. The molecular mechanism underlying this difference remains elusive. We have characterized the histone modification profiles of the intronic region surrounding rs12041331 and identified H3K4Me1 enhancer-specific enrichment for the region that covers the CpG-SNP. Interestingly, methylation studies revealed that the CpG site is fully methylated in leukocytes of GG carriers. Nuclear protein extracts from megakaryocytes, endothelial cells, vs control HEK-293 cells show a 3-fold higher affinity for the methylated G allele compared with nonmethylated G or A alleles in a gel electrophoretic mobility shift assay. To understand the positive relationship between methylation and gene expression, we studied DNA methylation at 4 different loci of PEAR1 during in vitro megakaryopoiesis. During differentiation, the CpG-SNP remained fully methylated, while we observed rapid methylation increases at the CpG-island overlapping the first 5'-untranslated region exon, paralleling the increased PEAR1 expression. In the same region, A-allele carriers of rs12041331 showed significantly lower DNA methylation at CGI1 compared with GG homozygote. This CpG-island contains binding sites for the methylation-sensitive transcription factor CTCF, whose binding is known to play a role in enhancer activation and/or repression. In conclusion, we report the molecular characterization of the first platelet function-related CpG-SNP, a genetic predisposition that reinforces PEAR1 enhancer activity through allele-specific DNA methylation. PMID:27313330

  6. Educator Exchange Resource Guide.

    ERIC Educational Resources Information Center

    Garza, Cris; Rodriguez, Victor

    This resource guide was developed for teachers and administrators interested in participating in intercultural and international exchange programs or starting an exchange program. An analysis of an exchange program's critical elements discusses exchange activities; orientation sessions; duration of exchange; criteria for participation; travel,…

  7. A common allele on chromosome 9 associated with coronary heartdisease

    SciTech Connect

    McPherson, Ruth; Pertsemlidis, Alexander; Kavaslar, Nihan; Stewart, Alexandre; Roberts, Robert; Cox, David R.; Hinds, David; Pennachio, Len; Tybjaerg-Hansen, Anne; Folsom, Aaron R.; Boerwinkle,Eric; Hobbs, Helen H.; Cohen, Jonathan C.

    2007-03-01

    Coronary heart disease (CHD) is a major cause of death in Western countries. Here we used genome-wide association scanning to identify a 58 kb interval on chromosome 9 that was consistently associated with CHD in six independent samples. The interval contains no annotated genes and is not associated with established CHD risk factors such as plasma lipoproteins, hypertension or diabetes. Homozygotes for the risk allele comprise 20-25% of Caucasians and have a {approx}30-40% increased risk of CHD. These data indicate that the susceptibility allele acts through a novel mechanism to increase CHD risk in a large fraction of the population.

  8. Data-adaptive algorithms for calling alleles in repeat polymorphisms.

    PubMed

    Stoughton, R; Bumgarner, R; Frederick, W J; McIndoe, R A

    1997-01-01

    Data-adaptive algorithms are presented for separating overlapping signatures of heterozygotic allele pairs in electrophoresis data. Application is demonstrated for human microsatellite CA-repeat polymorphisms in LiCor 4000 and ABI 373 data. The algorithms allow overlapping alleles to be called correctly in almost every case where a trained observer could do so, and provide a fast automated objective alternative to human reading of the gels. The algorithm also supplies an indication of confidence level which can be used to flag marginal cases for verification by eye, or as input to later stages of statistical analysis. PMID:9059812

  9. Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders

    PubMed Central

    Fitzpatrick, Benjamin M; Johnson, Jarrett R; Kump, D Kevin; Shaffer, H Bradley; Smith, Jeramiah J; Voss, S Randal

    2009-01-01

    Background Hybrid zones represent valuable opportunities to observe evolution in systems that are unusually dynamic and where the potential for the origin of novelty and rapid adaptation co-occur with the potential for dysfunction. Recently initiated hybrid zones are particularly exciting evolutionary experiments because ongoing natural selection on novel genetic combinations can be studied in ecological time. Moreover, when hybrid zones involve native and introduced species, complex genetic patterns present important challenges for conservation policy. To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into the range of California Tiger Salamanders. Results At three of 64 markers, introduced alleles have largely displaced native alleles within the hybrid populations. Another marker (GNAT1) showed consistent heterozygote deficits in the wild, and this marker was associated with embryonic mortality in laboratory F2's. Other deviations from equilibrium expectations were idiosyncratic among breeding ponds, consistent with highly stochastic demographic effects. Conclusion While most markers retain native and introduced alleles in expected proportions, strong selection appears to be eliminating native alleles at a smaller set of loci. Such rapid fixation of alleles is detectable only in recently formed hybrid zones, though it might be representative of dynamics that frequently occur in nature. These results underscore the variable and mosaic nature of hybrid genomes and illustrate the potency of recombination and selection in promoting variable, and often unpredictable genetic outcomes. Introgression of a few, strongly selected introduced alleles should not necessarily affect the conservation status of California Tiger Salamanders, but suggests that genetically pure populations of this endangered species will be difficult to maintain. PMID:19630983

  10. Clonal Ordering of 17p and 5q Allelic Losses in Barrett Dysplasia and Adenocarcinoma

    NASA Astrophysics Data System (ADS)

    Blount, Patricia L.; Meltzer, Stephen J.; Yin, Jing; Huang, Ying; Krasna, Mark J.; Reid, Brian J.

    1993-04-01

    Both 17p and 5q allelic losses appear to be involved in the pathogenesis or progression of many human solid tumors. In colon carcinogenesis, there is strong evidence that the targets of the 17p and 5q allelic losses are TP53, the gene encoding p53, and APC, respectively. It is widely accepted that 5q allelic losses precede 17p allelic losses in the progression to colonic carcinoma. The data, however, supporting this proposed order are largely based on the prevalence of 17p and 5q allelic losses in adenomas and unrelated adenocarcinomas from different patients. We investigated the order in which 17p and 5q allelic losses developed during neoplastic progression in Barrett esophagus by evaluating multiple aneuploid cell populations from the same patient. Using DNA content flow cytometric cell sorting and polymerase chain reaction, 38 aneuploid cell populations from 14 patients with Barrett esophagus who had high grade dysplasia, cancer or both were evaluated for 17p and 5q allelic losses. 17p allelic losses preceded 5q allelic losses in 7 patients, both 17p and 5q allelic losses were present in all aneuploid populations of 4 patients, and only 17p (without 5q) allelic losses were present in the aneuploid populations of 3 patients. In no patient did we find that a 5q allelic loss preceded a 17p allelic loss. Our data suggest that 17p allelic losses typically occur before 5q allelic losses during neoplastic progression in Barrett esophagus.

  11. Synthesis and Small Molecule Exchange Studies of a Magnesium Bisformate Metal-Organic Framework: An Experiment in Host-Guest Chemistry for the Undergraduate Laboratory

    ERIC Educational Resources Information Center

    Rood, Jeffrey A.; Henderson, Kenneth W.

    2013-01-01

    concepts of host-guest chemistry and size exclusion in porous metal-organic frameworks (MOFs). The experiment has been successfully carried out in both introductory and advanced-level inorganic chemistry laboratories. Students synthesized the porous MOF, alpha-Mg[subscript…

  12. Ion Exchange and Thin Layer Chromatographic Separation and Identification of Amino Acids in a Mixture: An Experiment for General Chemistry and Biotechnology Laboratories

    ERIC Educational Resources Information Center

    Brunauer, Linda S.; Caslavka, Katelyn E.; Van Groningen, Karinne

    2014-01-01

    A multiday laboratory exercise is described that is suitable for first-year undergraduate chemistry, biochemistry, or biotechnology students. Students gain experience in performing chromatographic separations of biomolecules, in both a column and thin layer chromatography (TLC) format. Students chromatographically separate amino acids (AA) in an…

  13. Corrosive resistant heat exchanger

    DOEpatents

    Richlen, Scott L.

    1989-01-01

    A corrosive and errosive resistant heat exchanger which recovers heat from a contaminated heat stream. The heat exchanger utilizes a boundary layer of innocuous gas, which is continuously replenished, to protect the heat exchanger surface from the hot contaminated gas. The innocuous gas is conveyed through ducts or perforations in the heat exchanger wall. Heat from the heat stream is transferred by radiation to the heat exchanger wall. Heat is removed from the outer heat exchanger wall by a heat recovery medium.

  14. Registration of two allelic erect leaf mutants of sorghum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two allelic sorghum [Sorghum bicolor (L.) Moench] erect leaf (erl) mutants were isolated from an Annotated Individually-pedigreed Mutagenized Sorghum (AIMS) mutant library developed at the Plant Stress and Germplasm Development Unit, at Lubbock, Texas. The two mutants, erl1-1 and erl1-2, were isol...

  15. Efficient nonmeiotic allele introgression in livestock using custom endonucleases

    PubMed Central

    Tan, Wenfang; Carlson, Daniel F.; Lancto, Cheryl A.; Garbe, John R.; Webster, Dennis A.; Hackett, Perry B.; Fahrenkrug, Scott C.

    2013-01-01

    We have expanded the livestock gene editing toolbox to include transcription activator-like (TAL) effector nuclease (TALEN)- and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-stimulated homology-directed repair (HDR) using plasmid, rAAV, and oligonucleotide templates. Toward the genetic dehorning of dairy cattle, we introgressed a bovine POLLED allele into horned bull fibroblasts. Single nucleotide alterations or small indels were introduced into 14 additional genes in pig, goat, and cattle fibroblasts using TALEN mRNA and oligonucleotide transfection with efficiencies of 10–50% in populations. Several of the chosen edits mimic naturally occurring performance-enhancing or disease- resistance alleles, including alteration of single base pairs. Up to 70% of the fibroblast colonies propagated without selection harbored the intended edits, of which more than one-half were homozygous. Edited fibroblasts were used to generate pigs with knockout alleles in the DAZL and APC genes to model infertility and colon cancer. Our methods enable unprecedented meiosis-free intraspecific and interspecific introgression of select alleles in livestock for agricultural and biomedical applications. PMID:24014591

  16. Generation of mice with a conditional Lbh null allele.

    PubMed

    Lindley, Linsey E; Briegel, Karoline J

    2013-07-01

    Limb bud and heart (LBH) is a developmentally expressed, tissue-specific transcription cofactor in vertebrates that acts in the WNT signaling pathway, a genetic program critical for embryogenesis and adult tissue homeostasis. Aberrant gain-of-function of LBH is implicated in both human congenital disease and cancer. The normal physiological function of LBH has remained elusive owing to a lack of genetic loss-of-function models. Here, we have generated mice with a conditional null allele of Lbh by flanking exon 2 with loxP sites (Lbh(flox)). Homozygous Lbh(flox) and Lbh(loxP) mice, in which the Neo cassette was removed through FLPe-mediated recombination, were viable and fertile, indicating that these conditional Lbh alleles are fully functional. Lbh(loxP) mice were then crossed with a Rosa26-Cre line, resulting in ubiquitous deletion of exon 2 and abolishment of LBH protein expression. Mice homozygous for the Lbh null allele (Lbh(Δ)(2)) displayed normal embryonic development and postnatal growth with morphologies indistinguishable from wild-type littermates. However, mammary gland development, which occurs primarily after birth, was perturbed. Thus, the conditional Lbh allele will be a valuable tool to uncover the currently unknown tissue-specific roles of LBH in postnatal development and disease. PMID:23495064

  17. MHC class II DR allelic diversity in bighorn sheep

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We hypothesized that decreased diversity and/or unique polymorphisms in MHC class II alleles of bighorn sheep (BHS, Ovis canadensis) are responsible for lower titer of antibodies against Mannheimia haemolytica leukotoxin, in comparison to domestic sheep (DS, Ovis aries). To test this hypothesis, DRA...

  18. Multifragment alleles in DNA fingerprints of the parrot, Amazona ventralis

    USGS Publications Warehouse

    Brock, M.K.; White, B.N.

    1991-01-01

    Human DNA probes that identify variable numbers of tandem repeat loci are being used to generate DNA fingerprints in many animal and plant species. In most species the majority of the sc rable autoradiographic bands of the DNA fingerprint represent alleles from numerous unlinked loci. This study was initiated to use DNA fingerprints to determine the amount of band-sharing among captive Hispaniolan parrots (Amazona ventralis) with known genetic relationships. This would form the data base to examine DNA fingerprints of the closely related and endangered Puerto Rican parrot (A. vittata) and to estimate the degree of inbreeding in the relic population. We found by segregation analysis of the bands scored in the DNA fingerprints of the Hispaniolan parrots that there may be as few as two to five loci identified by the human 33.15 probe. Furthermore, at one locus we identified seven alleles, one of which is represented by as many as 19 cosegregating bands. It is unknown how common multiband alleles might be in natural populations, and their existence will cause problems in the assessment of relatedness by band-sharing analysis. We believe, therefore, that a pedigree analysis should be included in all DNA fingerprinting studies, where possible, in order to estimate the number of loci identified by a minisatellite DNA probe and to examine the nature of their alleles.

  19. Functional Allelic Variation at Key Photoperiod Response QTL in Maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tropical maize represents a valuable genetic resource containing unique alleles not present in elite temperate maize. The strong delay in flowering in response to long daylength photoperiods exhibited by most tropical maize hinders its incorporation into temperate maize breeding programs. We tested ...

  20. RECOVERY OF EXOTIC ALLELES IN ENHANCED TROPICAL YELLOW GERMPLASM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enhancement of overall diversity levels and the incorporation of new favorable traits are major benefits of using exotic germplasm in elite breeding programs. Agronomic deficiencies and poor adaptation often limits use of exotic germplasm in plant breeding programs. To introgress exotic alleles into...

  1. PUTATIVE ALLELES FOR INCREASED YIELD FROM SOYBEAN PLANT INTRODUCTIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Improving seed yield of soybean [Glycine max (L.) Merr.] cultivars is an important goal of breeding programs. The objective of this study was to evaluate two soybean plant introductions (PIs) as sources of alleles for the enhancement of seed yield in North American cultivars. A soybean population ...

  2. Distribution of forensic marker allelic frequencies in Pernambuco, Northestern Brazil.

    PubMed

    Santos, S M; Souza, C A; Rabelo, K C N; Souza, P R E; Moura, R R; Oliveira, T C; Crovella, S

    2015-01-01

    Pernambuco is one of the 27 federal units of Brazil, ranking seventh in the number of inhabitants. We examined the allele frequencies of 13 short tandem repeat loci (CFS1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, vWA, and TPOX), the minimum recommended by the Federal Bureau of Investigation and commonly used in forensic genetics laboratories in Brazil, in a sample of 609 unrelated individuals from all geographic regions of Pernambuco. The allele frequencies ranged from 5 to 47.2%. No significant differences for any loci analyzed were observed compared with other publications in other various regions of Brazil. Most of the markers observed were in Hardy-Weinberg equilibrium. The occurrence of the allele 47.2 (locus FGA) and alleles 35.1 and 39 (locus D21S11), also described in a single study of the Brazilian population, was observed. The other forensic parameters analyzed (matching probability, power of discrimination, polymorphic information content, paternity exclusion, complement factor I, observed heterozygosity, expected heterozygosity) indicated that the studied markers are very informative for human forensic identification purposes in the Pernambuco population. PMID:25966202

  3. Natural allelic variations in highly polyploidy Saccharum complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane (Saccharum spp.) as important sugar and biofuel crop are highly polypoid with complex genomes. A large amount of natural phenotypic variation exists in sugarcane germplasm. Understanding its allelic variance has been challenging but is a critical foundation for discovery of the genomic seq...

  4. Tissue-specific patterns of allelically-skewed DNA methylation

    PubMed Central

    Marzi, Sarah J.; Meaburn, Emma L.; Dempster, Emma L.; Lunnon, Katie; Paya-Cano, Jose L.; Smith, Rebecca G.; Volta, Manuela; Troakes, Claire; Schalkwyk, Leonard C.; Mill, Jonathan

    2016-01-01

    ABSTRACT While DNA methylation is usually thought to be symmetrical across both alleles, there are some notable exceptions. Genomic imprinting and X chromosome inactivation are two well-studied sources of allele-specific methylation (ASM), but recent research has indicated a more complex pattern in which genotypic variation can be associated with allelically-skewed DNA methylation in cis. Given the known heterogeneity of DNA methylation across tissues and cell types we explored inter- and intra-individual variation in ASM across several regions of the human brain and whole blood from multiple individuals. Consistent with previous studies, we find widespread ASM with > 4% of the ∼220,000 loci interrogated showing evidence of allelically-skewed DNA methylation. We identify ASM flanking known imprinted regions, and show that ASM sites are enriched in DNase I hypersensitivity sites and often located in an extended genomic context of intermediate DNA methylation. We also detect examples of genotype-driven ASM, some of which are tissue-specific. These findings contribute to our understanding of the nature of differential DNA methylation across tissues and have important implications for genetic studies of complex disease. As a resource to the community, ASM patterns across each of the tissues studied are available in a searchable online database: http://epigenetics.essex.ac.uk/ASMBrainBlood. PMID:26786711

  5. Further evidence for allelic heterogeneity in Hartnup disorder.

    PubMed

    Azmanov, Dimitar N; Kowalczuk, Sonja; Rodgers, Helen; Auray-Blais, Christiane; Giguère, Robert; Rasko, John E J; Bröer, Stefan; Cavanaugh, Juleen A

    2008-10-01

    Hartnup disorder is an autosomal recessive impairment of amino acid transport in kidney and intestine. Mutations in SLC6A19 have been shown to cosegregate with the disease in the predicted recessive manner; however, in two previous studies (Seow et al., Nat Genet 2004;36:1003-1007; Kleta et al., Nat Genet 2004;36:999-1002), not all causative alleles were identified in all affected individuals, raising the possibility that other genes may contribute to Hartnup disorder. We have now investigated six newly acquired families of Australian and Canadian (Province of Quebec) origin and resequenced the entire coding region of SLC6A19 in families with only a single disease allele identified. We also studied one American family in whom no mutations had been identified in a previous study (Kleta et al., Nat Genet 2004;36:999-1002). We have identified seven novel mutations in SLC6A19 that show functional obliteration of the protein in vitro, explaining Hartnup disorder in all reported families so far. We demonstrate that Hartnup disorder is allelically heterogeneous with two mutated SLC6A19 alleles, whether identical or not, necessary for manifestation of the characteristic aminoaciduria in affected individuals. This study resolves the previous hypothesis that other genes contribute to the Hartnup phenotype. PMID:18484095

  6. Recovery of Exotic Alleles in Enhanced Tropical Yellow Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enhancement of overall diversity levels and the incorporation of new favorable traits are major benefits of using exotic germplasm in elite breeding programs. Agronomic deficiencies and poor adaptation often limits use of exotic germplasm in plant breeding programs. To introgress exotic alleles into...

  7. Estimating the age of alleles by use of intraallelic variability

    SciTech Connect

    Slatkin, M.; Rannala, B.

    1997-02-01

    A method is presented for estimating the age of an allele by use of its frequency and the extent of variation among different copies. The method uses the joint distribution of the number of copies in a population sample and the coalescence times of the intraallelic gene genealogy conditioned on the number of copies. The linear birth-death process is used to approximate the dynamics of a rare allele in a finite population. A maximum-likelihood estimate of the age of the allele is obtained by Monte Carlo integration over the coalescence times. The method is applied to two alleles at the cystic fibrosis (CFTR) locus, {Delta}F508 and G542X, for which intraallelic variability at three intronic microsatellite loci has been examined. Our results indicate that G542X is somewhat older than {Delta}F508. Although absolute estimates depend on the mutation rates at the microsatellite loci, our results support the hypothesis that {Delta}F508 arose <500 generations ({approx}10,000 years) ago. 32 refs., 4 figs.

  8. Increase in NRAS mutant allele percentage during metastatic melanoma progression.

    PubMed

    Funck-Brentano, Elisa; Hélias-Rodzewicz, Zofia; Longvert, Christine; Mokhtari, Karima; Saiag, Philippe; Emile, Jean-François

    2016-06-01

    One-fifth of cutaneous melanomas have dominant gain-of-function mutations of the NRAS oncogene. We report the first two cases of increasing NRAS mutant allele frequency in melanoma metastases and show that the chromosomal mechanism of this homozygosity is an increased polysomy of chromosome 1. We observed an increase in NRAS mutant allele percentage (NRAS-MA%) in the metastatic melanoma progression from 2 patients with melanomas harbouring a NRAS mutation (p.Q61K in case 1 and p.Q61R in case 2). In case 1, we observed a NRAS-MA% increase from 18% within the first metastatic node to 81%, 92% and 85% respectively in the three subsequent metastases: lymph node, brain and subcutaneous metastases biopsied 1, 6 and 17 months, respectively, after the initial lymph node biopsy. In case 2, we observed an increase in NRAS-MA% from 40% within the primary melanoma to 63% within the metastatic lymph node. FISH analysis showed the same results in both cases: a frequent polysomy of chromosome 1 in metastasis samples with NRAS mutant allele percentage >60%, while most cells were disomic in the samples with well-balanced heterozygous mutations. The percentage of NRAS mutant allele may increase during metastatic progression and may be associated with chromosomal instability. Further studies are needed to evaluate the prognostic impact of the NRAS homozygous status and/or polyploidy in metastatic cutaneous melanomas. PMID:26990546

  9. Nomenclature for alleles of the thiopurine methyltransferase gene.

    PubMed

    Appell, Malin L; Berg, Jonathan; Duley, John; Evans, William E; Kennedy, Martin A; Lennard, Lynne; Marinaki, Tony; McLeod, Howard L; Relling, Mary V; Schaeffeler, Elke; Schwab, Matthias; Weinshilboum, Richard; Yeoh, Allen E J; McDonagh, Ellen M; Hebert, Joan M; Klein, Teri E; Coulthard, Sally A

    2013-04-01

    The drug-metabolizing enzyme thiopurine methyltransferase (TPMT) has become one of the best examples of pharmacogenomics to be translated into routine clinical practice. TPMT metabolizes the thiopurines 6-mercaptopurine, 6-thioguanine, and azathioprine, drugs that are widely used for treatment of acute leukemias, inflammatory bowel diseases, and other disorders of immune regulation. Since the discovery of genetic polymorphisms in the TPMT gene, many sequence variants that cause a decreased enzyme activity have been identified and characterized. Increasingly, to optimize dose, pretreatment determination of TPMT status before commencing thiopurine therapy is now routine in many countries. Novel TPMT sequence variants are currently numbered sequentially using PubMed as a source of information; however, this has caused some problems as exemplified by two instances in which authors' articles appeared on PubMed at the same time, resulting in the same allele numbers given to different polymorphisms. Hence, there is an urgent need to establish an order and consensus to the numbering of known and novel TPMT sequence variants. To address this problem, a TPMT nomenclature committee was formed in 2010, to define the nomenclature and numbering of novel variants for the TPMT gene. A website (http://www.imh.liu.se/tpmtalleles) serves as a platform for this work. Researchers are encouraged to submit novel TPMT alleles to the committee for designation and reservation of unique allele numbers. The committee has decided to renumber two alleles: nucleotide position 106 (G>A) from TPMT*24 to TPMT*30 and position 611 (T>C, rs79901429) from TPMT*28 to TPMT*31. Nomenclature for all other known alleles remains unchanged. PMID:23407052

  10. KIR2DL2/2DL3-E35 alleles are functionally stronger than -Q35 alleles

    NASA Astrophysics Data System (ADS)

    Bari, Rafijul; Thapa, Rajoo; Bao, Ju; Li, Ying; Zheng, Jie; Leung, Wing

    2016-03-01

    KIR2DL2 and KIR2DL3 segregate as alleles of a single locus in the centromeric motif of the killer cell immunoglobulin-like receptor (KIR) gene family. Although KIR2DL2/L3 polymorphism is known to be associated with many human diseases and is an important factor for donor selection in allogeneic hematopoietic stem cell transplantation, the molecular determinant of functional diversity among various alleles is unclear. In this study we found that KIR2DL2/L3 with glutamic acid at position 35 (E35) are functionally stronger than those with glutamine at the same position (Q35). Cytotoxicity assay showed that NK cells from HLA-C1 positive donors with KIR2DL2/L3-E35 could kill more target cells lacking their ligands than NK cells with the weaker -Q35 alleles, indicating better licensing of KIR2DL2/L3+ NK cells with the stronger alleles. Molecular modeling analysis reveals that the glutamic acid, which is negatively charged, interacts with positively charged histidine located at position 55, thereby stabilizing KIR2DL2/L3 dimer and reducing entropy loss when KIR2DL2/3 binds to HLA-C ligand. The results of this study will be important for future studies of KIR2DL2/L3-associated diseases as well as for donor selection in allogeneic stem cell transplantation.

  11. KIR2DL2/2DL3-E35 alleles are functionally stronger than -Q35 alleles

    PubMed Central

    Bari, Rafijul; Thapa, Rajoo; Bao, Ju; Li, Ying; Zheng, Jie; Leung, Wing

    2016-01-01

    KIR2DL2 and KIR2DL3 segregate as alleles of a single locus in the centromeric motif of the killer cell immunoglobulin-like receptor (KIR) gene family. Although KIR2DL2/L3 polymorphism is known to be associated with many human diseases and is an important factor for donor selection in allogeneic hematopoietic stem cell transplantation, the molecular determinant of functional diversity among various alleles is unclear. In this study we found that KIR2DL2/L3 with glutamic acid at position 35 (E35) are functionally stronger than those with glutamine at the same position (Q35). Cytotoxicity assay showed that NK cells from HLA-C1 positive donors with KIR2DL2/L3-E35 could kill more target cells lacking their ligands than NK cells with the weaker -Q35 alleles, indicating better licensing of KIR2DL2/L3+ NK cells with the stronger alleles. Molecular modeling analysis reveals that the glutamic acid, which is negatively charged, interacts with positively charged histidine located at position 55, thereby stabilizing KIR2DL2/L3 dimer and reducing entropy loss when KIR2DL2/3 binds to HLA-C ligand. The results of this study will be important for future studies of KIR2DL2/L3-associated diseases as well as for donor selection in allogeneic stem cell transplantation. PMID:27030405

  12. Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Though sugarcane cultivars (Saccharum spp. hybrids) are complex aneu-polyploid hybrids, genetic evaluation and tracking of clone- or cultivar-specific alleles become possible due to capillary electrophoregrams (CE) using fluorescence-labeled SSR primer pairs. Twenty-four sugarcane cultivars, 12 each...

  13. Mineral Separation in a CELSS by Ion-exchange Chromatography

    NASA Technical Reports Server (NTRS)

    Ballou, E. V.; Spitze, L. A.; Wong, F. W.; Wydeven, T.; Johnson, C. C.

    1982-01-01

    Operational parameters pertinent to ion exchange chromatography separation were identified. The experiments were performed with 9 mm diameter ion exchange columns and conventional column accessories. The cation separation beds were packed with AG 50W-X2 strong acid cation exchange resin in H(+) form and 200-400 dry mesh particle size. The stripper beds used in some experiments were packed with AG 1-XB strong base cation exchange resin in OH(-) form and 200-400 dry mesh particle size.

  14. Transvection in the Drosophila Ultrabithorax Gene: A Cbx(1) Mutant Allele Induces Ectopic Expression of a Normal Allele in Trans

    PubMed Central

    Castelli-Gair, J. E.; Micol, J. L.; Garcia-Bellido, A.

    1990-01-01

    In wild-type Drosophila melanogaster larvae, the Ultrabithorax (Ubx) gene is expressed in the haltere imaginal discs but not in the majority of cells of the wing imaginal discs. Ectopic expression of the Ubx gene in wing discs can be elicited by the presence of Contrabithorax (Cbx) gain-of-function alleles of the Ubx gene or by loss-of-function mutations in Polycomb (Pc) or in other trans-regulatory genes which behave as repressors of Ubx gene activity. Several Ubx loss-of-function alleles cause the absence of detectable Ubx proteins (UBX) or the presence of truncated UBX lacking the homeodomain. We have compared adult wing phenotypes with larval wing disc UBX patterns in genotypes involving double mutant chromosomes carrying in cis one of those Ubx mutations and the Cbx(1) mutation. We show that such double mutant genes are (1) active in the same cells in which the single mutant Cbx(1) is expressed, although they are unable to yield functional proteins, and (2) able to induce ectopic expression of a normal homologous Ubx allele in a part of the cells in which the single mutant Cbx(1) is active. That induction is conditional upon pairing of the homologous chromosomes (the phenomenon known as transvection), and it is not mediated by UBX. Depletion of Pc gene products by Pc(3) mutation strongly enhances the induction phenomenon, as shown by (1) the increase of the number of wing disc cells in which induction of the homologous allele is detectable, and (2) the induction of not only a paired normal allele but also an unpaired one. PMID:2121595

  15. Greenhouse (III): Gas-Exchange and Seed-to-Seed Experiments on the Russian Space Station MIR and Earth-grown, Ethylene-Treated Wheat Plants

    NASA Technical Reports Server (NTRS)

    Campbell, William F.; Bingham, Gail; Carman, John; Bubenheim, David; Levinskikh, Margarita; Sytchev, Vladimir N.; Podolsky, Igor B.; Chernova, Lola; Nefodova, Yelena

    2001-01-01

    The Mir Space Station provided an outstanding opportunity to study long-term plant responses when exposed to a microgravity environment. Furthermore, if plants can be grown to maturity in a microgravity environment, they might be used in future bioregenerative life-support systems (BLSS). The primary objective of the Greenhouse experiment onboard Mir was to grow Super Dwarf and Apogee wheat through complete life cycles in microgravity; i.e., from seed-to-seed-to-seed. Additional objectives were to study chemical, biochemical, and structural changes in plant tissues as well as photosynthesis, respiration, and transpiration (evaporation of water from plants). Another major objective was to evaluate the suitability clothe facilities on Mir for advanced research with plants. The Greenhouse experiment was conducted in the Russian/Bulgarian plant growth chamber, the Svet, to which the United States added instrumentation systems to monitor changes in CO2 and water vapor caused by the plants (with four infrared gas analyzers monitoring air entering and leaving two small plastic chambers). In addition, the US instrumentation also monitored O2; air, leaf (IR), cabin pressure; photon flux; and substrate temperature and substrate moisture (16 probes in the root module). Facility modifications were first performed during the summer of 1995 during Mir 19, which began after STS-72 left Mir. Plant development was monitored by daily observations and some photographs.

  16. FACTORS AFFECTING AIR EXCHANGE IN TWO HOUSES

    EPA Science Inventory

    Air exchange rate is critical to determining the relationship between indoor and outdoor concentrations of hazardous pollutants. Approximately 150 air exchange experiments were completed in two residences: a two-story detached house located in Redwood City, CA and a three-story...

  17. Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression.

    PubMed

    Cavalli, Marco; Pan, Gang; Nord, Helena; Wallerman, Ola; Wallén Arzt, Emelie; Berggren, Olof; Elvers, Ingegerd; Eloranta, Maija-Leena; Rönnblom, Lars; Lindblad Toh, Kerstin; Wadelius, Claes

    2016-05-01

    Genome-wide association studies (GWAS) have identified a large number of disease-associated SNPs, but in few cases the functional variant and the gene it controls have been identified. To systematically identify candidate regulatory variants, we sequenced ENCODE cell lines and used public ChIP-seq data to look for transcription factors binding preferentially to one allele. We found 9962 candidate regulatory SNPs, of which 16 % were rare and showed evidence of larger functional effect than common ones. Functionally rare variants may explain divergent GWAS results between populations and are candidates for a partial explanation of the missing heritability. The majority of allele-specific variants (96 %) were specific to a cell type. Furthermore, by examining GWAS loci we found >400 allele-specific candidate SNPs, 141 of which were highly relevant in our cell types. Functionally validated SNPs support identification of an SNP in SYNGR1 which may expose to the risk of rheumatoid arthritis and primary biliary cirrhosis, as well as an SNP in the last intron of COG6 exposing to the risk of psoriasis. We propose that by repeating the ChIP-seq experiments of 20 selected transcription factors in three to ten people, the most common polymorphisms can be interrogated for allele-specific binding. Our strategy may help to remove the current bottleneck in functional annotation of the genome. PMID:26993500

  18. DRD2 Schizophrenia-Risk Allele Is Associated With Impaired Striatal Functioning in Unaffected Siblings of Schizophrenia Patients.

    PubMed

    Vink, Matthijs; de Leeuw, Max; Luykx, Jurjen J; van Eijk, Kristel R; van den Munkhof, Hanna E; van Buuren, Mariët; Kahn, René S

    2016-05-01

    A recent Genome-Wide Association Study showed that the rs2514218 single nucleotide polymorphism (SNP) in close proximity to dopamine receptor D2 is strongly associated with schizophrenia. Further, an in silico experiment showed that rs2514218 has a cis expression quantitative trait locus effect in the basal ganglia. To date, however, the functional consequence of this SNP is unknown. Here, we used functional Magnetic resonance imaging to investigate the impact of this risk allele on striatal activation during proactive and reactive response inhibition in 45 unaffected siblings of schizophrenia patients. We included siblings to circumvent the illness specific confounds affecting striatal functioning independent from gene effects. Behavioral analyses revealed no differences between the carriers (n= 21) and noncarriers (n= 24). Risk allele carriers showed a diminished striatal response to increasing proactive inhibitory control demands, whereas overall level of striatal activation in carriers was elevated compared to noncarriers. Finally, risk allele carriers showed a blunted striatal response during successful reactive inhibition compared to the noncarriers. These data are consistent with earlier reports showing similar deficits in schizophrenia patients, and point to a failure to flexibly engage the striatum in response to contextual cues. This is the first study to demonstrate an association between impaired striatal functioning and the rs2514218 polymorphism. We take our findings to indicate that striatal functioning is impaired in carriers of the DRD2 risk allele, likely due to dopamine dysregulation at the DRD2 location. PMID:26598739

  19. Woven heat exchanger

    DOEpatents

    Piscitella, Roger R.

    1987-05-05

    In a woven ceramic heat exchanger using the basic tube-in-shell design, each heat exchanger consisting of tube sheets and tube, is woven separately. Individual heat exchangers are assembled in cross-flow configuration. Each heat exchanger is woven from high temperature ceramic fiber, the warp is continuous from tube to tube sheet providing a smooth transition and unitized construction.

  20. Human Leukocyte Antigen Alleles and Cytomegalovirus Infection After Renal Transplantation

    PubMed Central

    Futohi, Farzaneh; Saber, Azadeh; Nemati, Eglim; Einollahi, Behzad; Rostami, Zohre

    2015-01-01

    Background: Several studies have been conducted on the relationship between a number of human leukocyte antigen (HLA) alleles and cytomegalovirus infection (CMV), in kidney transplant recipients, after transplantation. However, only a limited number of HLAs have been investigated, so far, and the results have been contradictory. Objectives: This study aimed to investigate the relationship between 59 HLA alleles and the CMV infection, in transplant recipients, after kidney transplantation. Patients and Methods: This retrospective cohort study was conducted on 200 patients, receiving a kidney transplant, in Baqiyatallah Hospital, in Tehran, during 2013. Throughout a one-year follow-up of kidney transplant recipients, in case of detecting the CMV antigen in patients’ blood, at any time, they were placed in the group of patients with CMV infection, whereas, if no CMV-specific antigen was developed, over a year, patients were placed in the group of patients without CMV infection, after transplantation. This study investigated the relationship between CMV infection in kidney transplant recipients and 59 HLA alleles, including 14 HLA-A, 28 HLA-B, and 17 HLA-DRB1 cases. Results: Of all participants, 104 patients (52%) were diagnosed with CMV infection. There was no significant difference between the two groups, with and without CMV infection, in terms of patient’s characteristics. The CMV infection, in patients receiving a transplanted organ from deceased donor, was significantly more prevalent than in those receiving kidney transplant from living donor (63% vs. 39%, respectively, P = 0.001). Recipients with HLA-B44 were more infected with CMV compared with patients without this allele (80% vs. 50%, respectively, P = 0.024); on the contrary, kidney recipients with HLA-DRB1-1 were less infected with CMV than patients without this allele (31% vs. 55%, respectively, P = 0.020). There was no significant relationship between CMV infection and other HLA alleles. Results of

  1. Quantitative trait locus mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower.

    PubMed

    Whitney, Kenneth D; Broman, Karl W; Kane, Nolan C; Hovick, Stephen M; Randell, Rebecca A; Rieseberg, Loren H

    2015-05-01

    The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 single nucleotide polymorphism (SNP) markers and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favoured in the wild. QTL for a number of other ecophysiological, phenological and architectural traits colocalized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence. PMID:25522096

  2. Woven heat exchanger

    DOEpatents

    Piscitella, R.R.

    1984-07-16

    This invention relates to a heat exchanger for waste heat recovery from high temperature industrial exhaust streams. In a woven ceramic heat exchanger using the basic tube-in-shell design, each heat exchanger consisting of tube sheets and tube, is woven separately. Individual heat exchangers are assembled in cross-flow configuration. Each heat exchanger is woven from high temperature ceramic fiber, the warp is continuous from tube to tube sheet providing a smooth transition and unitized construction.

  3. Designing health insurance exchanges: key decisions.

    PubMed

    Starc, Amanda; Kolstad, Jonathan T

    2012-02-01

    A cornerstone of health care reform is the establishment of state-level insurance exchanges where individuals and small businesses can purchase health insurance in an online marketplace. States are required to develop an exchange by 2014, or participate in a federal one. The exchanges will help people without employer-sponsored insurance find and choose a health plan to meet their needs. This Issue Brief reviews the experience of Massachusetts in developing a health insurance exchange and offers policymakers guidance on key features and likely consumer responses. PMID:22451998

  4. Attenuated APC alleles produce functional protein from internal translation initiation

    PubMed Central

    Heppner Goss, Kathleen; Trzepacz, Chris; Tuohy, Thérèse M. F.; Groden, Joanna

    2002-01-01

    Some truncating mutations of the APC tumor suppressor gene are associated with an attenuated phenotype of familial adenomatous polyposis coli (AAPC). This work demonstrates that APC alleles with 5′ mutations produce APC protein that down-regulates β-catenin, inhibits β-catenin/T cell factor-mediated transactivation, and induces cell-cycle arrest. Transfection studies demonstrate that cap-independent translation is initiated internally at an AUG at codon 184 of APC. Furthermore, APC coding sequence between AAPC mutations and AUG 184 permits internal ribosome entry in a bicistronic vector. These data suggest that AAPC alleles in vivo may produce functional APC by internal initiation and establish a functional correlation between 5′ APC mutations and their associated clinical phenotype. PMID:12034871

  5. High throughput automated allele frequency estimation by pyrosequencing.

    PubMed

    Doostzadeh, Julie; Shokralla, Shadi; Absalan, Farnaz; Jalili, Roxana; Mohandessi, Sharareh; Langston, James W; Davis, Ronald W; Ronaghi, Mostafa; Gharizadeh, Baback

    2008-01-01

    Pyrosequencing is a DNA sequencing method based on the principle of sequencing-by-synthesis and pyrophosphate detection through a series of enzymatic reactions. This bioluminometric, real-time DNA sequencing technique offers unique applications that are cost-effective and user-friendly. In this study, we have combined a number of methods to develop an accurate, robust and cost efficient method to determine allele frequencies in large populations for association studies. The assay offers the advantage of minimal systemic sampling errors, uses a general biotin amplification approach, and replaces dTTP for dATP-apha-thio to avoid non-uniform higher peaks in order to increase accuracy. We demonstrate that this newly developed assay is a robust, cost-effective, accurate and reproducible approach for large-scale genotyping of DNA pools. We also discuss potential improvements of the software for more accurate allele frequency analysis. PMID:18628978

  6. High Throughput Automated Allele Frequency Estimation by Pyrosequencing

    PubMed Central

    Absalan, Farnaz; Jalili, Roxana; Mohandessi, Sharareh; Langston, James W.; Davis, Ronald W.; Ronaghi, Mostafa; Gharizadeh, Baback

    2008-01-01

    Pyrosequencing is a DNA sequencing method based on the principle of sequencing-by-synthesis and pyrophosphate detection through a series of enzymatic reactions. This bioluminometric, real-time DNA sequencing technique offers unique applications that are cost-effective and user-friendly. In this study, we have combined a number of methods to develop an accurate, robust and cost efficient method to determine allele frequencies in large populations for association studies. The assay offers the advantage of minimal systemic sampling errors, uses a general biotin amplification approach, and replaces dTTP for dATP-apha-thio to avoid non-uniform higher peaks in order to increase accuracy. We demonstrate that this newly developed assay is a robust, cost-effective, accurate and reproducible approach for large-scale genotyping of DNA pools. We also discuss potential improvements of the software for more accurate allele frequency analysis. PMID:18628978

  7. Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli

    PubMed Central

    Mortazavi, Pooneh; Knight, Rob; Gill, Ryan T.

    2016-01-01

    Chemical genomics expands our understanding of microbial tolerance to inhibitory chemicals, but its scope is often limited by the throughput of genome-scale library construction and genotype-phenotype mapping. Here we report a method for rapid, parallel, and deep characterization of the response to antibiotics in Escherichia coli using a barcoded genome-scale library, next-generation sequencing, and streamlined bioinformatics software. The method provides quantitative growth data (over 200,000 measurements) and identifies contributing antimicrobial resistance and susceptibility alleles. Using multivariate analysis, we also find that subtle differences in the population responses resonate across multiple levels of functional hierarchy. Finally, we use machine learning to identify a unique allelic and proteomic fingerprint for each antibiotic. The method can be broadly applied to tolerance for any chemical from toxic metabolites to next-generation biofuels and antibiotics. PMID:26771672

  8. Early allelic selection in maize as revealed by ancient DNA.

    PubMed

    Jaenicke-Després, Viviane; Buckler, Ed S; Smith, Bruce D; Gilbert, M Thomas P; Cooper, Alan; Doebley, John; Pääbo, Svante

    2003-11-14

    Maize was domesticated from teosinte, a wild grass, by approximately 6300 years ago in Mexico. After initial domestication, early farmers continued to select for advantageous morphological and biochemical traits in this important crop. However, the timing and sequence of character selection are, thus far, known only for morphological features discernible in corn cobs. We have analyzed three genes involved in the control of plant architecture, storage protein synthesis, and starch production from archaeological maize samples from Mexico and the southwestern United States. The results reveal that the alleles typical of contemporary maize were present in Mexican maize by 4400 years ago. However, as recently as 2000 years ago, allelic selection at one of the genes may not yet have been complete. PMID:14615538

  9. Mammalian interspecies substitution of immune modulatory alleles by genome editing

    PubMed Central

    Lillico, Simon G.; Proudfoot, Chris; King, Tim J.; Tan, Wenfang; Zhang, Lei; Mardjuki, Rachel; Paschon, David E.; Rebar, Edward J.; Urnov, Fyodor D.; Mileham, Alan J.; McLaren, David G.; Whitelaw, C. Bruce A.

    2016-01-01

    We describe a fundamentally novel feat of animal genetic engineering: the precise and efficient substitution of an agronomic haplotype into a domesticated species. Zinc finger nuclease in-embryo editing of the RELA locus generated live born domestic pigs with the warthog RELA orthologue, associated with resilience to African Swine Fever. The ability to efficiently achieve interspecies allele introgression in one generation opens unprecedented opportunities for agriculture and basic research. PMID:26898342

  10. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    PubMed Central

    Song, Jian; Yang, Xiping; Resende, Marcio F. R.; Neves, Leandro G.; Todd, James; Zhang, Jisen; Comstock, Jack C.; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes. PMID:27375658

  11. Triploidy with cyclopia and identical HLA alleles in the parents.

    PubMed Central

    Lambert, J C; Philip, P; Charpentier, G; Ferrari, M; Donzeau, M; Ayraud, N

    1984-01-01

    A 22-week pregnancy was terminated after discovery of serious echographic abnormalities. Fetal examination showed cyclopia, sacral meningocele, and syndactyly. The karyotype was 69,XXX. The parents had identical HLA alleles A1, A2, and Bw21. The mechanism of the triploidy was determined by chromosome marker analysis to be digyny. The association of triploidy with holoprosencephaly and the parents' identical immunological status are discussed. Images PMID:6607355

  12. Mammalian interspecies substitution of immune modulatory alleles by genome editing.

    PubMed

    Lillico, Simon G; Proudfoot, Chris; King, Tim J; Tan, Wenfang; Zhang, Lei; Mardjuki, Rachel; Paschon, David E; Rebar, Edward J; Urnov, Fyodor D; Mileham, Alan J; McLaren, David G; Whitelaw, C Bruce A

    2016-01-01

    We describe a fundamentally novel feat of animal genetic engineering: the precise and efficient substitution of an agronomic haplotype into a domesticated species. Zinc finger nuclease in-embryo editing of the RELA locus generated live born domestic pigs with the warthog RELA orthologue, associated with resilience to African Swine Fever. The ability to efficiently achieve interspecies allele introgression in one generation opens unprecedented opportunities for agriculture and basic research. PMID:26898342

  13. Natural Allelic Variations in Highly Polyploidy Saccharum Complex.

    PubMed

    Song, Jian; Yang, Xiping; Resende, Marcio F R; Neves, Leandro G; Todd, James; Zhang, Jisen; Comstock, Jack C; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes. PMID:27375658

  14. Fast spatial ancestry via flexible allele frequency surfaces

    PubMed Central

    Rañola, John Michael; Novembre, John; Lange, Kenneth

    2014-01-01

    Motivation: Unique modeling and computational challenges arise in locating the geographic origin of individuals based on their genetic backgrounds. Single-nucleotide polymorphisms (SNPs) vary widely in informativeness, allele frequencies change non-linearly with geography and reliable localization requires evidence to be integrated across a multitude of SNPs. These problems become even more acute for individuals of mixed ancestry. It is hardly surprising that matching genetic models to computational constraints has limited the development of methods for estimating geographic origins. We attack these related problems by borrowing ideas from image processing and optimization theory. Our proposed model divides the region of interest into pixels and operates SNP by SNP. We estimate allele frequencies across the landscape by maximizing a product of binomial likelihoods penalized by nearest neighbor interactions. Penalization smooths allele frequency estimates and promotes estimation at pixels with no data. Maximization is accomplished by a minorize–maximize (MM) algorithm. Once allele frequency surfaces are available, one can apply Bayes’ rule to compute the posterior probability that each pixel is the pixel of origin of a given person. Placement of admixed individuals on the landscape is more complicated and requires estimation of the fractional contribution of each pixel to a person’s genome. This estimation problem also succumbs to a penalized MM algorithm. Results: We applied the model to the Population Reference Sample (POPRES) data. The model gives better localization for both unmixed and admixed individuals than existing methods despite using just a small fraction of the available SNPs. Computing times are comparable with the best competing software. Availability and implementation: Software will be freely available as the OriGen package in R. Contact: ranolaj@uw.edu or klange@ucla.edu Supplementary information: Supplementary data are available at

  15. Inferring Selection Intensity and Allele Age from Multilocus Haplotype Structure

    PubMed Central

    Chen, Hua; Slatkin, Montgomery

    2013-01-01

    It is a challenging task to infer selection intensity and allele age from population genetic data. Here we present a method that can efficiently estimate selection intensity and allele age from the multilocus haplotype structure in the vicinity of a segregating mutant under positive selection. We use a structured-coalescent approach to model the effect of directional selection on the gene genealogies of neutral markers linked to the selected mutant. The frequency trajectory of the selected allele follows the Wright-Fisher model. Given the position of the selected mutant, we propose a simplified multilocus haplotype model that can efficiently model the dynamics of the ancestral haplotypes under the joint influence of selection and recombination. This model approximates the ancestral genealogies of the sample, which reduces the number of states from an exponential function of the number of single-nucleotide polymorphism loci to a quadratic function. That allows parameter inference from data covering DNA regions as large as several hundred kilo-bases. Importance sampling algorithms are adopted to evaluate the probability of a sample by exploring the space of both allele frequency trajectories of the selected mutation and gene genealogies of the linked sites. We demonstrate by simulation that the method can accurately estimate selection intensity for moderate and strong positive selection. We apply the method to a data set of the G6PD gene in an African population and obtain an estimate of 0.0456 (95% confidence interval 0.0144−0.0769) for the selection intensity. The proposed method is novel in jointly modeling the multilocus haplotype pattern caused by recombination and mutation, allowing the analysis of haplotype data in recombining regions. Moreover, the method is applicable to data from populations under exponential growth and a variety of other demographic histories. PMID:23797107

  16. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    DOE PAGESBeta

    Song, Jian; Yang, Xiping; Resende, Marcio F. R.; Neves, Leandro G.; Todd, James; Zhang, Jisen; Comstock, Jack C.; Wang, Jianping

    2016-06-08

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed basedmore » on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWAmem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non -redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp, diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.« less

  17. Application of current steps and design of experiments methodology to the detection of water management faults in a proton exchange membrane fuel cell stack

    NASA Astrophysics Data System (ADS)

    Moçotéguy, Philippe; Ludwig, Bastian; Yousfi Steiner, Nadia

    2016-01-01

    We apply a 25-1 fractional factorial Design of Experiments (DoE) test plan in order to discriminate the direct effects and interactions of five factors on the water management of a 500 We PEMFC stack. The stack is submitted to current steps between different operating levels and several responses are extracted for the DoE analysis. A strong ageing effect on stack and cell performances is observed. Therefore, in order to perform the DoE analysis, responses which values are too strongly affected by ageing are "corrected" prior to the analysis. A "virtual" stack, considered as "healthy", is also "reconstructed" by "putting in series" the cells exhibiting very low performance drop. The results show that stacks and cells' resistivities are mostly impacted by direct effects of both temperature and cathodic inlet relative humidity and by compensating interaction between temperature and anodic overstoichiometric ratio. It also appears that two responses are able to distinguish a "healthy" stack from a degraded stack: heterogeneities in cell voltages and cell resistivities distributions. They are differently impacted by considered effects and interactions. Thus, a customised water management strategy could be developed, depending on the stack's state of health to maintain it in the best possible operating conditions.

  18. Exchanging expertise, theory and practice at Master's level healthcare education between Russia and Finland - experiences from an intensive course in St. Petersburg.

    PubMed

    Hopia, Hanna; Liimatainen, Leena; Turkina, Natalija Victorovna; Filenkov, Anton

    2011-01-01

    The aim of this article is to raise discussion on the internationalisation possibilities of master's students who study while working. The objective of the article is to describe and share experiences on how to make the development of students' internationalisation competence possible through collaboration with representatives of different cultures during a one-week intensive course. Internationalisation is an essential component in the competence-based curriculum of master's level social and healthcare education. On the other hand, it has been a difficult task for adult students to enhance their internationalisation competence when they pursue studies alongside work. In addition, internationalisation in master's level education has been a key feature both in Finland and in Russia. An intensive course is one educational method to share students' existing professional know-how in an international multi-professional student group and to enable adult students' mobility. This paper describes a one-week intensive course which was carried out in St. Petersburg, Russia in autumn 2008. The course was evaluated by the adult students and their teachers participating in the course. The intensive course increased the degree of transparency and compatibility between higher education and advanced professional education qualifications gained in postgraduate healthcare education in the partner organisations. It seems that an intensive course is a good pedagogical method for enhancing the internationalisation competence of adult students. PMID:20538523

  19. The Franck-Hertz Experiments, 1911-1914 Experimentalists in Search of a Theory. With an appendix, "On the History of our Experiments on the Energy Exchange between Slow Electrons and Atoms" by Gustav Hertz

    NASA Astrophysics Data System (ADS)

    Gearhart, Clayton A.

    2014-09-01

    In 1911, James Franck and Gustav Hertz began a collaboration to investigate the nature of collisions of slow electrons with gas molecules that led to a series of carefully planned and executed experiments, culminating in their discovery of inelastic collisions of electrons with mercury vapor atoms in 1914. This paper tells the story of their collaboration and the eventual reinterpretation of their results as a confirmation of Niels Bohr's new atomic theory, largely as a result of experiments done in North America during the Great War.

  20. The Franck-Hertz Experiments, 1911-1914 Experimentalists in Search of a Theory - With an appendix, "On the History of our Experiments on the Energy Exchange between Slow Electrons and Atoms" by Gustav Hertz

    NASA Astrophysics Data System (ADS)

    Gearhart, Clayton A.

    2014-09-01

    In 1911, James Franck and Gustav Hertz began a collaboration to investigate the nature of collisions of slow electrons with gas molecules that led to a series of carefully planned and executed experiments, culminating in their discovery of inelastic collisions of electrons with mercury vapor atoms in 1914. This paper tells the story of their collaboration and the eventual reinterpretation of their results as a confirmation of Niels Bohr's new atomic theory, largely as a result of experiments done in North America during the Great War.

  1. Tracing pastoralist migrations to southern Africa with lactase persistence alleles.

    PubMed

    Macholdt, Enrico; Lede, Vera; Barbieri, Chiara; Mpoloka, Sununguko W; Chen, Hua; Slatkin, Montgomery; Pakendorf, Brigitte; Stoneking, Mark

    2014-04-14

    Although southern African Khoisan populations are often assumed to have remained largely isolated during prehistory, there is growing evidence for a migration of pastoralists from eastern Africa some 2,000 years ago, prior to the arrival of Bantu-speaking populations in southern Africa. Eastern Africa harbors distinctive lactase persistence (LP) alleles, and therefore LP alleles in southern African populations may be derived from this eastern African pastoralist migration. We sequenced the lactase enhancer region in 457 individuals from 18 Khoisan and seven Bantu-speaking groups from Botswana, Namibia, and Zambia and additionally genotyped four short tandem repeat (STR) loci that flank the lactase enhancer region. We found nine single-nucleotide polymorphisms, of which the most frequent is -14010(∗)C, which was previously found to be associated with LP in Kenya and Tanzania and to exhibit a strong signal of positive selection. This allele occurs in significantly higher frequency in pastoralist groups and in Khoe-speaking groups in our study, supporting the hypothesis of a migration of eastern African pastoralists that was primarily associated with Khoe speakers. Moreover, we find a signal of ongoing positive selection in all three pastoralist groups in our study, as well as (surprisingly) in two foraging groups. PMID:24704073

  2. Pollution-tolerant allele in fingernail clams (Musculium transversum).

    PubMed

    Sloss, B L; Romano, M A; Anderson, R V

    1998-08-01

    For nearly 50 years, the fingernail clam (Musculium transversum) was believed to be virtually eliminated from the Illinois River. In 1991, workers began finding substantial populations of M. transversum in the Illinois River including several beds in and around the highly polluted Chicago Sanitary District. In order to determine if populations of M. transversum from polluted sites exhibited any genetic response to the high levels of toxins and to examine the genetic structure of several populations of M. transversum for any changes due to the population crash, starch-gel electrophoresis was performed on M. transversum from three Illinois River localities and four Mississippi River basin locations. The sampled populations produced an inbreeding coefficient (FIS) of 0.929, indicating that the populations were highly inbred. The results of a suspected founder effect due to a bottleneck was suggested by an FST = 0.442. The isozyme Glucose-6-phosphate isomerase-2 (Gpi-2) produced allelic frequency patterns that were consistent with expected patterns of a pollution-tolerant allele. Polluted sites exhibited elevated frequencies of Gpi-2(100) whereas nonpolluted sites exhibited elevated frequencies of Gpi-2(74). This frequency pattern suggested that natural selection was occurring in populations under severe toxic pressures, leading to an increase in the frequency of the allele Gpi-2(100). Therefore, Gpi-2(100) is a possible pollution-tolerant mutation in M. transversum. PMID:9680522

  3. Allele-specific tumor spectrum in pten knockin mice.

    PubMed

    Wang, Hui; Karikomi, Matt; Naidu, Shan; Rajmohan, Ravi; Caserta, Enrico; Chen, Hui-Zi; Rawahneh, Maysoon; Moffitt, Julie; Stephens, Julie A; Fernandez, Soledad A; Weinstein, Michael; Wang, Danxin; Sadee, Wolfgang; La Perle, Krista; Stromberg, Paul; Rosol, Thomas J; Eng, Charis; Ostrowski, Michael C; Leone, Gustavo

    2010-03-16

    Germline mutations in the tumor suppressor gene PTEN (phosphatase and tensin homology deleted on chromosome 10) cause Cowden and Bannayan-Riley-Ruvalcaba (BRR) syndromes, two dominantly inherited disorders characterized by mental retardation, multiple hamartomas, and variable cancer risk. Here, we modeled three sentinel mutant alleles of PTEN identified in patients with Cowden syndrome and show that the nonsense Pten(4-5) and missense Pten(C124R) and Pten(G129E) alleles lacking lipid phosphatase activity cause similar developmental abnormalities but distinct tumor spectra with varying severity and age of onset. Allele-specific differences may be accounted for by loss of function for Pten(4-5), hypomorphic function for Pten(C124R), and gain of function for Pten(G129E). These data demonstrate that the variable tumor phenotypes observed in patients with Cowden and BRR syndromes can be attributed to specific mutations in PTEN that alter protein function through distinct mechanisms. PMID:20194734

  4. Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis

    PubMed Central

    2005-01-01

    Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly high resolution. Similarly, loss-of-heterozygosity events have been finely mapped using high-throughput genotyping technologies. We have developed a probe-level allele-specific quantitation procedure that extracts both copy number and allelotype information from single nucleotide polymorphism (SNP) array data to arrive at allele-specific copy number across the genome. Our approach applies an expectation-maximization algorithm to a model derived from a novel classification of SNP array probes. This method is the first to our knowledge that is able to (a) determine the generalized genotype of aberrant samples at each SNP site (e.g., CCCCT at an amplified site), and (b) infer the copy number of each parental chromosome across the genome. With this method, we are able to determine not just where amplifications and deletions occur, but also the haplotype of the region being amplified or deleted. The merit of our model and general approach is demonstrated by very precise genotyping of normal samples, and our allele-specific copy number inferences are validated using PCR experiments. Applying our method to a collection of lung cancer samples, we are able to conclude that amplification is essentially monoallelic, as would be expected under the mechanisms currently believed responsible for gene amplification. This suggests that a specific parental chromosome may be targeted for amplification, whether because of germ line or somatic variation. An R software package containing the methods described in this paper is freely available at http://genome.dfci.harvard.edu/~tlaframb/PLASQ. PMID:16322765

  5. Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles.

    PubMed

    Hoffert, Jason D; Pisitkun, Trairak; Miller, R Lance

    2012-06-01

    Transgenic and conditional knockout mouse models play an important role in biomedical research and their use has grown exponentially in the last 5-10 years. Generating conditional knockouts often requires breeding multiple alleles onto the background of a single mouse or group of mice. Breeding these mice depends on parental genotype, litter size, transmission frequency, and the number of breeding rounds. Therefore, a well planned breeding strategy is critical for keeping costs to a minimum. However, designing a viable breeding strategy can be challenging. With so many different variables this would be an ideal task for a computer program. To facilitate this process, we created a Java-based program called Conditional Allele Mouse Planner (CAMP). CAMP is designed to provide an estimate of the number of breeders, amount of time, and costs associated with generating mice of a particular genotype. We provide a description of CAMP, how to use it, and offer it freely as an application. PMID:21870117

  6. Increasing long-term response by selecting for favorable minor alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Long-term response of genomic selection can be improved by considering allele frequencies of selected markers or quantitative trait loci (QTLs). A previous formula to weight allele frequency of favorable minor alleles was tested, and 2 new formulas were developed. The previous formula used nonlinear...

  7. Allele Name Translation Tool and Update NomenCLature: software tools for the automated translation of HLA allele names between successive nomenclatures.

    PubMed

    Mack, S J; Hollenbach, J A

    2010-05-01

    In this brief communication, we describe the Allele Name Translation Tool (antt) and Update NomenCLature (uncl), free programs developed to facilitate the translation of human leukocyte antigen (HLA) allele names recorded using the December 2002 version of the HLA allele nomenclature (e.g. A*01010101) to those recorded using the colon-delimited version of the HLA allele nomenclature (e.g. A*01:01:01:01) that was adopted in April 2010. In addition, the antt and uncl translate specific HLA allele-name changes (e.g. DPB1*0502 is translated to DPB1*104:01), as well as changes to the locus prefix for HLA-C (i.e. Cw* is translated to C*). The antt and uncl will also translate allele names that have been truncated to two, four, or six digits, as well as ambiguous allele strings. The antt is a locally installed and run application, while uncl is a web-based tool that requires only an Internet connection and a modern browser. The antt accepts a variety of HLA data-presentation and allele-name formats. In addition, the antt can translate using user-defined conversion settings (e.g. the names of alleles that encode identical peptide binding domains can be translated to a common 'P-code'), and can serve as a preliminary data-sanity tool. The antt is available for download, and uncl for use, at www.igdawg.org/software. PMID:20412076

  8. Meiotic Instability of the R-R Complex Arising from Displaced Intragenic Exchange and Intrachromosomal Rearrangement

    PubMed Central

    Robbins, T. P.; Walker, E. L.; Kermicle, J. L.; Alleman, M.; Dellaporta, S. L.

    1991-01-01

    The R complex of Zea mays encodes a tissue-specific transcriptional activator of the anthocyanin pigment biosynthetic pathway. Certain R alleles comprise two genetically distinct components that confer the plant (P) and seed (S) aspects of the pigmentation pattern. These alleles are meiotically unstable, losing (P) or (S) function, often accompanied by exchange of flanking markers. We show that the (P) component consists of a single gene within the R-r complex, whereas the (S) component is part of a more complex arrangement of multiple R genes or gene subfragments. A third, cryptic region of the complex, termed (Q), consists of a truncated R sequence. The analysis of R-r crossover derivative alleles shows they arise from unequal exchange between the (P) gene and one of several distinct regions of the R-r complex. Restriction site polymorphisms were used to show that most of these unequal exchanges are intragenic. The frequency of displaced intragenic recombination is comparable to previous estimates for intragenic recombination in maize involving genes that are not duplicated. These exchange events have been used to determine the arrangement of components within the complex and their orientation in the chromosome. We also show that localized rearrangements in the (P) or (S) components are responsible for noncrossover derivative alleles. The organization of R-r has implications for these noncrossover derivatives and models for their origin are discussed. PMID:1682214

  9. [Male reproductive behavior in Drosophila melanogaster strains with different alleles of the flamenco gene].

    PubMed

    Subocheva, E A; Romanova, N I; Karpova, N N; Iuneva, A O; Kim, A I

    2003-05-01

    The allelic state of gene flamenco has been determined in a number of Drosophila melanogaster strains using the ovoD test. The presence of an active copy of gypsy in these strains was detected by restriction analysis. Then male reproduction behavior was studied in the strains carrying a mutation in gene flamenco. In these experiments mating success has been experimentally estimated in groups of flies. It has been demonstrated that the presence of mutant allele flamMS decreases male mating activity irrespective of the presence or absence of mutation white. The active copy of gypsy does not affect mating activity in the absence of the mutation in gene flamenco. Individual analysis has demonstrated that that mutation flamMS results in characteristic changes in courtship: flamMS males exhibit a delay in the transition from the orientation stage to the vibration stage (the so-called vibration delay). The role of locus flamenco in the formation of male mating behavior in Drosophila is discussed. PMID:12838614

  10. Allele-specific RNAi Mitigates Phenotypic Progression in a Transgenic Model of Alzheimer's Disease

    PubMed Central

    Rodríguez-Lebrón, Edgardo; Gouvion, Cynthia M; Moore, Steven A; Davidson, Beverly L; Paulson, Henry L

    2009-01-01

    Despite recent advances suggesting new therapeutic targets, Alzheimer's disease (AD) remains incurable. Aberrant production and accumulation of the Aβ peptide resulting from altered processing of the amyloid precursor protein (APP) is central to the pathogenesis of disease, particularly in dominantly inherited forms of AD. Thus, modulating the production of APP is a potential route to effective AD therapy. Here, we describe the successful use of an allele-specific RNA interference (RNAi) approach targeting the Swedish variant of APP (APPsw) in a transgenic mouse model of AD. Using recombinant adeno-associated virus (rAAV), we delivered an anti-APPsw short-hairpin RNA (shRNA) to the hippocampus of AD transgenic mice (APP/PS1). In short- and long-term transduction experiments, reduced levels of APPsw transprotein were observed throughout targeted regions of the hippocampus while levels of wild-type murine APP remained unaltered. Moreover, intracellular production of transfer RNA (tRNA)-valine promoter–driven shRNAs did not lead to detectable neuronal toxicity. Finally, long-term bilateral hippocampal expression of anti-APPsw shRNA mitigated abnormal behaviors in this mouse model of AD. The difference in phenotype progression was associated with reduced levels of soluble Aβ but not with a reduced number of amyloid plaques. Our results support the development of allele-specific RNAi strategies to treat familial AD and other dominantly inherited neurodegenerative diseases. PMID:19532137

  11. Indiana Health Information Exchange

    Cancer.gov

    The Indiana Health Information Exchange is comprised of various Indiana health care institutions, established to help improve patient safety and is recognized as a best practice for health information exchange.

  12. Wheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene Pm3: a large scale allele mining project

    PubMed Central

    2010-01-01

    Background In the last hundred years, the development of improved wheat cultivars has led to the replacement of landraces and traditional varieties by modern cultivars. This has resulted in a decline in the genetic diversity of agriculturally used wheat. However, the diversity lost in the elite material is somewhat preserved in crop gene banks. Therefore, the gene bank accessions provide the basis for genetic improvement of crops for specific traits and and represent rich sources of novel allelic variation. Results We have undertaken large scale molecular allele mining to isolate new alleles of the powdery mildew resistance gene Pm3 from wheat gene bank accessions. The search for new Pm3 alleles was carried out on a geographically diverse set of 733 wheat accessions originating from 20 countries. Pm3 specific molecular tools as well as classical pathogenicity tests were used to characterize the accessions. Two new functional Pm3 alleles were identified out of the eight newly cloned Pm3 sequences. These new resistance alleles were isolated from accessions from China and Nepal. Thus, the repertoire of functional Pm3 alleles now includes 17 genes, making it one of the largest allelic series of plant resistance genes. The combined information on resistant and susceptible Pm3 sequences will allow to study molecular function and specificity of functional Pm3 alleles. Conclusions This study demonstrates that molecular allele mining on geographically defined accessions is a useful strategy to rapidly characterize the diversity of gene bank accessions at a specific genetic locus of agronomical importance. The identified wheat accessions with new resistance specificities can be used for marker-assisted transfer of the Pm3 alleles to modern wheat lines. PMID:20470444

  13. Charge exchange system

    DOEpatents

    Anderson, Oscar A.

    1978-01-01

    An improved charge exchange system for substantially reducing pumping requirements of excess gas in a controlled thermonuclear reactor high energy neutral beam injector. The charge exchange system utilizes a jet-type blanket which acts simultaneously as the charge exchange medium and as a shield for reflecting excess gas.

  14. Bovine Polledness – An Autosomal Dominant Trait with Allelic Heterogeneity

    PubMed Central

    Medugorac, Ivica; Seichter, Doris; Graf, Alexander; Russ, Ingolf; Blum, Helmut; Göpel, Karl Heinrich; Rothammer, Sophie; Förster, Martin; Krebs, Stefan

    2012-01-01

    The persistent horns are an important trait of speciation for the family Bovidae with complex morphogenesis taking place briefly after birth. The polledness is highly favourable in modern cattle breeding systems but serious animal welfare issues urge for a solution in the production of hornless cattle other than dehorning. Although the dominant inhibition of horn morphogenesis was discovered more than 70 years ago, and the causative mutation was mapped almost 20 years ago, its molecular nature remained unknown. Here, we report allelic heterogeneity of the POLLED locus. First, we mapped the POLLED locus to a ∼381-kb interval in a multi-breed case-control design. Targeted re-sequencing of an enlarged candidate interval (547 kb) in 16 sires with known POLLED genotype did not detect a common allele associated with polled status. In eight sires of Alpine and Scottish origin (four polled versus four horned), we identified a single candidate mutation, a complex 202 bp insertion-deletion event that showed perfect association to the polled phenotype in various European cattle breeds, except Holstein-Friesian. The analysis of the same candidate interval in eight Holsteins identified five candidate variants which segregate as a 260 kb haplotype also perfectly associated with the POLLED gene without recombination or interference with the 202 bp insertion-deletion. We further identified bulls which are progeny tested as homozygous polled but bearing both, 202 bp insertion-deletion and Friesian haplotype. The distribution of genotypes of the two putative POLLED alleles in large semi-random sample (1,261 animals) supports the hypothesis of two independent mutations. PMID:22737241

  15. Chromosome 5 allele loss in human colorectal carcinomas.

    PubMed

    Solomon, E; Voss, R; Hall, V; Bodmer, W F; Jass, J R; Jeffreys, A J; Lucibello, F C; Patel, I; Rider, S H

    That the sporadic and inherited forms of a particular cancer could both result from mutations in the same gene was first proposed by Knudson. He further proposed that these mutations act recessively at the cellular level, and that both copies of the gene must be lost for the cancer to develop. In sporadic cases both events occur somatically whereas in dominant familial cases susceptibility is inherited through a germline mutation and the cancer develops after a somatic change in the homologous allele. This model has since been substantiated in the case of retinoblastoma, Wilms tumour, acoustic neuroma and several other tumours, in which loss of heterozygosity was shown in tumour material compared to normal tissue from the same patient. The dominantly inherited disorder, familial adenomatous polyposis (FAP, also called familial polyposis coli), which gives rise to multiple adenomatous polyps in the colon that have a relatively high probability of progressing to a malignant adenocarcinoma, provides a basis for studying recessive genes in the far more common colorectal carcinomas using this approach. Following a clue as to the location of the FAP gene given by a case report of an individual with an interstitial deletion of chromosome 5q, who had FAP and multiple developmental abnormalities, we have examined sporadic colorectal adenocarcinomas for loss of alleles on chromosome 5. Using a highly polymorphic 'minisatellite' probe which maps to chromosome 5q we have shown that at least 20% of this highly heterogeneous set of tumours lose one of the alleles present in matched normal tissue. This parallels the assignment of the FAP gene to chromosome 5 (see accompanying paper) and suggests that becoming recessive for this gene may be a critical step in the progression of a relatively high proportion of colorectal cancers. PMID:2886919

  16. Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo)

    PubMed Central

    2010-01-01

    Background Land plant genomes contain multiple members of a eukaryote-specific gene family encoding proteins with pentatricopeptide repeat (PPR) motifs. Some PPR proteins were shown to participate in post-transcriptional events involved in organellar gene expression, and this type of function is now thought to be their main biological role. Among PPR genes, restorers of fertility (Rf) of cytoplasmic male sterility systems constitute a peculiar subgroup that is thought to evolve in response to the presence of mitochondrial sterility-inducing genes. Rf genes encoding PPR proteins are associated with very close relatives on complex loci. Results We sequenced a non-restoring allele (L7rfo) of the Rfo radish locus whose restoring allele (D81Rfo) was previously described, and compared the two alleles and their PPR genes. We identified a ca 13 kb long fragment, likely originating from another part of the radish genome, inserted into the L7rfo sequence. The L7rfo allele carries two genes (PPR-1 and PPR-2) closely related to the three previously described PPR genes of the restorer D81Rfo allele (PPR-A, PPR-B, and PPR-C). Our results indicate that alleles of the Rfo locus have experienced complex evolutionary events, including recombination and insertion of extra-locus sequences, since they diverged. Our analyses strongly suggest that present coding sequences of Rfo PPR genes result from intragenic recombination. We found that the 10 C-terminal PPR repeats in Rfo PPR gene encoded proteins result from the tandem duplication of a 5 PPR repeat block. Conclusions The Rfo locus appears to experience more complex evolution than its flanking sequences. The Rfo locus and PPR genes therein are likely to evolve as a result of intergenic and intragenic recombination. It is therefore not possible to determine which genes on the two alleles are direct orthologs. Our observations recall some previously reported data on pathogen resistance complex loci. PMID:20178653

  17. Analysis of the distribution of HLA-A alleles in populations from five continents.

    PubMed

    Middleton, D; Williams, F; Meenagh, A; Daar, A S; Gorodezky, C; Hammond, M; Nascimento, E; Briceno, I; Perez, M P

    2000-10-01

    The variation and frequency of HLA-A genotypes were established by PCR-SSOP typing in diverse geographically distributed populations: Brazilian, Colombian Kogui, Cuban, Mexican, Omani, Singapore Chinese, and South African Zulu. HLA-A allelic families with only one allele were identified for HLA-A*01, -A*23, -A*25, -A*31, -A*32, -A*36, -A*43, -A*69, -A*80; and with two alleles for HLA-A*03, -A*11, -A*26, -A*29, -A*33, -A*34, and -A*66. Greater variation was detected for HLA-A*02, -A*24, and -A*68 allele families. Colombian Kogui and Mexican Seris showed the least diversity with respect to HLA-A alleles, albeit with small numbers tested, with only four and five HLA-A alleles identified, respectively. It would appear by their presence in all populations studied, either rural or indigenous, that certain alleles are very important in pathogen peptide presentation. PMID:11082518

  18. Lipid exchange between membranes.

    PubMed Central

    Jähnig, F

    1984-01-01

    The exchange of lipid molecules between vesicle bilayers in water and a monolayer forming at the water surface was investigated theoretically within the framework of thermodynamics. The total number of exchanged molecules was found to depend on the bilayer curvature as expressed by the vesicle radius and on the boundary condition for exchange, i.e., whether during exchange the radius or the packing density of the vesicles remains constant. The boundary condition is determined by the rate of flip-flop within the bilayer relative to the rate of exchange between bi- and monolayer. If flip-flop is fast, exchange is independent of the vesicle radius; if flip-flop is slow, exchange increases with the vesicle radius. Available experimental results agree with the detailed form of this dependence. When the theory was extended to exchange between two bilayers of different curvature, the direction of exchange was also determined by the curvatures and the boundary conditions for exchange. Due to the dependence of the boundary conditions on flip-flop and, consequently, on membrane fluidity, exchange between membranes may partially be regulated by membrane fluidity. PMID:6518251

  19. Inferring the age of a fixed beneficial allele.

    PubMed

    Ormond, Louise; Foll, Matthieu; Ewing, Gregory B; Pfeifer, Susanne P; Jensen, Jeffrey D

    2016-01-01

    Estimating the age and strength of beneficial alleles is central to understanding how adaptation proceeds in response to changing environmental conditions. Several haplotype-based estimators exist for inferring the age of segregating beneficial mutations. Here, we develop an approximate Bayesian-based approach that rather estimates these parameters for fixed beneficial mutations in single populations. We integrate a range of existing diversity, site frequency spectrum, haplotype- and linkage disequilibrium-based summary statistics. We show that for strong selective sweeps on de novo mutations the method can estimate allele age and selection strength even in nonequilibrium demographic scenarios. We extend our approach to models of selection on standing variation, and co-infer the frequency at which selection began to act upon the mutation. Finally, we apply our method to estimate the age and selection strength of a previously identified mutation underpinning cryptic colour adaptation in a wild deer mouse population, and compare our findings with previously published estimates as well as with geological data pertaining to the presumed shift in selective pressure. PMID:26576754

  20. Allele mining and enhanced genetic recombination for rice breeding.

    PubMed

    Leung, Hei; Raghavan, Chitra; Zhou, Bo; Oliva, Ricardo; Choi, Il Ryong; Lacorte, Vanica; Jubay, Mona Liza; Cruz, Casiana Vera; Gregorio, Glenn; Singh, Rakesh Kumar; Ulat, Victor Jun; Borja, Frances Nikki; Mauleon, Ramil; Alexandrov, Nickolai N; McNally, Kenneth L; Sackville Hamilton, Ruaraidh

    2015-12-01

    Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources. PMID:26606925

  1. A bird's eye view of a deleterious recessive allele.

    PubMed

    Ekblom, Robert

    2016-07-01

    In the endangered Scottish chough (Pyrrhocorax pyrrhocorax) population, a lethal blindness syndrome is found to be caused by a deleterious recessive allele. Photo: Gordon Yates. In Focus: Trask, A.E., Bignal, E.M., McCracken, D.I., Monaghan, P., Piertney, S.B. & Reid, J.M. (2016) Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern. Journal of Animal Ecology, 85, 879-891. In this issue of Journal of Animal Ecology, Trask et al. () report on a strange, lethal, blindness that regularly affects chicks of an endangered bird population. The authors show that the inheritance mode of this blindness disease precisely matches the expectations of a recessive deleterious mutation. Intriguingly, there is also an indication that the disease-causing variant might be maintained in the population by balancing selection, due to a selective advantage for heterozygotes. Could this finding have consequences for conservation actions implemented for the population? PMID:27279331

  2. Assessment of PAX6 alleles in 66 families with aniridia.

    PubMed

    Bobilev, A M; McDougal, M E; Taylor, W L; Geisert, E E; Netland, P A; Lauderdale, J D

    2016-06-01

    We report on PAX6 alleles associated with a clinical diagnosis of classical aniridia in 81 affected individuals representing 66 families. Allelic variants expected to affect PAX6 function were identified in 61 families (76 individuals). Ten cases of sporadic aniridia (10 families) had complete (8 cases) or partial (2 cases) deletion of the PAX6 gene. Sequence changes that introduced a premature termination codon into the open reading frame of PAX6 occurred in 47 families (62 individuals). Three individuals with sporadic aniridia (three families) had sequence changes (one deletion, two run-on mutations) expected to result in a C-terminal extension. An intronic deletion of unknown functional significance was detected in one case of sporadic aniridia (one family), but not in unaffected relatives. Within these 61 families, single nucleotide substitutions accounted for 30/61 (49%), indels for 23/61 (38%), and complete deletion of the PAX6 locus for 8/61 (13%). In five cases of sporadic aniridia (five families), no disease-causing mutation in the coding region was detected. In total, 23 unique variants were identified that have not been reported in the Leiden Open Variation Database (LOVD) database. Within the group assessed, 92% had sequence changes expected to reduce PAX6 function, confirming the primacy of PAX6 haploinsufficiency as causal for aniridia. PMID:26661695

  3. An allele of the crm gene blocks cyanobacterial circadian rhythms

    PubMed Central

    Boyd, Joseph S.; Bordowitz, Juliana R.; Bree, Anna C.; Golden, Susan S.

    2013-01-01

    The SasA-RpaA two-component system constitutes a key output pathway of the cyanobacterial Kai circadian oscillator. To date, rhythm of phycobilisome associated (rpaA) is the only gene other than kaiA, kaiB, and kaiC, which encode the oscillator itself, whose mutation causes completely arrhythmic gene expression. Here we report a unique transposon insertion allele in a small ORF located immediately upstream of rpaA in Synechococcus elongatus PCC 7942 termed crm (for circadian rhythmicity modulator), which results in arrhythmic promoter activity but does not affect steady-state levels of RpaA. The crm ORF complements the defect when expressed in trans, but only if it can be translated, suggesting that crm encodes a small protein. The crm1 insertion allele phenotypes are distinct from those of an rpaA null; crm1 mutants are able to grow in a light:dark cycle and have no detectable oscillations of KaiC phosphorylation, whereas low-amplitude KaiC phosphorylation rhythms persist in the absence of RpaA. Levels of phosphorylated RpaA in vivo measured over time are significantly altered compared with WT in the crm1 mutant as well as in the absence of KaiC. Taken together, these results are consistent with the hypothesis that the Crm polypeptide modulates a circadian-specific activity of RpaA. PMID:23918383

  4. Allele frequency of CODIS 13 in Indonesian population.

    PubMed

    Untoro, Evi; Atmadja, Djaja Surya; Pu, Chang-En; Wu, Fang-Chi

    2009-04-01

    Since the first application of DNA technology in 1985 in forensic cases, and the acceptance of this technology in 1988 at court, the DNA typing is widely used in personal identification, parentage cases and tracing the source of biological samples found in the crime scene. The FBI on 1990 had recommended the forensic labs to used 13 loci of Short Tandem Repeats (STR), known as CODIS 13, as the loci of choice for forensic use. The research on the population DNA database on these loci is extremely important for calculating the Paternity Index as well as Matching Probability for forensic application of DNA technology. As many as 402 unrelated persons, consisted of 322 from western part of Indonesia and 80 from eastern part of Indonesia, were chosen as the respondents of this research, after signing the informed consent. The peripheral blood sample was taken using sterile lancets and dropped onto FTA classic cards. The DNA was extracted by FTA purification solution (3x) and TE(-1) (2x), and amplified by PCR mix, either Cofiler or Profiler Plus (Perkin Elmers), followed by sequencing using ABI Prism type 3100 Avant Genetic Analyzer. The analysis showed that the alleles frequencies of Indonesian is specific, different with the other Asian populations with some specific alleles and microvariant were found. PMID:19261522

  5. Cytochrome allelic variants and clopidogrel metabolism in cardiovascular diseases therapy.

    PubMed

    Jarrar, Mohammed; Behl, Shalini; Manyam, Ganiraju; Ganah, Hany; Nazir, Mohammed; Nasab, Reem; Moustafa, Khaled

    2016-06-01

    Clopidogrel and aspirin are among the most prescribed dual antiplatelet therapies to treat the acute coronary syndrome and heart attacks. However, their potential clinical impacts are a subject of intense debates. The therapeutic efficiency of clopidogrel is controlled by the actions of hepatic cytochrome P450 (CYPs) enzymes and impacted by individual genetic variations. Inter-individual polymorphisms in CYPs enzymes affect the metabolism of clopidogrel into its active metabolites and, therefore, modify its turnover and clinical outcome. So far, clinical trials fail to confirm higher or lower adverse cardiovascular effects in patients treated with combinations of clopidogrel and proton pump inhibitors, compared with clopidogrel alone. Such inconclusive findings may be due to genetic variations in the cytochromes CYP2C19 and CYP3A4/5. To investigate potential interactions/effects of these cytochromes and their allele variants on the treatment of acute coronary syndrome with clopidogrel alone or in combination with proton pump inhibitors, we analyze recent literature and discuss the potential impact of the cytochrome allelic variants on cardiovascular events and stent thrombosis treated with clopidogrel. The diversity of CYP2C19 polymorphisms and prevalence span within various ethnic groups, subpopulations and demographic areas are also debated. PMID:27072373

  6. Insulin Like Growth Factor 2 Expression in the Rat Brain Both in Basal Condition and following Learning Predominantly Derives from the Maternal Allele

    PubMed Central

    Ye, Xiaojing; Kohtz, Amy; Pollonini, Gabriella; Riccio, Andrea; Alberini, Cristina M.

    2015-01-01

    Insulin like growth factor 2 (Igf2) is known as a maternally imprinted gene involved in growth and development. Recently, Igf2 was found to also be regulated and required in the adult rat hippocampus for long-term memory formation, raising the question of its allelic regulation in adult brain regions following experience and in cognitive processes. We show that, in adult rats, Igf2 is abundantly expressed in brain regions involved in cognitive functions, like hippocampus and prefrontal cortex, compared to the peripheral tissues. In contrast to its maternal imprinting in peripheral tissues, Igf2 is mainly expressed from the maternal allele in these brain regions. The training-dependent increase in Igf2 expression derives proportionally from both parental alleles, and, hence, is mostly maternal. Thus, Igf2 parental expression in the adult rat brain does not follow the imprinting rules found in peripheral tissues, suggesting differential expression regulation and functions of imprinted genes in the brain. PMID:26495851

  7. PAP-LMPCR for improved, allele-specific footprinting and automated chromatin fine structure analysis

    PubMed Central

    Ingram, R.; Gao, C.; LeBon, J.; Liu, Q.; Mayoral, R. J.; Sommer, S. S.; Hoogenkamp, M.; Riggs, A. D.; Bonifer, C.

    2008-01-01

    The analysis of chromatin fine structure and transcription factor occupancy of differentially expressed genes by in vivo footprinting and ligation-mediated-PCR (LMPCR) is a powerful tool to understand the impact of chromatin on gene expression. However, as with all PCR-based techniques, the accuracy of the experiments has often been reduced by sequence similarities and the presence of GC-rich or repeat sequences, and some sequences are completely refractory to analysis. Here we describe a novel method, pyrophosphorolysis activated polymerization LMPCR or PAP-LMPCR, which is capable of generating accurate and reproducible footprints specific for individual alleles and can read through sequences previously not accessible for analysis. In addition, we have adapted this technique for automation, thus enabling the simultaneous and rapid analysis of chromatin structure at many different genes. PMID:18208840

  8. Population-ethnic group specific genome variation allele frequency data: a querying and visualization journey.

    PubMed

    Viennas, Emmanouil; Gkantouna, Vassiliki; Ioannou, Marina; Georgitsi, Marianthi; Rigou, Maria; Poulas, Konstantinos; Patrinos, George P; Tzimas, Giannis

    2012-08-01

    National/ethnic mutation databases aim to document the genetic heterogeneity in various populations and ethnic groups worldwide. We have previously reported the development and upgrade of FINDbase (www.findbase.org), a database recording causative mutations and pharmacogenomic marker allele frequencies in various populations around the globe. Although this database has recently been upgraded, we continuously try to enhance its functionality by providing more advanced visualization tools that would further assist effective data querying and comparisons. We are currently experimenting in various visualization techniques on the existing FINDbase causative mutation data collection aiming to provide a dynamic research tool for the worldwide scientific community. We have developed an interactive web-based application for population-based mutation data retrieval. It supports sophisticated data exploration allowing users to apply advanced filtering criteria upon a set of multiple views of the underlying data collection and enables browsing the relationships between individual datasets in a novel and meaningful way. PMID:22659238

  9. Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes

    PubMed Central

    2014-01-01

    Background Pathogens and their vectors are organisms whose ecology is often only accessible through population genetics tools based on spatio-temporal variability of molecular markers. However, molecular tools may present technical difficulties due to the masking of some alleles (allelic dropouts and/or null alleles), which tends to bias the estimation of heterozygosity and thus the inferences concerning the breeding system of the organism under study. This is especially critical in clonal organisms in which deviation from panmixia, as measured by Wright’s FIS, can, in principle, be used to infer both the extent of clonality and structure in a given population. In particular, null alleles and allelic dropouts are locus specific and likely produce high variance of Wright’s FIS across loci, as rare sex is expected to do. In this paper we propose a tool enabling to discriminate between consequences of these technical problems and those of rare sex. Methods We have performed various simulations of clonal and partially clonal populations. We introduce allelic dropouts and null alleles in clonal data sets and compare the results with those that exhibit increasing rates of sexual recombination. We use the narrow relationship that links Wright’s FIS to genetic diversity in purely clonal populations as assessment criterion, since this relationship disappears faster with sexual recombination than with amplification problems of certain alleles. Results We show that the relevance of our criterion for detecting poorly amplified alleles depends partly on the population structure, the level of homoplasy and/or mutation rate. However, the interpretation of data becomes difficult when the number of poorly amplified alleles is above 50%. The application of this method to reinterpret published data sets of pathogenic clonal microbes (yeast and trypanosomes) confirms its usefulness and allows refining previous estimates concerning important pathogenic agents. Conclusion Our

  10. An Allele of Sequoia Dominantly Enhances a Trio Mutant Phenotype to Influence Drosophila Larval Behavior

    PubMed Central

    Liebl, Eric C.

    2013-01-01

    The transition of Drosophila third instar larvae from feeding, photo-phobic foragers to non-feeding, photo-neutral wanderers is a classic behavioral switch that precedes pupariation. The neuronal network responsible for this behavior has recently begun to be defined. Previous genetic analyses have identified signaling components for food and light sensory inputs and neuropeptide hormonal outputs as being critical for the forager to wanderer transition. Trio is a Rho-Guanine Nucleotide Exchange Factor integrated into a variety of signaling networks including those governing axon pathfinding in early development. Sequoia is a pan-neuronally expressed zinc-finger transcription factor that governs dendrite and axon outgrowth. Using pre-pupal lethality as an endpoint, we have screened for dominant second-site enhancers of a weakly lethal trio mutant background. In these screens, an allele of sequoia has been identified. While these mutants have no obvious disruption of embryonic central nervous system architecture and survive to third instar larvae similar to controls, they retain forager behavior and thus fail to pupariate at high frequency. PMID:24376789

  11. Tetra-allelic SNPs: Informative forensic markers compiled from public whole-genome sequence data.

    PubMed

    Phillips, C; Amigo, J; Carracedo, Á; Lareu, M V

    2015-11-01

    Multiple-allele single nucleotide polymorphisms (SNPs) are potentially useful for forensic DNA analysis as they can provide more discrimination power than normal binary SNPs. In addition, the presence in a profile of more than two alleles per marker provides a clearer indication of mixed DNA than assessments of imbalanced signals in the peak pairs of binary SNPs. Using the 1000 Genomes Phase III human variant data release of 2014 as the starting point, this study collated 961 tetra-allelic SNPs that pass minimum sequence quality thresholds and where four separate nucleotide substitution alleles were detected. Although most of these loci had three of the four alleles in combined frequencies of 2% or less, 160 had high heterozygosities with 50 exceeding those of 'ideal' 0.5:0.5 binary SNPs. From this set of most polymorphic tetra-allelic SNPs, we identified markers most informative for forensic purposes and explored these loci in detail. Subsets of the most polymorphic tetra-allelic SNPs will make useful additions to current panels of forensic identification SNPs and ancestry-informative SNPs. The 24 most discriminatory tetra-allelic SNPs were estimated to detect more than two alleles in at least one marker per profile in 99.9% of mixtures of African contributors. In European contributor mixtures 99.4% of profiles would show multiple allele patterns, but this drops to 92.6% of East Asian contributor mixtures due to reduced levels of polymorphism for the 24 SNPs in this population group. PMID:26209763

  12. Bhlhb5::flpo allele uncovers a requirement for Bhlhb5 for the development of the dorsal cochlear nucleus.

    PubMed

    Cai, Xiaoyun; Kardon, Adam P; Snyder, Lindsey M; Kuzirian, Marissa S; Minestro, Sam; de Souza, Luiza; Rubio, Maria E; Maricich, Stephen M; Ross, Sarah E

    2016-06-15

    Auditory information is initially processed in the cochlear nuclei before being relayed to the brain. The cochlear nuclei are subdivided into dorsal, anterior ventral, and posterior ventral domains, each containing several subtypes of neurons that are thought to play discrete roles in the processing of sound. However, the ontogeny of these neurons is poorly understood, and this gap in knowledge hampers efforts to understand the basic neural circuitry of this nucleus. Here, we reveal that Bhlhb5 is expressed in both excitatory (unipolar brush cells) and inhibitory neurons (cartwheel cells) of the DCN during development. To gain genetic access to Bhlhb5-expressing neurons in the DCN, we generated a Bhlhb5::flpo knockin allele. Using an intersectional genetic strategy, we labeled cartwheel cells, thereby providing proof of concept that subpopulations of Bhlhb5-expressing neurons can be genetically targeted. Moreover, fate-mapping experiments using this allele revealed that Bhlhb5 is required for the proper development of the DCN, since mice lacking Bhlhb5 showed a dramatically diminished number of neurons, including unipolar brush and cartwheel cells. Intriguingly, the Bhlhb5::flpo allele also genetically labels numerous other regions of the nervous system that process sensory input, including the dorsal horn, the retina, and the nucleus of the lateral olfactory tract, hinting at a more general role for Bhlhb5 in the development of neurons that mediate sensory integration. PMID:27151208

  13. Bhlhb5::flpo allele uncovers a requirement for Bhlhb5 for the development of the dorsal cochlear nucleus

    PubMed Central

    Cai, Xiaoyun; Kardon, Adam P.; Snyder, Lindsey M.; Kuzirian, Marissa S.; Minestro, Sam; de Souza, Luiza; Rubio, Maria E.; Maricich, Stephen M.; Ross, Sarah E.

    2016-01-01

    Auditory information is initially processed in the cochlear nuclei before being relayed to the brain. The cochlear nuclei are subdivided into dorsal, anterior ventral, and posterior ventral domains, each containing several subtypes of neurons that are thought to play discrete roles in the processing of sound. However, the ontogeny of these neurons is poorly understood, and this gap in knowledge hampers efforts to understand the basic neural circuitry of this nucleus. Here, we reveal that Bhlhb5 is expressed in both excitatory (unipolar brush cells) and inhibitory neurons (cartwheel cells) of the DCN during development. To gain genetic access to Bhlhb5-expressing neurons in the DCN, we generated a Bhlhb5::flpo knockin allele. Using an intersectional genetic strategy, we labeled cartwheel cells, thereby providing proof of concept that subpopulations of Bhlhb5-expressing neurons can be genetically targeted. Moreover, fate-mapping experiments using this allele revealed that Bhlhb5 is required for the proper development of the DCN, since mice lacking Bhlhb5 showed a dramatically diminished number of neurons, including unipolar brush and cartwheel cells. Intriguingly, the Bhlhb5::flpo allele also genetically labels numerous other regions of the nervous system that process sensory input, including the dorsal horn, the retina, and the nucleus of the lateral olfactory tract, hinting at a more general role for Bhlhb5 in the development of neurons that mediate sensory integration. PMID:27151208

  14. Ethylnitrosourea Mutagenesis and the Isolation of Mutant Alleles for Specific Genes Located in the t Region of Mouse Chromosome 17

    PubMed Central

    Bode, Vernon C.

    1984-01-01

    Ethylnitrosourea mutagenesis of spermatogonia in male mice is very efficient and makes it practical to isolate new desired mutant alleles by subsequent progeny screening. This is demonstrated for three genes in the t region of chromosome 17. The first, a mutation designated t-int, interacts with the dominant mutation, T (Brachyury), to produce a tailless mouse. Previously, mutant alleles of the t-int gene were available only in t haplotypes, where they are part of a t chromatin block within which recombination with wild-type chromosomes is inhibited. In addition to t-int, new mutations at the quaking and tufted loci were obtained, as well as at several loci not on chromosome 17, e.g., an X-linked lethal that causes a mottled phenotype in the heterozygote and four new mutant W alleles on chromosome 5. In the experiment, an average of one fertilizing spermatozoan in 1500 was mutant at a given locus and an average of one male in five was able to sire mutants at that locus. PMID:6500258

  15. Two Photon Exchange for Exclusive Pion Electroproduction

    SciTech Connect

    Afanaciev, Andrei V.; Aleksejevs, Aleksandrs G.; Barkanova, Svetlana G.

    2013-09-01

    We perform detailed calculations of two-photon-exchange QED corrections to the cross section of pion electroproduction. The results are obtained with and without the soft-photon approximation; analytic expressions for the radiative corrections are derived. The relative importance of the two-photon correction is analyzed for the kinematics of several experiments at Jefferson Lab. A significant, over 20%, effect due to two-photon exchange is predicted for the backward angles of electron scattering at large transferred momenta.

  16. The induction of nitric oxide response of carp macrophages by transferrin is influenced by the allelic diversity of the molecule.

    PubMed

    Jurecka, Patrycja; Irnazarow, Ilgiz; Stafford, James L; Ruszczyk, Aleksandra; Taverne, Nico; Belosevic, Miodrag; Savelkoul, Huub F J; Wiegertjes, Geert F

    2009-04-01

    The central role of transferrin (Tf) as an iron transporting protein has been extended by observations that modified versions of Tf also participate in the regulation of innate immunity. We report on the isolation of two carp Tf proteins (alleles D and G) to purity using rivanol precipitation and ion-exchange chromatography, and describe the activation of head kidney-derived carp macrophages by cleaved Tf. We demonstrate the superiority of the D-type over the G-type Tf in inducing nitric oxide (NO) and confirm previous observations that full-length Tf cannot induce NO in fish macrophages. We believe that cleaved Tf fragments should be considered to be "alarmins". We discuss the possibility that parasites such as Trypanoplasma borreli cleave Tf and use Tf fragments to their advantage by modulating the NO induction in carp macrophages. PMID:18996204

  17. Insect gas exchange patterns: a phylogenetic perspective.

    PubMed

    Marais, Elrike; Klok, C Jaco; Terblanche, John S; Chown, Steven L

    2005-12-01

    Most investigations of insect gas exchange patterns and the hypotheses proposed to account for their evolution have been based either on small-scale, manipulative experiments, or comparisons of a few closely related species. Despite their potential utility, no explicit, phylogeny-based, broad-scale comparative studies of the evolution of gas exchange in insects have been undertaken. This may be due partly to the preponderance of information for the endopterygotes, and its scarcity for the apterygotes and exopterygotes. Here we undertake such a broad-scale study. Information on gas exchange patterns for the large majority of insects examined to date (eight orders, 99 species) is compiled, and new information on 19 exemplar species from a further ten orders, not previously represented in the literature (Archaeognatha, Zygentoma, Ephemeroptera, Odonata, Mantodea, Mantophasmatodea, Phasmatodea, Dermaptera, Neuroptera, Trichoptera), is provided. These data are then used in a formal, phylogeny-based parsimony analysis of the evolution of gas exchange patterns at the order level. Cyclic gas exchange is likely to be the ancestral gas exchange pattern at rest (recognizing that active individuals typically show continuous gas exchange), and discontinuous gas exchange probably originated independently a minimum of five times in the Insecta. PMID:16339869

  18. DOE/ANL/HTRI heat exchanger tube vibration data bank

    SciTech Connect

    Halle, H.; Chenoweth, J.M.; Wambsganss, M.W.

    1981-01-01

    This addendum to the DOE/ANL/HTRI Heat Exchanger Tube Vibration Data Bank includes 16 new case histories of field experiences. The cases include several exchangers that did not experience vibration problems and several for which acoustic vibration was reported.

  19. Nonsurvivable momentum exchange system

    NASA Technical Reports Server (NTRS)

    Roder, Russell (Inventor); Ahronovich, Eliezer (Inventor); Davis, III, Milton C. (Inventor)

    2007-01-01

    A demiseable momentum exchange system includes a base and a flywheel rotatably supported on the base. The flywheel includes a web portion defining a plurality of web openings and a rim portion. The momentum exchange system further includes a motor for driving the flywheel and a cover for engaging the base to substantially enclose the flywheel. The system may also include components having a melting temperature below 1500 degrees Celsius. The momentum exchange system is configured to demise on reentry.

  20. Allelic diversity at the DLA-88 locus in Golden Retriever and Boxer breeds is limited.

    PubMed

    Ross, P; Buntzman, A S; Vincent, B G; Grover, E N; Gojanovich, G S; Collins, E J; Frelinger, J A; Hess, P R

    2012-08-01

    In the dog, previous analyses of major histocompatibility complex class I genes suggest a single polymorphic locus, dog leukocyte antigen (DLA)-88. While 51 alleles have been reported, estimates of prevalence have not been made. We hypothesized that, within a breed, DLA-88 diversity would be restricted, and one or more dominant alleles could be identified. Accordingly, we determined allele usage in 47 Golden Retrievers and 39 Boxers. In each population, 10 alleles were found; 4 were shared. Seven novel alleles were identified. DLA-88*05101 and *50801 predominated in Golden Retrievers, while most Boxers carried *03401. In these breeds, DLA-88 polymorphisms are limited and largely non-overlapping. The finding of highly prevalent alleles fulfills an important prerequisite for studying canine CD8+ T-cell responses. PMID:22571293

  1. An Allele Real-Coded Quantum Evolutionary Algorithm Based on Hybrid Updating Strategy.

    PubMed

    Zhang, Yu-Xian; Qian, Xiao-Yi; Peng, Hui-Deng; Wang, Jian-Hui

    2016-01-01

    For improving convergence rate and preventing prematurity in quantum evolutionary algorithm, an allele real-coded quantum evolutionary algorithm based on hybrid updating strategy is presented. The real variables are coded with probability superposition of allele. A hybrid updating strategy balancing the global search and local search is presented in which the superior allele is defined. On the basis of superior allele and inferior allele, a guided evolutionary process as well as updating allele with variable scale contraction is adopted. And H ε gate is introduced to prevent prematurity. Furthermore, the global convergence of proposed algorithm is proved by Markov chain. Finally, the proposed algorithm is compared with genetic algorithm, quantum evolutionary algorithm, and double chains quantum genetic algorithm in solving continuous optimization problem, and the experimental results verify the advantages on convergence rate and search accuracy. PMID:27057159

  2. An Allele Real-Coded Quantum Evolutionary Algorithm Based on Hybrid Updating Strategy

    PubMed Central

    Zhang, Yu-Xian; Qian, Xiao-Yi; Peng, Hui-Deng; Wang, Jian-Hui

    2016-01-01

    For improving convergence rate and preventing prematurity in quantum evolutionary algorithm, an allele real-coded quantum evolutionary algorithm based on hybrid updating strategy is presented. The real variables are coded with probability superposition of allele. A hybrid updating strategy balancing the global search and local search is presented in which the superior allele is defined. On the basis of superior allele and inferior allele, a guided evolutionary process as well as updating allele with variable scale contraction is adopted. And Hε gate is introduced to prevent prematurity. Furthermore, the global convergence of proposed algorithm is proved by Markov chain. Finally, the proposed algorithm is compared with genetic algorithm, quantum evolutionary algorithm, and double chains quantum genetic algorithm in solving continuous optimization problem, and the experimental results verify the advantages on convergence rate and search accuracy. PMID:27057159

  3. Two classes of deleterious recessive alleles in a natural population of zebrafish, Danio rerio.

    PubMed Central

    McCune, Amy R.; Houle, David; McMillan, Kyle; Annable, Rebecca; Kondrashov, Alexey S.

    2004-01-01

    Natural populations carry deleterious recessive alleles which cause inbreeding depression. We compared mortality and growth of inbred and outbred zebrafish, Danio rerio, between 6 and 48 days of age. Grandparents of the studied fish were caught in the wild. Inbred fish were generated by brother-sister mating. Mortality was 9% in outbred fish, and 42% in inbred fish, which implies at least 3.6 lethal equivalents of deleterious recessive alleles per zygote. There was no significant inbreeding depression in the growth, perhaps because the surviving inbred fish lived under less crowded conditions. In contrast to alleles that cause embryonic and early larval mortality in the same population, alleles responsible for late larval and early juvenile mortality did not result in any gross morphological abnormalities. Thus, deleterious recessive alleles that segregate in a wild zebrafish population belong to two sharply distinct classes: early-acting, morphologically overt, unconditional lethals; and later-acting, morphologically cryptic, and presumably milder alleles. PMID:15451692

  4. Allelic diversity at the DLA-88 locus in Golden Retriever and Boxer breeds is limited

    PubMed Central

    Ross, Peter; Buntzman, Adam S.; Vincent, Benjamin G.; Grover, Elise N.; Gojanovich, Gregory S.; Collins, Edward J.; Frelinger, Jeffrey A.; Hess, Paul R.

    2012-01-01

    In the dog, previous analyses of major histocompatibility complex (MHC) class I genes suggest a single polymorphic locus, Dog Leukocyte Antigen (DLA)-88. While 51 alleles have been reported, estimates of prevalence have not been made. We hypothesized that, within a breed, DLA-88 diversity would be restricted, and one or more dominant alleles could be identified. Accordingly, we determined allele usage in 47 Golden Retrievers and 39 Boxers. In each population, 10 alleles were found; 4 were shared. Seven novel alleles were identified. DLA-88*05101 and *50801 predominated in Golden Retrievers, while most Boxers carried *03401. In these breeds DLA-88 polymorphisms are limited and largely non-overlapping. The finding of highly prevalent alleles fulfills an important prerequisite for studying canine CD8+ T-cell responses. PMID:22571293

  5. Introgressive hybridization: brown bears as vectors for polar bear alleles.

    PubMed

    Hailer, Frank

    2015-03-01

    The dynamics and consequences of introgression can inform about numerous evolutionary processes. Biologists have therefore long been interested in hybridization. One challenge, however, lies in the identification of nonadmixed genotypes that can serve as a baseline for accurate quantification of admixture. In this issue of Molecular Ecology, Cahill et al. (2015) analyse a genomic data set of 28 polar bears, eight brown bears and one American black bear. Polar bear alleles are found to be introgressed into brown bears not only near a previously identified admixture zone on the Alaskan Admiralty, Baranof and Chichagof (ABC) Islands, but also far into the North American mainland. Elegantly contrasting admixture levels at autosomal and X chromosomal markers, Cahill and colleagues infer that male-biased dispersal has spread these introgressed alleles away from the Late Pleistocene contact zone. Compared to a previous study on the ABC Island population in which an Alaskan brown bear served as a putatively admixture-free reference, Cahill et al. (2015) utilize a newly sequenced Swedish brown bear as admixture baseline. This approach reveals that brown bears have been impacted by introgression from polar bears to a larger extent (up to 8.8% of their genome), than previously known, including the bear that had previously served as admixture baseline. No evidence for introgression of brown bear into polar bear is found, which the authors argue could be a consequence of selection. Besides adding new exciting pieces to the puzzle of polar/brown bear evolutionary history, the study by Cahill and colleagues highlights that wildlife genomics is moving from analysing single genomes towards a landscape genomics approach. PMID:25775930

  6. Text Exchange System

    NASA Technical Reports Server (NTRS)

    Snyder, W. V.; Hanson, R. J.

    1986-01-01

    Text Exchange System (TES) exchanges and maintains organized textual information including source code, documentation, data, and listings. System consists of two computer programs and definition of format for information storage. Comprehensive program used to create, read, and maintain TES files. TES developed to meet three goals: First, easy and efficient exchange of programs and other textual data between similar and dissimilar computer systems via magnetic tape. Second, provide transportable management system for textual information. Third, provide common user interface, over wide variety of computing systems, for all activities associated with text exchange.

  7. Allelic Spectra of Risk SNPs Are Different for Environment/Lifestyle Dependent versus Independent Diseases

    PubMed Central

    Amos, Christopher I.

    2015-01-01

    Genome-wide association studies (GWAS) have generated sufficient data to assess the role of selection in shaping allelic diversity of disease-associated SNPs. Negative selection against disease risk variants is expected to reduce their frequencies making them overrepresented in the group of minor (<50%) alleles. Indeed, we found that the overall proportion of risk alleles was higher among alleles with frequency <50% (minor alleles) compared to that in the group of major alleles. We hypothesized that negative selection may have different effects on environment (or lifestyle)-dependent versus environment (or lifestyle)-independent diseases. We used an environment/lifestyle index (ELI) to assess influence of environmental/lifestyle factors on disease etiology. ELI was defined as the number of publications mentioning “environment” or “lifestyle” AND disease per 1,000 disease-mentioning publications. We found that the frequency distributions of the risk alleles for the diseases with strong environmental/lifestyle components follow the distribution expected under a selectively neutral model, while frequency distributions of the risk alleles for the diseases with weak environmental/lifestyle influences is shifted to the lower values indicating effects of negative selection. We hypothesized that previously selectively neutral variants become risk alleles when environment changes. The hypothesis of ancestrally neutral, currently disadvantageous risk-associated alleles predicts that the distribution of risk alleles for the environment/lifestyle dependent diseases will follow a neutral model since natural selection has not had enough time to influence allele frequencies. The results of our analysis suggest that prediction of SNP functionality based on the level of evolutionary conservation may not be useful for SNPs associated with environment/lifestyle dependent diseases. PMID:26201053

  8. Sex differences in the JAK2V617F allele burden in chronic myeloproliferative disorders

    PubMed Central

    Stein, Brady L.; Williams, Donna M.; Wang, Nae-Yuh; Rogers, Ophelia; Isaacs, Mary Ann; Pemmaraju, Naveen; Spivak, Jerry L.; Moliterno, Alison R.

    2010-01-01

    Background The JAK2V617F allele burden is a variable measure, determined by the frequency of mitotic recombination events and the expansion of JAK2V617F clones. Since variability in the JAK2V617F allele burden is partly responsible for the distinct phenotypes seen in the myeloproliferative disorders, the objective of this study was to identify modifiers of the allele burden. Design and Methods Blood samples were obtained between May 2005 and January 2009 from 272 patients with essential thrombocytosis, polycythemia vera, and myelofibrosis. The JAK2V617F allele burden was measured by an allele-specific quantitative polymerase chain reaction using DNA from purified neutrophils. Repeated measures, on average 2 years apart, were available for 104 patients. Results Sex, age at diagnosis, and disease duration all independently influenced the JAK2V617F allele burden. When considering all patients with myeloproliferative disorders, women had significantly lower allele burdens than men (P=0.04). In those patients with repeated measures, the increase in allele burden per year between the first and second evaluations was significantly less in females than in males. Among those who experienced disease evolution, females were 4.5 times more likely to have evolution from essential thrombocytosis to polycythemia vera, but 0.23 times as likely to have evolution from essential thrombocytosis to myelofibrosis. Conclusions Sex is an independent factor accounting for variability in the JAK2V617F allele burden. We speculate that lower allele burdens in females reflect a lower frequency of mitotic recombination events in females than in males, and should be considered when evaluating the relationship of allele burden to disease phenotype and also in evaluating responses to JAK2V617F-inhibitors. Because sex may influence genotype and/or clonal expansion, underpinning the variability in JAK2V617F allele burden, it will be important to explore factors that determine susceptibility to

  9. Association of apolipoprotein E allele {epsilon}4 with late-onset sporadic Alzheimer`s disease

    SciTech Connect

    Lucotte, G.; David, F.; Berriche, S.

    1994-09-15

    Apolipoprotein E, type {epsilon}4 allele (ApoE {epsilon}4), is associated with late-onset sporadic Alzheimer`s disease (AD) in French patients. The association is highly significant (0.45 AD versus 0.12 controls for {epsilon}4 allele frequencies). These data support the involvement of ApoE {epsilon}4 allele as a very important risk factor for the clinical expression of AD. 22 refs., 1 fig., 3 tabs.

  10. Identification of alleles of carotenoid pathway genes important for zeaxanthin accumulation in potato tubers

    PubMed Central

    Uitdewilligen, Jan G. A. M. L.; Kloosterman, Bjorn A.; Hutten, Ronald C. B.; Visser, Richard G. F.; van Eck, Herman J.

    2010-01-01

    We have investigated the genetics and molecular biology of orange flesh colour in potato (Solanum tuberosum L.). To this end the natural diversity in three genes of the carotenoid pathway was assessed by SNP analyses. Association analysis was performed between SNP haplotypes and flesh colour phenotypes in diploid and tetraploid potato genotypes. We observed that among eleven beta-carotene hydroxylase 2 (Chy2) alleles only one dominant allele has a major effect, changing white into yellow flesh colour. In contrast, none of the lycopene epsilon cyclase (Lcye) alleles seemed to have a large effect on flesh colour. Analysis of zeaxanthin epoxidase (Zep) alleles showed that all (diploid) genotypes with orange tuber flesh were homozygous for one specific Zep allele. This Zep allele showed a reduced level of expression. The complete genomic sequence of the recessive Zep allele, including the promoter, was determined, and compared with the sequence of other Zep alleles. The most striking difference was the presence of a non-LTR retrotransposon sequence in intron 1 of the recessive Zep allele, which was absent in all other Zep alleles investigated. We hypothesise that the presence of this large sequence in intron 1 caused the lower expression level, resulting in reduced Zep activity and accumulation of zeaxanthin. Only genotypes combining presence of the dominant Chy2 allele with homozygosity for the recessive Zep allele produced orange-fleshed tubers that accumulated large amounts of zeaxanthin. Electronic supplementary material The online version of this article (doi:10.1007/s11103-010-9647-y) contains supplementary material, which is available to authorized users. PMID:20490894

  11. Functional alleles of the flowering time regulator FRIGIDA in the Brassica oleracea genome

    PubMed Central

    2012-01-01

    Background Plants adopt different reproductive strategies as an adaptation to growth in a range of climates. In Arabidopsis thaliana FRIGIDA (FRI) confers a vernalization requirement and thus winter annual habit by increasing the expression of the MADS box transcriptional repressor FLOWERING LOCUS C (FLC). Variation at FRI plays a major role in A. thaliana life history strategy, as independent loss-of-function alleles that result in a rapid-cycling habit in different accessions, appear to have evolved many times. The aim of this study was to identify and characterize orthologues of FRI in Brassica oleracea. Results We describe the characterization of FRI from Brassica oleracea and identify the two B. oleracea FRI orthologues (BolC.FRI.a and BolC.FRI.b). These show extensive amino acid conservation in the central and C-terminal regions to FRI from other Brassicaceae, including A. thaliana, but have a diverged N-terminus. The genes map to two of the three regions of B. oleracea chromosomes syntenic to part of A. thaliana chromosome 5 suggesting that one of the FRI copies has been lost since the ancient triplication event that formed the B. oleracea genome. This genomic position is not syntenic with FRI in A. thaliana and comparative analysis revealed a recombination event within the A. thaliana FRI promoter. This relocated A. thaliana FRI to chromosome 4, very close to the nucleolar organizer region, leaving a fragment of FRI in the syntenic location on A. thaliana chromosome 5. Our data show this rearrangement occurred after the divergence from A. lyrata. We explored the allelic variation at BolC.FRI.a within cultivated B. oleracea germplasm and identified two major alleles, which appear equally functional both to each other and A. thaliana FRI, when expressed as fusions in A. thaliana. Conclusions We identify the two Brassica oleracea FRI genes, one of which we show through A. thaliana complementation experiments is functional, and show their genomic location is

  12. HLA Allele Frequencies in 5802 Koreans: Varied Allele Types Associated with SJS/TEN According to Culprit Drugs

    PubMed Central

    Park, Hye Jung; Kim, Young Joo; Kim, Dong Hyun; Kim, Junho; Park, Kyung Hee; Park, Jung-Won

    2016-01-01

    Purpose Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are very serious forms of drug-induced cutaneous adverse reaction. SJS/TEN induced by certain drug is well known to be associated with some human leukocyte antigen (HLA) gene type. We aimed to explore HLA allele frequencies and their association with SJS/TEN according to culprit drugs in Korea. Materials and Methods We enrolled 5802 subjects who had results of HLA typing test from August 2005 to July 2014. Total 28 SJS/TEN patients were categorized based on culprit drugs (allopurinol, lamotrigine, carbamazepine) and identified the presence of HLA-B*58:01, HLA-B*44:03, HLA-B*15:02, and HLA-A*31:01. Results HLA-A*24:02 (20.5%), HLA-B*44:03 (10.0%), and HLA-Cw*01:02 (17.1%) were the most frequent type in HLA-A, -B, and -C genes, respectively. Allele frequencies of HLA-B*58:01, HLA-B*44:03, HLA-A*31:01, and HLA-B*15:02 were 7.0%, 10.0%, 5.0%, and 0.3%, respectively. In 958 allopurinol users, 9 subjects (0.9%) were diagnosed with SJS/TEN. Among them, 8 subjects possessed HLA-B*58:01 allele. SJS/TEN induced by allopurinol was more frequently developed in subjects with HLA-B*58:01 than in subjects without it [odds ratio: 57.4; confidence interval (CI) 7.12-463.50; p<0.001]. Allopurinol treatment, based on screening by HLA-B*58:01 genotyping, could be more cost-effective than that not based on screening. HLA-B*44:03 may be associated with lamotrigine-induced SJS/TEN (odds ratio: 12.75; CI 1.03-157.14; p=0.053). Among carbamazepine users, only two patients experienced SJS/TEN and possessed neither HLA-B*15:02 nor HLA-A*31:03. Conclusion HLA gene frequencies varied in Korea. Screening of HLA-B*58:01 before the use of allopurinol might be needed to anticipate probability of SJS/TEN. PMID:26632391

  13. Are ‘Endurance’ Alleles ‘Survival’ Alleles? Insights from the ACTN3 R577X Polymorphism

    PubMed Central

    Fiuza-Luces, Carmen; Ruiz, Jonatan R.; Rodríguez-Romo, Gabriel; Santiago, Catalina; Gómez-Gallego, Félix; Yvert, Thomas; Cano-Nieto, Amalia; Garatachea, Nuria

    2011-01-01

    Exercise phenotypes have played a key role for ensuring survival over human evolution. We speculated that some genetic variants that influence exercise phenotypes could be associated with exceptional survival (i.e. reaching ≥100years of age). Owing to its effects on muscle structure/function, a potential candidate is the Arg(R)577Ter(X) polymorphism (rs1815739) in ACTN3, the structural gene encoding the skeletal muscle protein α-actinin-3. We compared the ACTN3 R577X genotype/allele frequencies between the following groups of ethnically-matched (Spanish) individuals: centenarians (cases, n = 64; 57 female; age range: 100–108 years), young healthy controls (n = 283, 67 females, 216 males; 21±2 years), and humans who are at the two end-points of exercise capacity phenotypes, i.e. muscle endurance (50 male professional road cyclists) and muscle power (63 male jumpers/sprinters). Although there were no differences in genotype/allele frequencies between centenarians (RR:28.8%; RX:47.5%; XX:23.7%), and controls (RR:31.8%; RX:49.8%; XX:18.4%) or endurance athletes (RR:28.0%; RX:46%; XX:26.0%), we observed a significantly higher frequency of the X allele (P = 0.019) and XX genotype (P = 0.011) in centenarians compared with power athletes (RR:47.6%; RX:36.5%;XX:15.9%). Notably, the frequency of the null XX (α-actinin-3 deficient) genotype in centenarians was the highest ever reported in non-athletic Caucasian populations. In conclusion, despite there were no significant differences with the younger, control population, overall the ACTN3 genotype of centenarians resembles that of world-class elite endurance athletes and differs from that of elite power athletes. Our preliminary data would suggest a certain ‘survival’ advantage brought about by α-actinin-3 deficiency and the ‘endurance’/oxidative muscle phenotype that is commonly associated with this condition. PMID:21407828

  14. Allele-specific enzymatic amplification of. beta. -globin genomic DNA for diagnosis of sickle cell anemia

    SciTech Connect

    Wu, D.Y.; Ugozzoli, L.; Pal, B.K.; Wallace, B. )

    1989-04-01

    A rapid nonradioactive approach to the diagnosis of sickle cell anemia is described based on an allele-specific polymerase chain reaction (ASPCR). This method allows direct detection of the normal or the sickle cell {beta}-globin allele in genomic DNA without additional steps of probe hybridization, ligation, or restriction enzyme cleavage. Two allele-specific oligonucleotide primers, one specific for the sickle cell allele and one specific for the normal allele, together with another primer complementary to both alleles were used in the polymerase chain reaction with genomic DNA templates. The allele-specific primers differed from each other in their terminal 3{prime} nucleotide. Under the proper annealing temperature and polymerase chain reaction conditions, these primers only directed amplification on their complementary allele. In a single blind study of DNA samples from 12 individuals, this method correctly and unambiguously allowed for the determination of the genotypes with no false negatives or positives. If ASPCR is able to discriminate all allelic variation (both transition and transversion mutations), this method has the potential to be a powerful approach for genetic disease diagnosis, carrier screening, HLA typing, human gene mapping, forensics, and paternity testing.

  15. How-To-Do-It: Multiple Allelic Frequencies in Populations at Equilibrium: Algorithms and Applications.

    ERIC Educational Resources Information Center

    Nussbaum, Francis, Jr.

    1988-01-01

    Presents an algorithm for solving problems related to multiple allelic frequencies in populations at equilibrium. Considers sample problems and provides their solution using this tabular algorithm. (CW)

  16. Persistence of the common Hartnup disease D173N allele in populations of European origin.

    PubMed

    Azmanov, Dimitar N; Rodgers, Helen; Auray-Blais, Christiane; Giguère, Robert; Bailey, Charles; Bröer, Stefan; Rasko, John E J; Cavanaugh, Juleen A

    2007-11-01

    Hartnup disorder is an aminoaciduria that results from mutations in the recently described gene SLC6A19 on chromosome 5p15.33. The disease is inherited in a simple recessive manner and ten different mutations have been described to date. One mutation, the D173N allele, is present in 42% of Hartnup chromosomes from apparently unrelated families from both Australia and North America. We report an investigation of the origins of the D173N allele using a unique combination of variants including SNPs, microsatellites, and a VNTR across 211 Kb spanning the SLC6A19 locus. All individuals who carry the mutant allele share an identical core haplotype suggesting a single common ancestor, indicating that the elevated frequency of the D173N allele is not a result of recurrent mutation. Analyses of these data indicate that the allele is more than 1000 years old. We compare the reasons for survival of this allele with other major alleles in some other common autosomal recessive diseases occurring in European Caucasians. We postulate that survival of this allele may be a consequence of failure of the allele to completely inactivate the transport of neutral amino acids. PMID:17555458

  17. Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles

    PubMed Central

    Lockhart, David W.; Listgarten, Jennifer; Maley, Stephen N.; Kadie, Carl; Learn, Gerald H.; Nickle, David C.; Heckerman, David E.; Deng, Wenjie; Brander, Christian; Ndung'u, Thumbi; Coovadia, Hoosen; Goulder, Philip J.R.; Korber, Bette T.; Walker, Bruce D.; Mullins, James I.

    2009-01-01

    Abstract HIV-1 can evolve HLA-specific escape variants in response to HLA-mediated cellular immunity. HLA alleles that are common in the host population may increase the frequency of such escape variants at the population level. When loss of viral fitness is caused by immune escape variation, these variants may revert upon infection of a new host who does not have the corresponding HLA allele. Furthermore, additional escape variants may appear in response to the nonconcordant HLA alleles. Because individuals with rare HLA alleles are less likely to be infected by a partner with concordant HLA alleles, viral populations infecting hosts with rare HLA alleles may undergo a greater amount of evolution than those infecting hosts with common alleles due to the loss of preexisting escape variants followed by new immune escape. This hypothesis was evaluated using maximum likelihood phylogenetic trees of each gene from 272 full-length HIV-1 sequences. Recent viral evolution, as measured by the external branch length, was found to be inversely associated with HLA frequency in nef (p < 0.02), env (p < 0.03), and pol (p ≤ 0.05), suggesting that rare HLA alleles provide a disproportionate force driving viral evolution compared to common alleles, likely due to the loss of preexisting escape variants during early stages postinfection. PMID:19327049

  18. HtrA1 Proteolysis of ApoE In Vitro Is Allele Selective.

    PubMed

    Chu, Qian; Diedrich, Jolene K; Vaughan, Joan M; Donaldson, Cynthia J; Nunn, Michael F; Lee, Kuo-Fen; Saghatelian, Alan

    2016-08-01

    Apolipoprotein E (ApoE) belongs to a large class of proteins that solubilize lipids for physiological transport. Humans have three different APOE alleles, APOE ε2, APOE ε3, and APOE ε4, and genetic studies identified ApoE4 as the strongest genetic risk factor for Alzheimer's disease (AD). People who are homozygous for ApoE4 (i.e., ApoE4/E4) are an order of magnitude more likely to develop late-onset AD (LOAD) than ApoE3/E3 carriers. Several differences between ApoE3 and ApoE4 may contribute to AD including the observation that ApoE4 is degraded to a greater extent than ApoE3 in the human brain. Experiments with high-temperature requirement serine peptidase A1 (HtrA1), which is found in the nervous system, demonstrate that HtrA1 is an allele-selective ApoE-degrading enzyme that degrades ApoE4 more quickly than ApoE3. This activity is specific to HtrA1, as similar assays with HtrA2 showed minimal ApoE4 proteolysis and trypsin had no preference between ApoE4 and ApoE3. HtrA1 has also been reported to cleave the tau protein (Tau) and the amyloid protein precursor (APP) to hinder the formation of toxic amyloid deposits associated with AD. Competition assays with ApoE4, ApoE3, and Tau revealed that ApoE4 inhibits Tau degradation. Thus, the identification of ApoE4 as an in vitro HtrA1 substrate suggests a potential biochemical mechanism that links ApoE4 regulation of AD proteins such as Tau. PMID:27379525

  19. Overall and allele-specific expression of the SMC1A gene in female Cornelia de Lange syndrome patients and healthy controls

    PubMed Central

    Parenti, Ilaria; Rovina, Davide; Masciadri, Maura; Cereda, Anna; Azzollini, Jacopo; Picinelli, Chiara; Limongelli, Giuseppe; Finelli, Palma; Selicorni, Angelo; Russo, Silvia; Gervasini, Cristina; Larizza, Lidia

    2014-01-01

    Cornelia de Lange syndrome (CdLS) is a rare multisystem disorder characterized by facial dysmorphisms, limb anomalies, and growth and cognitive deficits. Mutations in genes encoding subunits (SMC1A, SMC3, RAD21) or regulators (NIPBL, HDAC8) of the cohesin complex account for approximately 65% of clinically diagnosed CdLS cases. The SMC1A gene (Xp11.22), responsible for 5% of CdLS cases, partially escapes X chromosome inactivation in humans and the allele on the inactive X chromosome is variably expressed. In this study, we evaluated overall and allele-specific SMC1A expression. Real-time PCR analysis conducted on 17 controls showed that SMC1A expression in females is 50% higher than in males. Immunoblotting experiments confirmed a 44% higher protein level in healthy females than in males, and showed no significant differences in SMC1A protein levels between controls and patients. Pyrosequencing was used to assess the reciprocal level of allelic expression in six female carriers of different SMC1A mutations and 15 controls who were heterozygous at a polymorphic transcribed SMC1A locus. The two alleles were expressed at a 1:1 ratio in the control group and at a 2:1 ratio in favor of the wild type allele in the test group. Since a dominant negative effect is considered the pathogenic mechanism in SMC1A-defective female patients, the level of allelic preferential expression might be one of the factors contributing to the wide phenotypic variability observed in these patients. An extension of this study to a larger cohort containing mild to borderline cases could enhance our understanding of the clinical spectrum of SMC1A-linked CdLS. PMID:24756084

  20. Higher Education Exchange, 2008

    ERIC Educational Resources Information Center

    Brown, David W., Ed.; Witte, Deborah, Ed.

    2008-01-01

    "Higher Education Exchange" publishes case studies, analyses, news, and ideas about efforts within higher education to develop more democratic societies. Contributors to this issue of the "Higher Education Exchange" examine whether institutions of higher learning are doing anything to increase the capacity of citizens to shape their future.…

  1. Higher Education Exchange, 2010

    ERIC Educational Resources Information Center

    Brown, David W., Ed.; Witte, Deborah, Ed.

    2010-01-01

    "Higher Education Exchange" publishes case studies, analyses, news, and ideas about efforts within higher education to develop more democratic societies. Contributors to this issue of the "Higher Education Exchange" examine whether institutions of higher learning are doing anything to increase the capacity of citizens to shape their future.…

  2. Direct fired heat exchanger

    DOEpatents

    Reimann, Robert C.; Root, Richard A.

    1986-01-01

    A gas-to-liquid heat exchanger system which transfers heat from a gas, generally the combustion gas of a direct-fired generator of an absorption machine, to a liquid, generally an absorbent solution. The heat exchanger system is in a counterflow fluid arrangement which creates a more efficient heat transfer.

  3. Building Relationships through Exchange

    ERIC Educational Resources Information Center

    Primavera, Angi; Hall, Ellen

    2011-01-01

    From the moment of birth, children form and develop relationships with others in their world based on exchange. Children recognize that engaging in such encounters offers them the opportunity to enter into a relationship with another individual and to nurture that relationship through the exchange of messages and gifts, items and ideas. At Boulder…

  4. Higher Education Exchange, 2011

    ERIC Educational Resources Information Center

    Brown, David W., Ed.; Witte, Deborah, Ed.

    2011-01-01

    "Higher Education Exchange" publishes case studies, analyses, news, and ideas about efforts within higher education to develop more democratic societies. Contributors to this issue of the "Higher Education Exchange" examine whether institutions of higher learning are doing anything to increase the capacity of citizens to shape their future.…

  5. Higher Education Exchange, 2012

    ERIC Educational Resources Information Center

    Brown, David W., Ed.; Witte, Deborah, Ed.

    2012-01-01

    "Higher Education Exchange" publishes case studies, analyses, news, and ideas about efforts within higher education to develop more democratic societies. Contributors to this issue of the "Higher Education Exchange" examine whether institutions of higher learning are doing anything to increase the capacity of citizens to shape their future.…

  6. Higher Education Exchange, 2007

    ERIC Educational Resources Information Center

    Brown, David W., Ed.; Witte, Deborah, Ed.

    2007-01-01

    "Higher Education Exchange" publishes case studies, analyses, news, and ideas about efforts within higher education to develop more democratic societies. Contributors to this issue of the "Higher Education Exchange" discuss the concept of growing public scholars; each contribution incorporates a student component. Articles include: (1) "Foreword"…

  7. Money and Exchange.

    ERIC Educational Resources Information Center

    Walstad, William B.; And Others

    1982-01-01

    This teaching guide begins with an explanation of the role of money in the economy, focusing on its circulation or exchange. The use of money as a unit of account, a store of value, and a medium of exchange are explained. Three brief teaching units are included. The grade K-2 unit, "Money Counts," provides games and activities which develop the…

  8. Disagreement in genotyping results of drug resistance alleles of the Plasmodium falciparum dihydrofolate reductase (Pfdhfr) gene by allele-specific PCR (ASPCR) assays and Sanger sequencing.

    PubMed

    Sharma, Divya; Lather, Manila; Dykes, Cherry L; Dang, Amita S; Adak, Tridibes; Singh, Om P

    2016-01-01

    The rapid spread of antimalarial drug resistance in Plasmodium falciparum over the past few decades has necessitated intensive monitoring of such resistance for an effective malaria control strategy. P. falciparum dihydropteroate synthase (Pfdhps) and P. falciparum dihydrofolate reductase (Pfdhfr) genes act as molecular markers for resistance against the antimalarial drugs sulphadoxine and pyrimethamine, respectively. Resistance to pyrimethamine which is used as a partner drug in artemisinin combination therapy (ACT) is associated with several mutations in the Pfdhfr gene, namely A16V, N51I, C59R, S108N/T and I164L. Therefore, routine monitoring of Pfdhfr-drug-resistant alleles in a population may help in effective drug resistance management. Allele-specific PCR (ASPCR) is one of the commonly used methods for molecular genotyping of these alleles. In this study, we genotyped 55 samples of P. falciparum for allele discrimination at four codons of Pfdhfr (N51, C59, S108 and I164) by ASPCR using published methods and by Sanger's DNA sequencing method. We found that the ASPCR identified a significantly higher number of mutant alleles as compared to the DNA sequencing method. Such discrepancies arise due to the non-specificity of some of the allele-specific primer sets and due to the lack of sensitivity of Sanger's DNA sequencing method to detect minor alleles present in multiple clone infections. This study reveals the need of a highly specific and sensitive method for genotyping and detecting minor drug-resistant alleles present in multiple clonal infections. PMID:26407876

  9. Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases.

    PubMed

    Chen, Rong; Corona, Erik; Sikora, Martin; Dudley, Joel T; Morgan, Alex A; Moreno-Estrada, Andres; Nilsen, Geoffrey B; Ruau, David; Lincoln, Stephen E; Bustamante, Carlos D; Butte, Atul J

    2012-01-01

    Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed

  10. Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project

    PubMed Central

    2010-01-01

    Background There is a lack of knowledge regarding the frequency of disease associated polymorphisms in populations and population attributable risk for many populations remains unknown. Factors that could affect the association of the allele with disease, either positively or negatively, such as race, ethnicity, and gender, may not be possible to determine without population based allele frequencies. Here we used a panel of 51 polymorphisms previously associated with at least one disease and determined the allele frequencies within the entire Personalized Medicine Research Project population based cohort. We compared these allele frequencies to those in dbSNP and other data sources stratified by race. Differences in allele frequencies between self reported race, region of origin, and sex were determined. Results There were 19544 individuals who self reported a single racial category, 19027 or (97.4%) self reported white Caucasian, and 11205 (57.3%) individuals were female. Of the 11,208 (57%) individuals with an identifiable region of origin 8337 or (74.4%) were German. 41 polymorphisms were significantly different between self reported race at the 0.05 level. Stratification of our Caucasian population by self reported region of origin revealed 19 polymorphisms that were significantly different (p = 0.05) between individuals of different origins. Further stratification of the population by gender revealed few significant differences in allele frequencies between the genders. Conclusions This represents one of the largest population based allele frequency studies to date. Stratification by self reported race and region of origin revealed wide differences in allele frequencies not only by race but also by region of origin within a single racial group. We report allele frequencies for our Asian/Hmong and American Indian populations; these two minority groups are not typically selected for population allele frequency detection. Population wide allele frequencies are

  11. Apolipoprotein E alleles in Alzheimer`s and Parkinson`s patients

    SciTech Connect

    Poduslo, S.E.; Schwankhaus, J.D.

    1994-09-01

    A number of investigators have found an association between the apolipoprotein E4 allele and Alzheimer`s disease. The E4 allele appears at a higher frequency in late onset familial Alzheimer`s patients. In our studies we obtained blood samples from early and late onset familial and sporadic Alzheimer`s patients and spouses, as well as from Parkinson`s patients. The patients were diagnosed as probable Alzheimer`s patients after a neurological examination, extensive blood work, and a CAT scan. The diagnosis was made according to the NINCDS-ADRDA criteria. The apolipoprotein E4 polymorphism was detected after PCR amplification of genomic DNA, restriction enzyme digestion with Hhal, and polyacrylamide gel electrophoresis. Ethidium bromide-stained bands at 91 bp were designated as allele 3, at 83 bp as allele 2, and at 72 bp as allele 4. Of the 84 probable Alzheimer`s patients (all of whom were Caucasian), 47 were heterozygous and 13 were homozygous for the E4 allele. There were 26 early onset patients; 13 were heterozygous and 7 homozygous for the E4 allele. The frequencies for the E4 allele for late onset familial patients was 0.45 and for sporadic patients was 0.37. We analyzed 77 spouses with an average age of 71.9 {plus_minus} 7.4 years as controls, and 15 were heterozygous for the E4 allele for an E4 frequency of 0.097. Of the 53 Parkinson`s patients, 11 had the E4 allele for a frequency of 0.113. Thus our findings support the association of the ApoE4 allele with Alzheimer`s disease.

  12. Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases

    PubMed Central

    Chen, Rong; Corona, Erik; Sikora, Martin; Dudley, Joel T.; Morgan, Alex A.; Moreno-Estrada, Andres; Nilsen, Geoffrey B.; Ruau, David; Lincoln, Stephen E.; Bustamante, Carlos D.; Butte, Atul J.

    2012-01-01

    Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed

  13. Origins, distribution and expression of the Duarte-2 (D2) allele of galactose-1-phosphate uridylyltransferase

    PubMed Central

    Carney, Amanda E.; Sanders, Rebecca D.; Garza, Kerry R.; McGaha, Lee Anne; Bean, Lora J. H.; Coffee, Bradford W.; Thomas, James W.; Cutler, David J.; Kurtkaya, Natalie L.; Fridovich-Keil, Judith L.

    2009-01-01

    Duarte galactosemia is a mild to asymptomatic condition that results from partial impairment of galactose-1-phosphate uridylyltransferase (GALT). Patients with Duarte galactosemia demonstrate reduced GALT activity and carry one profoundly impaired GALT allele (G) along with a second, partially impaired GALT allele (Duarte-2, D2). Molecular studies reveal at least five sequence changes on D2 alleles: a p.N314D missense substitution, three intronic base changes and a 4 bp deletion in the 5′ proximal sequence. The four non-coding sequence changes are unique to D2. The p.N314D substitution, however, is not; it is found together with a silent polymorphism, p.L218(TTA), on functionally normal Duarte-1 alleles (D1, also called Los Angeles or LA alleles). The HapMap database reveals that p.N314D is a common human variant, and cross-species comparisons implicate D314 as the ancestral allele. The p.N314D substitution is also functionally neutral in mammalian cell and yeast expression studies. In contrast, the 4 bp 5′ deletion characteristic of D2 alleles appears to be functionally impaired in reporter gene transfection studies. Here we present allele-specific qRT–PCR evidence that D2 alleles express less mRNA in vivo than their wild-type counterparts; the difference is small but statistically significant. Furthermore, we characterize the prevalence of the 4 bp deletion in GG, NN and DG populations; the deletion appears exclusive to D2 alleles. Combined, these data strongly implicate the 4 bp 5′ deletion as a causal mutation in Duarte galactosemia and suggest that direct tests for this deletion, as proposed here, could enhance or supplant current tests, which define D2 alleles on the basis of the presence and absence of linked coding sequence polymorphisms. PMID:19224951

  14. HLA-B allele dropout in PCR sequence-specific oligonucleotide probe typing due to intronic polymorphism in the novel B*58:01:01:02 allele.

    PubMed

    He, Y; Wang, W; Han, Z; He, J; Chen, N; Dong, L; Tao, S; Zhang, W; He, J; Zhu, F; Lv, H

    2016-06-01

    Currently, Luminex technology based on the PCR sequence-specific oligonucleotide (SSO) probe method has been widely used for HLA genotyping in the immunogenetics laboratories. Here, we reported a case with HLA-B allele dropout by Luminex technology. The initial HLA-B result of the Luminex method with a commercial agent kit was inconclusive, and then, the result of PCR-SBT technology indicated the dropout as a HLA-B*58 allele. Subsequently, the full-length sequence of HLA-B allele was determined by TOPO-TA cloning, and a novel allele B*58:01:01:02 was identified in the individual. Compared with HLA-B*58:01:01:01, the novel allele showed some nucleotides difference at 509 C>T, 521 T>G and CCC insertion in position 503 of intron 2. According to the full-length sequence, the new mutations of intron 2 were contributed to HLA-B locus allele dropout in the sample. Our results indicated multiplatform should be used to improve the HLA typing accuracy when a conclusive HLA genotype cannot be determined. PMID:27016176

  15. Cognitive and neural correlates of the 5-repeat allele of the dopamine D4 receptor gene in a population lacking the 7-repeat allele.

    PubMed

    Takeuchi, Hikaru; Tomita, Hiroaki; Taki, Yasuyuki; Kikuchi, Yoshie; Ono, Chiaki; Yu, Zhiqian; Sekiguchi, Atsushi; Nouchi, Rui; Kotozaki, Yuka; Nakagawa, Seishu; Miyauchi, Carlos Makoto; Iizuka, Kunio; Yokoyama, Ryoichi; Shinada, Takamitsu; Yamamoto, Yuki; Hanawa, Sugiko; Araki, Tsuyoshi; Hashizume, Hiroshi; Kunitoki, Keiko; Sassa, Yuko; Kawashima, Ryuta

    2015-04-15

    The 5-repeat allele of a common length polymorphism in the gene that encodes the dopamine D4 receptor (DRD4) is robustly associated with the risk of attention deficit hyperactivity disorder (ADHD) and substantially exists in Asian populations, which have a lower ADHD prevalence. In this study, we investigated the effect of this allele on microstructural properties of the brain and on its functional activity during externally directed attention-demanding tasks and creative performance in the 765 Asian subjects. For this purpose, we employed diffusion tensor imaging, N-back functional magnetic resonance imaging paradigms, and a test to measure creativity by divergent thinking. The 5-repeat allele was significantly associated with increased originality in the creative performance, increased mean diffusivity (the measure of how the tissue includes water molecules instead of neural and vessel components) in the widespread gray and white matter areas of extensive areas, particularly those where DRD4 is expressed, and reduced task-induced deactivation in the areas that are deactivated during the tasks in the course of both the attention-demanding working memory task and simple sensorimotor task. The observed neural characteristics of 5-repeat allele carriers may lead to an increased risk of ADHD and behavioral deficits. Furthermore, the increased originality of creative thinking observed in the 5-repeat allele carriers may support the notion of the side of adaptivity of the widespread risk allele of psychiatric diseases. PMID:25659462

  16. High heat flux single phase heat exchanger

    NASA Technical Reports Server (NTRS)

    Valenzuela, Javier A.; Izenson, Michael G.

    1990-01-01

    This paper presents the results obtained to date in a program to develop a high heat flux, single-phase heat exchanger for spacecraft thermal management. The intended application is a net generation interface heat exchanger to couple the crew module water thermal bus to the two-phase ammonia main thermal bus in the Space Station Freedom. The large size of the interface heat exchanger is dictated by the relatively poor water-side heat transfer characteristics. The objective of this program is to develop a single-phase heat transfer approach which can achieve heat fluxes and heat transfer coefficients comparable to those of the evaporation ammonia side. A new heat exchanger concept has been developed to meet these objecties. The main feature of this heat exchanger is that it can achieve very high heat fluxes with a pressure drop one to two orders of magnitude lower than those of previous microchannel or jet impingement high heat flux heat exchangers. This paper describes proof-of-concept experiments performed in air and water and presents analytical model of the heat exchanger.

  17. Extensive exchange of rat liver microsomal phospholipids.

    PubMed

    Zilversmit, D B; Hughes, M E

    1977-08-15

    Liver microsomal fractions were prepared from rats injected with a single dose of choline [14C]methylchloride or with single or multiple doses of 32Pi. Exchangeability of microsomal phospholipids was determined by incubation with an excess of mitochondria and phospholipid exchange proteins derived from beef heart, beef liver or rat liver. Labeled phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine and phosphatidylinositol were found to act as a single pool and were 85--95% exchangeable in 1--2h. High latencies of mannose-6-phosphate phosphohydrolase activities and impermeability of microsomes to EDTA proved that phospholipid exchange proteins did not have access to the intracisternal space. If microsomal membranes are largely composed of phospholipid bilayers, the experiments suggest that one or more of the phospholipid classes in microsomal membranes undergo rapid translocation between the inner and outer portions of the bilayer. PMID:889827

  18. Detection of 549 new HLA alleles in potential stem cell donors from the United States, Poland and Germany.

    PubMed

    Hernández-Frederick, C J; Cereb, N; Giani, A S; Ruppel, J; Maraszek, A; Pingel, J; Sauter, J; Schmidt, A H; Yang, S Y

    2016-01-01

    We characterized 549 new human leukocyte antigen (HLA) class I and class II alleles found in newly registered stem cell donors as a result of high-throughput HLA typing. New alleles include 101 HLA-A, 132 HLA-B, 105 HLA-C, 2 HLA-DRB1, 89 HLA-DQB1 and 120 HLA-DPB1 alleles. Mainly, new alleles comprised single nucleotide variations when compared with homologous sequences. We identified nonsynonymous nucleotide mutations in 70.7% of all new alleles, synonymous variations in 26.4% and nonsense substitutions in 2.9% (null alleles). Some new alleles (55, 10.0%) were found multiple times, HLA-DPB1 alleles being the most frequent among these. Furthermore, as several new alleles were identified in individuals from ethnic minority groups, the relevance of recruiting donors belonging to such groups and the importance of ethnicity data collection in donor centers and registries is highlighted. PMID:26812061

  19. Characterization of an exchange-based two-qubit gate for resonant exchange qubits

    NASA Astrophysics Data System (ADS)

    Wardrop, Matthew P.; Doherty, Andrew C.

    2016-02-01

    Resonant exchange qubits are a promising addition to the family of experimentally implemented encodings of single qubits using semiconductor quantum dots. We have shown previously that it ought to be straightforward to perform a CPHASE gate between two resonant exchange qubits with a single exchange pulse. This approach uses energy gaps to suppress leakage rather than conventional pulse sequences. In this paper we present analysis and simulations of our proposed two-qubit gate subject to charge and Overhauser field noise at levels observed in current experiments. Our main result is that we expect implementations of our two-qubit gate to achieve high fidelities, with errors at the percent level and gate times comparable to single-qubit operations. As such, exchange-coupled resonant exchange qubits remain an attractive approach for quantum computing.

  20. Comparison of Prion Allele Frequency found in Suffolk and Targhee Sheep

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Scrapie is a class of Transmissible Spongiform Encephalopathy that affects sheep and goats. The objective of this study was to compare genotypic and allelic frequencies among USSES Targhee and Suffolk sheep. A total of 122 sheep were genotyped for codon 171 with allele specific primers in 2 separate...

  1. Molecular detection and identification of intimin alleles in pathogenic Escherichia coli by multiplex PCR.

    PubMed

    Reid, S D; Betting, D J; Whittam, T S

    1999-08-01

    A multiplex PCR was designed to detect the eae gene and simultaneously identify specific alleles in pathogenic Escherichia coli. The method was tested on 87 strains representing the diarrheagenic E. coli clones. The results show that the PCR assay accurately detects eae and resolves alleles encoding the alpha, beta, and gamma intimin variants. PMID:10405431

  2. Molecular Detection and Identification of Intimin Alleles in Pathogenic Escherichia coli by Multiplex PCR

    PubMed Central

    Reid, Sean D.; Betting, David J.; Whittam, Thomas S.

    1999-01-01

    A multiplex PCR was designed to detect the eae gene and simultaneously identify specific alleles in pathogenic Escherichia coli. The method was tested on 87 strains representing the diarrheagenic E. coli clones. The results show that the PCR assay accurately detects eae and resolves alleles encoding the α, β, and γ intimin variants. PMID:10405431

  3. Retention of agronomically important variation in germplasm core collections: implications for allele mining

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The primary targets of allele mining efforts are loci of agronomic importance. Agronomic loci typically exhibit patterns of allelic diversity consistent with a history of natural or artificial selection. Natural or artificial selection causes the distribution of genetic diversity at such loci to d...

  4. Fixation probability and the crossing time in the Wright-Fisher multiple alleles model

    NASA Astrophysics Data System (ADS)

    Gill, Wonpyong

    2009-08-01

    The fixation probability and crossing time in the Wright-Fisher multiple alleles model, which describes a finite haploid population, were calculated by switching on an asymmetric sharply-peaked landscape with a positive asymmetric parameter, r, such that the reversal allele of the optimal allele has higher fitness than the optimal allele. The fixation probability, which was evaluated as the ratio of the first arrival time at the reversal allele to the origination time, was double the selective advantage of the reversal allele compared with the optimal allele in the strong selection region, where the fitness parameter, k, is much larger than the critical fitness parameter, kc. The crossing time in a finite population for r>0 and kallele in the first generation should be greater than one individual in an asymmetric sharply-peaked landscape. It was also found that the crossing time in a finite population for r>0 and k≫kc scaled as a power law in the fitness parameter with a similar scaling exponent as the crossing time in an infinite population for r=0, and that the critical fitness parameter decreased with increasing sequence length with a fixed population size.

  5. An Updated Collection of Sequence Barcoded Temperature-Sensitive Alleles of Yeast Essential Genes

    PubMed Central

    Kofoed, Megan; Milbury, Karissa L.; Chiang, Jennifer H.; Sinha, Sunita; Ben-Aroya, Shay; Giaever, Guri; Nislow, Corey; Hieter, Philip; Stirling, Peter C.

    2015-01-01

    Systematic analyses of essential gene function using mutant collections in Saccharomyces cerevisiae have been conducted using collections of heterozygous diploids, promoter shut-off alleles, through alleles with destabilized mRNA, destabilized protein, or bearing mutations that lead to a temperature-sensitive (ts) phenotype. We previously described a method for construction of barcoded ts alleles in a systematic fashion. Here we report the completion of this collection of alleles covering 600 essential yeast genes. This resource covers a larger gene repertoire than previous collections and provides a complementary set of strains suitable for single gene and genomic analyses. We use deep sequencing to characterize the amino acid changes leading to the ts phenotype in half of the alleles. We also use high-throughput approaches to describe the relative ts behavior of the alleles. Finally, we demonstrate the experimental usefulness of the collection in a high-content, functional genomic screen for ts alleles that increase spontaneous P-body formation. By increasing the number of alleles and improving the annotation, this ts collection will serve as a community resource for probing new aspects of biology for essential yeast genes. PMID:26175450

  6. An Updated Collection of Sequence Barcoded Temperature-Sensitive Alleles of Yeast Essential Genes.

    PubMed

    Kofoed, Megan; Milbury, Karissa L; Chiang, Jennifer H; Sinha, Sunita; Ben-Aroya, Shay; Giaever, Guri; Nislow, Corey; Hieter, Philip; Stirling, Peter C

    2015-09-01

    Systematic analyses of essential gene function using mutant collections in Saccharomyces cerevisiae have been conducted using collections of heterozygous diploids, promoter shut-off alleles, through alleles with destabilized mRNA, destabilized protein, or bearing mutations that lead to a temperature-sensitive (ts) phenotype. We previously described a method for construction of barcoded ts alleles in a systematic fashion. Here we report the completion of this collection of alleles covering 600 essential yeast genes. This resource covers a larger gene repertoire than previous collections and provides a complementary set of strains suitable for single gene and genomic analyses. We use deep sequencing to characterize the amino acid changes leading to the ts phenotype in half of the alleles. We also use high-throughput approaches to describe the relative ts behavior of the alleles. Finally, we demonstrate the experimental usefulness of the collection in a high-content, functional genomic screen for ts alleles that increase spontaneous P-body formation. By increasing the number of alleles and improving the annotation, this ts collection will serve as a community resource for probing new aspects of biology for essential yeast genes. PMID:26175450

  7. Sporadic inclusion body myositis: HLA-DRB1 allele interactions influence disease risk and clinical phenotype.

    PubMed

    Mastaglia, Frank L; Needham, Merrilee; Scott, Adrian; James, Ian; Zilko, Paul; Day, Timothy; Kiers, Lynette; Corbett, Alastair; Witt, Campbell S; Allcock, Richard; Laing, Nigel; Garlepp, Michael; Christiansen, Frank T

    2009-11-01

    Susceptibility to sIBM is strongly associated with the HLA-DRB1*03 allele and the 8.1 MHC ancestral haplotype (HLA-A1, B8, DRB1*03) but little is known about the effects of allelic interactions at the DRB1 locus or disease-modifying effects of HLA alleles. HLA-A, B and DRB1 genotyping was performed in 80 Australian sIBM cases and the frequencies of different alleles and allele combinations were compared with those in a group of 190 healthy controls. Genotype-phenotype correlations were also investigated. Amongst carriers of the HLA-DRB1*03 allele, DRB1*03/*01 heterozygotes were over-represented in the sIBM group (p<0.003) while. DRB1*03/*04 heterozygotes were under-represented (p<0.008). The mean age-at-onset (AAO) was 6.5 years earlier in DRB1*03/*01 heterozygotes who also had more severe quadriceps muscle weakness than the rest of the cohort. The findings indicate that interactions between the HLA-DRB1*03 allele and other alleles at the DRB1 locus can influence disease susceptibility and the clinical phenotype in sIBM. PMID:19720533

  8. Allelic effects of mouse Pas1 candidate genes in human lung cancer cell lines.

    PubMed

    Galbiati, Federica; Pettinicchio, Angela; Dragani, Tommaso A; Manenti, Giacomo

    2006-12-01

    Four of the six genes constituting the mouse Pulmonary adenoma susceptibility 1 (Pas1) locus haplotype carry amino acid variants: Lrmp, Casc1, Ghiso, and Lmna-rs1. In vitro colony formation assay of human lung cancer cell lines A549 and NCI-H520 transfected with the allelic variants of the four genes revealed allele-specific modulations of colony numbers by Lmna-rs1 and Casc1, but not by Lrmp or Ghiso. In A549 and NCI-H520 cells, the A/J allele of Lmna-rs1 produced approximately 4- and approximately 2-fold, respectively, more transfectants than did the C57BL/6J allele, whereas the A/J allele of Casc1 produced approximately 6- and approximately 5-fold fewer transfectants, respectively, as compared to the C57BL/6J allele. Inhibition of clonogenicity by allelic forms of Pas1 candidate genes was not mediated by induction of apoptosis. These findings provide evidence that allelic variants of mouse Pas1 candidate genes differentially modulate growth of human cancer cells. PMID:16458428

  9. Identification of novel alleles of the rice blast resistance gene Pi54

    NASA Astrophysics Data System (ADS)

    Vasudevan, Kumar; Gruissem, Wilhelm; Bhullar, Navreet K.

    2015-10-01

    Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. The rice blast resistance gene Pi54 initially identified in an Indian cultivar confers broad-spectrum resistance in India. We explored the allelic diversity of the Pi54 gene among 885 Indian rice genotypes that were found resistant in our screening against field mixture of naturally existing M. oryzae strains as well as against five unique strains. These genotypes are also annotated as rice blast resistant in the International Rice Genebank database. Sequence-based allele mining was used to amplify and clone the Pi54 allelic variants. Nine new alleles of Pi54 were identified based on the nucleotide sequence comparison to the Pi54 reference sequence as well as to already known Pi54 alleles. DNA sequence analysis of the newly identified Pi54 alleles revealed several single polymorphic sites, three double deletions and an eight base pair deletion. A SNP-rich region was found between a tyrosine kinase phosphorylation site and the nucleotide binding site (NBS) domain. Together, the newly identified Pi54 alleles expand the allelic series and are candidates for rice blast resistance breeding programs.

  10. Sensitivity of Allelic Divergence to Genomic Position: Lessons from the Drosophila tan Gene

    PubMed Central

    John, Alisha V.; Sramkoski, Lisa L.; Walker, Elizabeth A.; Cooley, Arielle M.; Wittkopp, Patricia J.

    2016-01-01

    To identify genetic variants underlying changes in phenotypes within and between species, researchers often utilize transgenic animals to compare the function of alleles in different genetic backgrounds. In Drosophila, targeted integration mediated by the ΦC31 integrase allows activity of alternative alleles to be compared at the same genomic location. By using the same insertion site for each transgene, position effects are generally assumed to be controlled for because both alleles are surrounded by the same genomic context. Here, we test this assumption by comparing the activity of tan alleles from two Drosophila species, D. americana and D. novamexicana, at five different genomic locations in D. melanogaster. We found that the relative effects of these alleles varied among insertion sites, with no difference in activity observed between them at two sites. One of these sites simply silenced both transgenes, but the other allowed expression of both alleles that was sufficient to rescue a mutant phenotype yet failed to reveal the functional differences between the two alleles. These results suggest that more than one insertion site should be used when comparing the activity of transgenes because failing to do so could cause functional differences between alleles to go undetected. PMID:27449514

  11. Identification of novel alleles of the rice blast resistance gene Pi54

    PubMed Central

    Vasudevan, Kumar; Gruissem, Wilhelm; Bhullar, Navreet K.

    2015-01-01

    Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. The rice blast resistance gene Pi54 initially identified in an Indian cultivar confers broad-spectrum resistance in India. We explored the allelic diversity of the Pi54 gene among 885 Indian rice genotypes that were found resistant in our screening against field mixture of naturally existing M. oryzae strains as well as against five unique strains. These genotypes are also annotated as rice blast resistant in the International Rice Genebank database. Sequence-based allele mining was used to amplify and clone the Pi54 allelic variants. Nine new alleles of Pi54 were identified based on the nucleotide sequence comparison to the Pi54 reference sequence as well as to already known Pi54 alleles. DNA sequence analysis of the newly identified Pi54 alleles revealed several single polymorphic sites, three double deletions and an eight base pair deletion. A SNP-rich region was found between a tyrosine kinase phosphorylation site and the nucleotide binding site (NBS) domain. Together, the newly identified Pi54 alleles expand the allelic series and are candidates for rice blast resistance breeding programs. PMID:26498172

  12. Salmonella Typhi shdA: pseudogene or allelic variant?

    PubMed

    Urrutia, I M; Fuentes, J A; Valenzuela, L M; Ortega, A P; Hidalgo, A A; Mora, G C

    2014-08-01

    ShdA from Salmonella Typhimurium (ShdASTm) is a large outer membrane protein that specifically recognizes and binds to fibronectin. ShdASTm is involved in the colonization of the cecum and the Peyer's patches of terminal ileum in mice. On the other hand, shdA gene from Salmonella Typhi (shdASTy) has been considered a pseudogene (i.e. a nonfunctional sequence of genomic DNA) due to the presence of deletions and mutations that gave rise to premature stop codons. In this work we show that, despite the deletions and mutations, shdASTy is fully functional. S. Typhi ΔshdA mutants presented an impaired adherence and invasion of HEp-2 pre-treated with TGF-β1, an inducer of fibronectin production. Moreover, shdA from S. Typhi and S. Typhimurium seem to be equivalent since shdASTm restored the adherence and invasion of S. Typhi ΔshdA mutant to wild type levels. In addition, anti-FLAG mAbs interfered with the adherence and invasion of the S. Typhi shdA-3xFLAG strain. Finally, shdASTy encodes a detectable protein when heterologously expressed in Escherichia coli DH5α. The data presented here show that shdASTy is not a pseudogene, but a different functional allele compared with shdASTm. PMID:24859062

  13. Immunoglobulin light chain allelic inclusion in systemic lupus erythematosus.

    PubMed

    Fraser, Louise D; Zhao, Yuan; Lutalo, Pamela M K; D'Cruz, David P; Cason, John; Silva, Joselli S; Dunn-Walters, Deborah K; Nayar, Saba; Cope, Andrew P; Spencer, Jo

    2015-08-01

    The principles of allelic exclusion state that each B cell expresses a single light and heavy chain pair. Here, we show that B cells with both kappa and lambda light chains (Igκ and Igλ) are enriched in some patients with the systemic autoimmune disease systemic lupus erythematosus (SLE), but not in the systemic autoimmune disease control granulomatosis with polyangiitis. Detection of dual Igκ and Igλ expression by flow cytometry could not be abolished by acid washing or by DNAse treatment to remove any bound polyclonal antibody or complexes, and was retained after two days in culture. Both surface and intracytoplasmic dual light chain expression was evident by flow cytometry and confocal microscopy. We observed reduced frequency of rearrangements of the kappa-deleting element (KDE) in SLE and an inverse correlation between the frequency of KDE rearrangement and the frequency of dual light chain expressing B cells. We propose that dual expression of Igκ and Igλ by a single B cell may occur in some patients with SLE when this may be a consequence of reduced activity of the KDE. PMID:26036683

  14. Anion exchange membrane

    DOEpatents

    Verkade, John G; Wadhwa, Kuldeep; Kong, Xueqian; Schmidt-Rohr, Klaus

    2013-05-07

    An anion exchange membrane and fuel cell incorporating the anion exchange membrane are detailed in which proazaphosphatrane and azaphosphatrane cations are covalently bonded to a sulfonated fluoropolymer support along with anionic counterions. A positive charge is dispersed in the aforementioned cations which are buried in the support to reduce the cation-anion interactions and increase the mobility of hydroxide ions, for example, across the membrane. The anion exchange membrane has the ability to operate at high temperatures and in highly alkaline environments with high conductivity and low resistance.

  15. Wound tube heat exchanger

    DOEpatents

    Ecker, Amir L.

    1983-01-01

    What is disclosed is a wound tube heat exchanger in which a plurality of tubes having flattened areas are held contiguous adjacent flattened areas of tubes by a plurality of windings to give a double walled heat exchanger. The plurality of windings serve as a plurality of effective force vectors holding the conduits contiguous heat conducting walls of another conduit and result in highly efficient heat transfer. The resulting heat exchange bundle is economical and can be coiled into the desired shape. Also disclosed are specific embodiments such as the one in which the tubes are expanded against their windings after being coiled to insure highly efficient heat transfer.

  16. Heat and mass exchanger

    SciTech Connect

    Lowenstein, Andrew; Sibilia, Marc J.; Miller, Jeffrey A.; Tonon, Thomas

    2011-06-28

    A mass and heat exchanger includes at least one first substrate with a surface for supporting a continuous flow of a liquid thereon that either absorbs, desorbs, evaporates or condenses one or more gaseous species from or to a surrounding gas; and at least one second substrate operatively associated with the first substrate. The second substrate includes a surface for supporting the continuous flow of the liquid thereon and is adapted to carry a heat exchange fluid therethrough, wherein heat transfer occurs between the liquid and the heat exchange fluid.

  17. Heat and mass exchanger

    SciTech Connect

    Lowenstein, Andrew; Sibilia, Marc J.; Miller, Jeffrey A.; Tonon, Thomas

    2007-09-18

    A mass and heat exchanger includes at least one first substrate with a surface for supporting a continuous flow of a liquid thereon that either absorbs, desorbs, evaporates or condenses one or more gaseous species from or to a surrounding gas; and at least one second substrate operatively associated with the first substrate. The second substrate includes a surface for supporting the continuous flow of the liquid thereon and is adapted to carry a heat exchange fluid therethrough, wherein heat transfer occurs between the liquid and the heat exchange fluid.

  18. Microtube strip heat exchanger

    SciTech Connect

    Doty, F.D.

    1991-10-16

    This progress report is for the September--October 1991 quarter. We have demonstrated feasibility of higher specific conductance by a factor of five than any other work in high-temperature gas-to-gas exchangers. These laminar-flow, microtube exchangers exhibit extremely low pressure drop compared to alternative compact designs under similar conditions because of their much shorter flow length and larger total flow area for lower flow velocities. The design appears to be amenable to mass production techniques, but considerable process development remains. The reduction in materials usage and the improved heat exchanger performance promise to be of enormous significance in advanced engine designs and in cryogenics.

  19. alpha1-antitrypsin (PI) alleles as markers of Westeuropean influence in the Baltic Sea region.

    PubMed

    Beckman, L; Sikström, C; Mikelsaar, A; Krumina, A; Kucinskas, V; Beckman, G

    1999-01-01

    The distribution of alpha1-antitrypsin (PI) alleles was studied in an attempt to elucidate migrations and admixture between populations in the Baltic Sea region. The frequency of the PI Z allele, a typically Northwesteuropean marker gene, showed a highly significant regional variation in the Baltic Sea region. The highest frequency (4.5%) was found in the western part of Latvia (Courland). The PI S allele, another marker of Westeuropean influence, also showed an increased frequency in the Courland population. These results indicate that among the populations east of the Baltic Sea the Curonian population has the most pronounced Westeuropean influence. Archaeological data have shown that from the 7th century and for several hundreds of years Courland received immigrations from mainland Sweden and the island of Gotland. We speculate that the increased frequencies of the PI Z alleles and S alleles in Courland may have been caused by these migrations. PMID:9858859

  20. Global distribution of allele frequencies at the human dopamine D4 receptor locus

    SciTech Connect

    Chang, F.M.; Kidd, J.R.; Livak, K.J.

    1994-09-01

    The dopamine D4 receptor (DRD4) is a candidate gene for schizophrenia because the dopaminergic system has been implicated in this neuropsychiatric disorder. Several research groups have reported an association between allelic variants at DRD4 and schizophrenia, while others have been unable to replicate that finding. Knowledge of the appropriate gene frequencies in the underlying populations may resolve these inconsistencies. We have determined the frequencies of 8 different alleles of the 48 bp imperfect tandem repeat of exon 3 at the DRD4 locus in samples from 33 populations around the world. The frequencies vary considerably in the different populations with the most common allele ranging from 16% to 95%. Frequencies and Fst values will be presented for the 3 most common alleles (4-, 7-, and 2- repeat) by continental groupings, but the individual populations vary significantly around the averages. The populations averaged 4.3 alleles (range 2 to 7).

  1. Heat transfer characteristics of a plate-fin type supercritical/liquid helium heat exchanger

    NASA Astrophysics Data System (ADS)

    Kato, T.; Miyake, A.; Hiyama, T.; Kawano, K.; Iwamoto, S.; Ebisu, H.; Takahashi, T.; Hamada, K.; Tsuji, H.; Tsukamoto, N.; Yamaguchi, M.; Ishida, H.; Honda, T.; Yamanishi, A.; Ohmori, T.; Mori, M.

    A compact supercritical-helium/liquid-helium heat exchanger composed of a plate-fin type was studied. The heat exchange limit performance was determined through the experiment. The pulse heating performance was observed to apply the pulse heating by an electric heater. A numerical heat exchanger simulating calculation was carried out, which successfully expresses the experiment results.

  2. The functional importance of sequence versus expression variability of MHC alleles in parasite resistance.

    PubMed

    Axtner, Jan; Sommer, Simone

    2012-12-01

    Understanding selection processes driving the pronounced allelic polymorphism of the major histocompatibility complex (MHC) genes and its functional associations to parasite load have been the focus of many recent wildlife studies. Two main selection scenarios are currently debated which explain the susceptibility or resistance to parasite infections either by the effects of (1) specific MHC alleles which are selected frequency-dependent in space and time or (2) a heterozygote or divergent allele advantage. So far, most studies have focused only on structural variance in co-evolutionary processes although this might not be the only trait subject to natural selection. In the present study, we analysed structural variance stretching from exon1 through exon3 of MHC class II DRB genes as well as genotypic expression variance in relation to the gastrointestinal helminth prevalence and infection intensity in wild yellow-necked mice (Apodemus flavicollis). We found support for the functional importance of specific alleles both on the sequence and expression level. By resampling a previously investigated study population we identified specific MHC alleles affected by temporal shifts in parasite pressure and recorded associated changes in allele frequencies. The allele Apfl-DRB*23 was associated with resistance to infections by the oxyurid nematode Syphacia stroma and at the same time with susceptibility to cestode infection intensity. In line with our expectation, MHC mRNA transcript levels tended to be higher in cestode-infected animals carrying the allele Apfl-DRB*23. However, no support for a heterozygote or divergent allele advantage on the sequence or expression level was detected. The individual amino acid distance of genotypes did not explain individual differences in parasite loads and the genetic distance had no effect on MHC genotype expression. For ongoing studies on the functional importance of expression variance in parasite resistance, allele

  3. Distribution of repeat unit differences between alleles at tandem repeat microsatellite loci

    SciTech Connect

    Jin, L. |; Zhong, Y.; Chakraborty, R.

    1994-09-01

    PCR-based assays of tandemly repeated microsatellite loci detect genetic variation from which alleles may be scored by their repeat unit lengths. Comparison of allele sizes from such data yields a probability distribution (P{sub k}) of repeat unit differences (k) between alleles segregating in a population. We show that this distribution (P{sub k}; k = 0, 1,2,...) provides insight regarding the mechanism of production of new alleles at such loci and the demographic history of populations, far better than that obtained from other summary measures (e.g., heterozygosity, number of alleles, and the range of allele sizes). The distributions of P{sub k} under multi-step stepwise models of mutation are analytically derived, which show that when a population is at equilibrium under the mutation-drift balance, the distribution of repeat unit differences between alleles is positively skewed with a mode larger than zero. However, when the heterozygosity at a locus is low (say, less than 40%), P{sub k} is a monotonically decreasing function of k. Applications of this theory to data on repeat unit sizes at over 1,240 microsatellite loci from the Caucasians, categorized by the average heterozygosity of loci, indicate that at most microsatellite loci new alleles are produced by stepwise mutations, and this is consistent with the replication slippage mechanism of mutations. The repeat size changes of mutants are probably within one or two units of alleles from which the mutants arise. Distributions of P{sub k} at microsatellite loci located within genes show evidence of allele size constraints. No significant evidence of recent expansion of population sizes in the Caucasians is detected by the distribution of P{sub k}.

  4. Distinct allelic patterns of nanog expression impart embryonic stem cell population heterogeneity.

    PubMed

    Wu, Jincheng; Tzanakakis, Emmanuel S

    2013-01-01

    Nanog is a principal pluripotency regulator exhibiting a disperse distribution within stem cell populations in vivo and in vitro. Increasing evidence points to a functional role of Nanog heterogeneity on stem cell fate decisions. Allelic control of Nanog gene expression was reported recently in mouse embryonic stem cells. To better understand how this mode of regulation influences the observed heterogeneity of NANOG in stem cell populations, we assembled a multiscale stochastic population balance equation framework. In addition to allelic control, gene expression noise and random partitioning at cell division were considered. As a result of allelic Nanog expression, the distribution of Nanog exhibited three distinct states but when combined with transcriptional noise the profile became bimodal. Regardless of their allelic expression pattern, initially uniform populations of stem cells gave rise to the same Nanog heterogeneity within ten cell cycles. Depletion of NANOG content in cells switching off both gene alleles was slower than the accumulation of intracellular NANOG after cells turned on at least one of their Nanog gene copies pointing to Nanog state-dependent dynamics. Allelic transcription of Nanog also raises issues regarding the use of stem cell lines with reporter genes knocked in a single allelic locus. Indeed, significant divergence was observed in the reporter and native protein profiles depending on the difference in their half-lives and insertion of the reporter gene in one or both alleles. In stem cell populations with restricted Nanog expression, allelic regulation facilitates the maintenance of fractions of self-renewing cells with sufficient Nanog content to prevent aberrant loss of pluripotency. Our findings underline the role of allelic control of Nanog expression as a prime determinant of stem cell population heterogeneity and warrant further investigation in the contexts of stem cell specification and cell reprogramming. PMID:23874182

  5. Diverged Alleles of the Anopheles gambiae Leucine-Rich Repeat Gene APL1A Display Distinct Protective Profiles against Plasmodium falciparum

    PubMed Central

    Mitri, Christian; Riehle, Michelle M.; Bischoff, Emmanuel; Brito-Fravallo, Emma; Takashima, Eizo; Thiery, Isabelle; Zettor, Agnes; Petres, Stephane; Bourgouin, Catherine; Vernick, Kenneth D.; Eiglmeier, Karin

    2012-01-01

    Functional studies have demonstrated a role for the Anopheles gambiae APL1A gene in resistance against the human malaria parasite, Plasmodium falciparum. Here, we exhaustively characterize the structure of the APL1 locus and show that three structurally different APL1A alleles segregate in the Ngousso colony. Genetic association combined with RNAi-mediated gene silencing revealed that APL1A alleles display distinct protective profiles against P. falciparum. One APL1A allele is sufficient to explain the protective phenotype of APL1A observed in silencing experiments. Epitope-tagged APL1A isoforms expressed in an in vitro hemocyte-like cell system showed that under assay conditions, the most protective APL1A isoform (APL1A2) localizes within large cytoplasmic vesicles, is not constitutively secreted, and forms only one protein complex, while a less protective isoform (APL1A1) is constitutively secreted in at least two protein complexes. The tested alleles are identical to natural variants in the wild A. gambiae population, suggesting that APL1A genetic variation could be a factor underlying natural heterogeneity of vector susceptibility to P. falciparum. PMID:23285147

  6. The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations.

    PubMed Central

    Marth, Gabor T; Czabarka, Eva; Murvai, Janos; Sherry, Stephen T

    2004-01-01

    We have studied a genome-wide set of single-nucleotide polymorphism (SNP) allele frequency measures for African-American, East Asian, and European-American samples. For this analysis we derived a simple, closed mathematical formulation for the spectrum of expected allele frequencies when the sampled populations have experienced nonstationary demographic histories. The direct calculation generates the spectrum orders of magnitude faster than coalescent simulations do and allows us to generate spectra for a large number of alternative histories on a multidimensional parameter grid. Model-fitting experiments using this grid reveal significant population-specific differences among the demographic histories that best describe the observed allele frequency spectra. European and Asian spectra show a bottleneck-shaped history: a reduction of effective population size in the past followed by a recent phase of size recovery. In contrast, the African-American spectrum shows a history of moderate but uninterrupted population expansion. These differences are expected to have profound consequences for the design of medical association studies. The analytical methods developed for this study, i.e., a closed mathematical formulation for the allele frequency spectrum, correcting the ascertainment bias introduced by shallow SNP sampling, and dealing with variable sample sizes provide a general framework for the analysis of public variation data. PMID:15020430

  7. Outdoor heat exchanger section

    SciTech Connect

    Kessler, A.F.; Smiley, W.A. III; Wendt, M.E.

    1988-02-09

    An outdoor section for an air conditioning system is described comprising: a compressor; a heat exchanger; a cabinet having an upper cabinet section, a lower cabinet section and a louvered lower section top cover, the heat exchanger and the compressor being housed in the lower cabinet section and the upper cabinet section having a solid top which overlies the louvers in the lower section top cover; and a fan disposed in the lower cabinet section to draw air through the sides of the lower cabinet section and through the heat exchanger housed therein, the fan discharging air, after having been drawn through the heat exchanger, upward through the louvers in the lower cabinet section top cover and into the interior of the upper cabinet section.

  8. Exchange transfusion - series (image)

    MedlinePlus

    ... her back, usually under a radiant warmer. The umbilical vein is catheterized with a fluid-filled catheter. ... plasma is injected. After the exchange transfusion, an umbilical catheter may be left in place in case ...

  9. Active microchannel heat exchanger

    DOEpatents

    Tonkovich, Anna Lee Y [Pasco, WA; Roberts, Gary L [West Richland, WA; Call, Charles J [Pasco, WA; Wegeng, Robert S [Richland, WA; Wang, Yong [Richland, WA

    2001-01-01

    The present invention is an active microchannel heat exchanger with an active heat source and with microchannel architecture. The microchannel heat exchanger has (a) an exothermic reaction chamber; (b) an exhaust chamber; and (c) a heat exchanger chamber in thermal contact with the exhaust chamber, wherein (d) heat from the exothermic reaction chamber is convected by an exothermic reaction exhaust through the exhaust chamber and by conduction through a containment wall to the working fluid in the heat exchanger chamber thereby raising a temperature of the working fluid. The invention is particularly useful as a liquid fuel vaporizer and/or a steam generator for fuel cell power systems, and as a heat source for sustaining endothermic chemical reactions and initiating exothermic reactions.

  10. Anion exchange polymer electrolytes

    SciTech Connect

    Kim, Yu Seung; Kim, Dae Sik

    2015-06-02

    Anion exchange polymer electrolytes that include guanidinium functionalized polymers may be used as membranes and binders for electrocatalysts in preparation of anodes for electrochemical cells such as solid alkaline fuel cells.

  11. Data exchange in metrology.

    PubMed

    Badger, P

    1996-01-01

    The adoption of the directives 71/316/EEC on measuring instruments and 90/384/EEC on non-automatic weighing instruments has resulted in a considerable quantity of certificates to be exchanged between the Central Metrological Authorities and the Local Metrological Authorities, in the member states. This requirement to exchange data, prompted the setting up of the WELMEC working group, to explore how computerisation could help the member states perform their tasks. PMID:10172832

  12. Microtube Strip Heat Exchanger

    SciTech Connect

    Doty, F.D.

    1990-12-27

    Doty Scientific (DSI) believes their Microtube-Strip Heat Exchanger will contribute significantly to (a) the closed Brayton cycles being pursued at MIT, NASA, and elsewhere; (b) reverse Brayton cycle cryocoolers, currently being investigated by NASA for space missions, being applied to MRI superconducting magnets; and (c) high-efficiency cryogenic gas separation schemes for CO{sub 2} removal from exhaust stacks. The goal of this current study is to show the potential for substantial progress in high-effectiveness, low-cost, gas-to-gas heat exchangers for diverse applications at temperatures from below 100 K to above 1000 K. To date, the highest effectiveness measured is about 98%, and relative pressure drops below 0.1% with a specific conductance of about 45 W/kgK are reported. During the pre-award period DSI built and tested a 3-module heat exchanger bank using 103-tube microtube strip (MTS) modules. To add to their analytical capabilities, DSI has acquired computational fluid dynamics (CFD) software. This report describes the pre-award work and the status of the ten tasks of the current project, which are: analyze flow distribution and thermal stresses within individual modules; design a heat exchanger bank of ten modules with 400 microtube per module; obtain production quality tubestrip die and AISI 304 tubestrips; obtain production quality microtubing; construct revised MTS heat exchanger; construct dies and fixtures for prototype heat exchanger; construct 100 MTS modules; assemble 8-10 prototype MTS heat exchangers; test prototype MTS heat exchanger; and verify test through independent means. 7 refs., 9 figs. 1 tab. (CK)

  13. Cryptographic Combinatorial Securities Exchanges

    NASA Astrophysics Data System (ADS)

    Thorpe, Christopher; Parkes, David C.

    We present a useful new mechanism that facilitates the atomic exchange of many large baskets of securities in a combinatorial exchange. Cryptography prevents information about the securities in the baskets from being exploited, enhancing trust. Our exchange offers institutions who wish to trade large positions a new alternative to existing methods of block trading: they can reduce transaction costs by taking advantage of other institutions’ available liquidity, while third party liquidity providers guarantee execution—preserving their desired portfolio composition at all times. In our exchange, institutions submit encrypted orders which are crossed, leaving a “remainder”. The exchange proves facts about the portfolio risk of this remainder to third party liquidity providers without revealing the securities in the remainder, the knowledge of which could also be exploited. The third parties learn either (depending on the setting) the portfolio risk parameters of the remainder itself, or how their own portfolio risk would change if they were to incorporate the remainder into a portfolio they submit. In one setting, these third parties submit bids on the commission, and the winner supplies necessary liquidity for the entire exchange to clear. This guaranteed clearing, coupled with external price discovery from the primary markets for the securities, sidesteps difficult combinatorial optimization problems. This latter method of proving how taking on the remainder would change risk parameters of one’s own portfolio, without revealing the remainder’s contents or its own risk parameters, is a useful protocol of independent interest.

  14. Radial flow heat exchanger

    DOEpatents

    Valenzuela, Javier

    2001-01-01

    A radial flow heat exchanger (20) having a plurality of first passages (24) for transporting a first fluid (25) and a plurality of second passages (26) for transporting a second fluid (27). The first and second passages are arranged in stacked, alternating relationship, are separated from one another by relatively thin plates (30) and (32), and surround a central axis (22). The thickness of the first and second passages are selected so that the first and second fluids, respectively, are transported with laminar flow through the passages. To enhance thermal energy transfer between first and second passages, the latter are arranged so each first passage is in thermal communication with an associated second passage along substantially its entire length, and vice versa with respect to the second passages. The heat exchangers may be stacked to achieve a modular heat exchange assembly (300). Certain heat exchangers in the assembly may be designed slightly differently than other heat exchangers to address changes in fluid properties during transport through the heat exchanger, so as to enhance overall thermal effectiveness of the assembly.

  15. Vacuum powered heat exchanger

    SciTech Connect

    Ruffolo, R.F.

    1986-06-24

    In an internal combustion engine including an oil lubrication system, a liquid cooling system, and an improved air intake system is described. The improved air intake system comprises: a housing including a first opening in one end, which opening is open to the atmosphere and a second opening comprising an air outlet opening in the other end open to the air intake manifold of the engine, a heat exchanger positioned in the first opening. The heat exchanger consists of a series of coils positioned in the flow path of the atmospheric air as it enters the housing, the heat exchanger being fluidly connected to either the engine lubrication system or the cooling system to provide a warm heat source for the incoming air to the housing, acceleration means positioned in the housing downstream of the heat exchanger, the acceleration means comprising a honeycomb structure positioned across the air intake flow path. The honey-comb structure includes a multitude of honey combed mini-venturi cells through which the heated air flows in an accelerated mode, a removable air filter positioned between the heat exchanger and the acceleration means and a single opening provided in the housing through which the air filter can be passed and removed, and additional openings in the housing positioned downstream of the heat exchanger and upstream of the air filter, the additional openings including removable flaps for opening and closing the openings to control the temperature of the air flowing through the housing.

  16. Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids

    PubMed Central

    2012-01-01

    Background Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles for any accession of an allopolyploid plant species. The method, named Microsatellite Allele Dose and Configuration Establishment (MADCE), can be applied to mapping populations and pedigreed (breeding) germplasm in allopolyploids. Results Two case studies are presented to demonstrate the power and robustness of the MADCE method. In the mapping case, five microsatellites were analysed. These microsatellites amplified 35 different alleles based on size. Using MADCE, we uncovered 30 highly informative segregating alleles. A conventional approach would have yielded only 19 fully informative and six partially informative alleles. Of the ten alleles that were present in all progeny (and thereby ignored or considered homozygous when using conventional approaches), six were found to segregate by dosage when analysed with MADCE. Moreover, the full allelic configuration of the mapping parents could be established, including null alleles, homozygous loci, and alleles that were present on multiple homoeologues. In the second case, 21 pedigreed cultivars were analysed using MADCE, resulting in the establishment of the full allelic configuration for all 21 cultivars and a tracing of allele flow over multiple generations. Conclusions The procedure described in this study (MADCE) enhances the efficiency and information content of mapping studies in allopolyploids. More importantly, it is the first technique to allow the determination of the full allelic configuration in pedigreed breeding germplasm from allopolyploid plants. This enables pedigree-based marker-trait association studies the use of algorithms developed for diploid crops, and it may increase the effectiveness of LD

  17. Demographic history and rare allele sharing among human populations.

    PubMed

    Gravel, Simon; Henn, Brenna M; Gutenkunst, Ryan N; Indap, Amit R; Marth, Gabor T; Clark, Andrew G; Yu, Fuli; Gibbs, Richard A; Bustamante, Carlos D

    2011-07-19

    High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2-4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence. PMID:21730125

  18. Naturally occurring allele diversity allows potato cultivation in northern latitudes.

    PubMed

    Kloosterman, Bjorn; Abelenda, José A; Gomez, María del Mar Carretero; Oortwijn, Marian; de Boer, Jan M; Kowitwanich, Krissana; Horvath, Beatrix M; van Eck, Herman J; Smaczniak, Cezary; Prat, Salomé; Visser, Richard G F; Bachem, Christian W B

    2013-03-14

    Potato (Solanum tuberosum L.) originates from the Andes and evolved short-day-dependent tuber formation as a vegetative propagation strategy. Here we describe the identification of a central regulator underlying a major-effect quantitative trait locus for plant maturity and initiation of tuber development. We show that this gene belongs to the family of DOF (DNA-binding with one finger) transcription factors and regulates tuberization and plant life cycle length, by acting as a mediator between the circadian clock and the StSP6A mobile tuberization signal. We also show that natural allelic variants evade post-translational light regulation, allowing cultivation outside the geographical centre of origin of potato. Potato is a member of the Solanaceae family and is one of the world's most important food crops. This annual plant originates from the Andean regions of South America. Potato develops tubers from underground stems called stolons. Its equatorial origin makes potato essentially short-day dependent for tuberization and potato will not make tubers in the long-day conditions of spring and summer in the northern latitudes. When introduced in temperate zones, wild material will form tubers in the course of the autumnal shortening of day-length. Thus, one of the first selected traits in potato leading to a European potato type is likely to have been long-day acclimation for tuberization. Potato breeders can exploit the naturally occurring variation in tuberization onset and life cycle length, allowing varietal breeding for different latitudes, harvest times and markets. PMID:23467094

  19. Demographic history and rare allele sharing among human populations

    PubMed Central

    Gravel, Simon; Henn, Brenna M.; Gutenkunst, Ryan N.; Indap, Amit R.; Marth, Gabor T.; Clark, Andrew G.; Yu, Fuli; Gibbs, Richard A.; Bustamante, Carlos D.; Altshuler, David L.; Durbin, Richard M.; Abecasis, Gonçalo R.; Bentley, David R.; Chakravarti, Aravinda; Clark, Andrew G.; Collins, Francis S.; De La Vega, Francisco M.; Donnelly, Peter; Egholm, Michael; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Knoppers, Bartha M.; Lander, Eric S.; Lehrach, Hans; Mardis, Elaine R.; McVean, Gil A.; Nickerson, Debbie A.; Peltonen, Leena; Schafer, Alan J.; Sherry, Stephen T.; Wang, Jun; Wilson, Richard K.; Gibbs, Richard A.; Deiros, David; Metzker, Mike; Muzny, Donna; Reid, Jeff; Wheeler, David; Wang, Jun; Li, Jingxiang; Jian, Min; Li, Guoqing; Li, Ruiqiang; Liang, Huiqing; Tian, Geng; Wang, Bo; Wang, Jian; Wang, Wei; Yang, Huanming; Zhang, Xiuqing; Zheng, Huisong; Lander, Eric S.; Altshuler, David L.; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Bentley, David R.; Gormley, Niall; Humphray, Sean; Kingsbury, Zoya; Koko-Gonzales, Paula; Stone, Jennifer; McKernan, Kevin J.; Costa, Gina L.; Ichikawa, Jeffry K.; Lee, Clarence C.; Sudbrak, Ralf; Lehrach, Hans; Borodina, Tatiana A.; Dahl, Andreas; Davydov, Alexey N.; Marquardt, Peter; Mertes, Florian; Nietfeld, Wilfiried; Rosenstiel, Philip; Schreiber, Stefan; Soldatov, Aleksey V.; Timmermann, Bernd; Tolzmann, Marius; Egholm, Michael; Affourtit, Jason; Ashworth, Dana; Attiya, Said; Bachorski, Melissa; Buglione, Eli; Burke, Adam; Caprio, Amanda; Celone, Christopher; Clark, Shauna; Conners, David; Desany, Brian; Gu, Lisa; Guccione, Lorri; Kao, Kalvin; Kebbel, Andrew; Knowlton, Jennifer; Labrecque, Matthew; McDade, Louise; Mealmaker, Craig; Minderman, Melissa; Nawrocki, Anne; Niazi, Faheem; Pareja, Kristen; Ramenani, Ravi; Riches, David; Song, Wanmin; Turcotte, Cynthia; Wang, Shally; Mardis, Elaine R.; Wilson, Richard K.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Weinstock, George; Durbin, Richard M.; Burton, John; Carter, David M.; Churcher, Carol; Coffey, Alison; Cox, Anthony; Palotie, Aarno; Quail, Michael; Skelly, Tom; Stalker, James; Swerdlow, Harold P.; Turner, Daniel; De Witte, Anniek; Giles, Shane; Gibbs, Richard A.; Wheeler, David; Bainbridge, Matthew; Challis, Danny; Sabo, Aniko; Yu, Fuli; Yu, Jin; Wang, Jun; Fang, Xiaodong; Guo, Xiaosen; Li, Ruiqiang; Li, Yingrui; Luo, Ruibang; Tai, Shuaishuai; Wu, Honglong; Zheng, Hancheng; Zheng, Xiaole; Zhou, Yan; Li, Guoqing; Wang, Jian; Yang, Huanming; Marth, Gabor T.; Garrison, Erik P.; Huang, Weichun; Indap, Amit; Kural, Deniz; Lee, Wan-Ping; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; Daly, Mark J.; DePristo, Mark A.; Altshuler, David L.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Cibulskis, Kristian; Fennell, Tim J.; Garimella, Kiran V.; Grossman, Sharon R.; Handsaker, Robert E.; Hanna, Matt; Hartl, Chris; Jaffe, David B.; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; McKenna, Aaron; Nemesh, James C.; Philippakis, Anthony A.; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis C.; Schaffner, Stephen F.; Shefler, Erica; Shlyakhter, Ilya A.; Cooper, David N.; Ball, Edward V.; Mort, Matthew; Phillips, Andrew D.; Stenson, Peter D.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Bustamante, Carlos D.; Clark, Andrew G.; Boyko, Adam; Degenhardt, Jeremiah; Gravel, Simon; Gutenkunst, Ryan N.; Kaganovich, Mark; Keinan, Alon; Lacroute, Phil; Ma, Xin; Reynolds, Andy; Clarke, Laura; Flicek, Paul; Cunningham, Fiona; Herrero, Javier; Keenen, Stephen; Kulesha, Eugene; Leinonen, Rasko; McLaren, William M.; Radhakrishnan, Rajesh; Smith, Richard E.; Zalunin, Vadim; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Stütz, Adrian M.; Humphray, Sean; Bauer, Markus; Cheetham, R. Keira; Cox, Tony; Eberle, Michael; James, Terena; Kahn, Scott; Murray, Lisa; Chakravarti, Aravinda; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Hyland, Fiona C. L.; Manning, Jonathan M.; McLaughlin, Stephen F.; Peckham, Heather E.; Sakarya, Onur; Sun, Yongming A.; Tsung, Eric F.; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Sudbrak, Ralf; Albrecht, Marcus W.; Amstislavskiy, Vyacheslav S.; Herwig, Ralf; Parkhomchuk, Dimitri V.; Sherry, Stephen T.; Agarwala, Richa; Khouri, Hoda M.; Morgulis, Aleksandr O.; Paschall, Justin E.; Phan, Lon D.; Rotmistrovsky, Kirill E.; Sanders, Robert D.; Shumway, Martin F.; Xiao, Chunlin; McVean, Gil A.; Auton, Adam; Iqbal, Zamin; Lunter, Gerton; Marchini, Jonathan L.; Moutsianas, Loukas; Myers, Simon; Tumian, Afidalina; Desany, Brian; Knight, James; Winer, Roger; Craig, David W.; Beckstrom-Sternberg, Steve M.; Christoforides, Alexis; Kurdoglu, Ahmet A.; Pearson, John V.; Sinari, Shripad A.; Tembe, Waibhav D.; Haussler, David; Hinrichs, Angie S.; Katzman, Sol J.; Kern, Andrew; Kuhn, Robert M.; Przeworski, Molly; Hernandez, Ryan D.; Howie, Bryan; Kelley, Joanna L.; Melton, S. Cord; Abecasis, Gonçalo R.; Li, Yun; Anderson, Paul; Blackwell, Tom; Chen, Wei; Cookson, William O.; Ding, Jun; Kang, Hyun Min; Lathrop, Mark; Liang, Liming; Moffatt, Miriam F.; Scheet, Paul; Sidore, Carlo; Snyder, Matthew; Zhan, Xiaowei; Zöllner, Sebastian; Awadalla, Philip; Casals, Ferran; Idaghdour, Youssef; Keebler, John; Stone, Eric A.; Zilversmit, Martine; Jorde, Lynn; Xing, Jinchuan; Eichler, Evan E.; Aksay, Gozde; Alkan, Can; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Kidd, Jeffrey M.; Sahinalp, S. Cenk; Sudmant, Peter H.; Mardis, Elaine R.; Chen, Ken; Chinwalla, Asif; Ding, Li; Koboldt, Daniel C.; McLellan, Mike D.; Dooling, David; Weinstock, George; Wallis, John W.; Wendl, Michael C.; Zhang, Qunyuan; Durbin, Richard M.; Albers, Cornelis A.; Ayub, Qasim; Balasubramaniam, Senduran; Barrett, Jeffrey C.; Carter, David M.; Chen, Yuan; Conrad, Donald F.; Danecek, Petr; Dermitzakis, Emmanouil T.; Hu, Min; Huang, Ni; Hurles, Matt E.; Jin, Hanjun; Jostins, Luke; Keane, Thomas M.; Le, Si Quang; Lindsay, Sarah; Long, Quan; MacArthur, Daniel G.; Montgomery, Stephen B.; Parts, Leopold; Stalker, James; Tyler-Smith, Chris; Walter, Klaudia; Zhang, Yujun; Gerstein, Mark B.; Snyder, Michael; Abyzov, Alexej; Balasubramanian, Suganthi; Bjornson, Robert; Du, Jiang; Grubert, Fabian; Habegger, Lukas; Haraksingh, Rajini; Jee, Justin; Khurana, Ekta; Lam, Hugo Y. K.; Leng, Jing; Mu, Xinmeng Jasmine; Urban, Alexander E.; Zhang, Zhengdong; Li, Yingrui; Luo, Ruibang; Marth, Gabor T.; Garrison, Erik P.; Kural, Deniz; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; McCarroll, Steven A.; Banks, Eric; DePristo, Mark A.; Handsaker, Robert E.; Hartl, Chris; Korn, Joshua M.; Li, Heng; Nemesh, James C.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Degenhardt, Jeremiah; Kaganovich, Mark; Clarke, Laura; Smith, Richard E.; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Humphray, Sean; Cheetham, R. Keira; Eberle, Michael; Kahn, Scott; Murray, Lisa; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Peckham, Heather E.; Sun, Yongming A.; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Xiao, Chunlin; Iqbal, Zamin; Desany, Brian; Blackwell, Tom; Snyder, Matthew; Xing, Jinchuan; Eichler, Evan E.; Aksay, Gozde; Alkan, Can; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Kidd, Jeffrey M.; Chen, Ken; Chinwalla, Asif; Ding, Li; McLellan, Mike D.; Wallis, John W.; Hurles, Matt E.; Conrad, Donald F.; Walter, Klaudia; Zhang, Yujun; Gerstein, Mark B.; Snyder, Michael; Abyzov, Alexej; Du, Jiang; Grubert, Fabian; Haraksingh, Rajini; Jee, Justin; Khurana, Ekta; Lam, Hugo Y. K.; Leng, Jing; Mu, Xinmeng Jasmine; Urban, Alexander E.; Zhang, Zhengdong; Gibbs, Richard A.; Bainbridge, Matthew; Challis, Danny; Coafra, Cristian; Dinh, Huyen; Kovar, Christie; Lee, Sandy; Muzny, Donna; Nazareth, Lynne; Reid, Jeff; Sabo, Aniko; Yu, Fuli; Yu, Jin; Marth, Gabor T.; Garrison, Erik P.; Indap, Amit; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Ward, Alistair N.; Wu, Jiantao; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Garimella, Kiran V.; Hartl, Chris; Shefler, Erica; Sougnez, Carrie L.; Wilkinson, Jane; Clark, Andrew G.; Gravel, Simon; Grubert, Fabian; Clarke, Laura; Flicek, Paul; Smith, Richard E.; Zheng-Bradley, Xiangqun; Sherry, Stephen T.; Khouri, Hoda M.; Paschall, Justin E.; Shumway, Martin F.; Xiao, Chunlin; McVean, Gil A.; Katzman, Sol J.; Abecasis, Gonçalo R.; Blackwell, Tom; Mardis, Elaine R.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Koboldt, Daniel C.; Durbin, Richard M.; Balasubramaniam, Senduran; Coffey, Allison; Keane, Thomas M.; MacArthur, Daniel G.; Palotie, Aarno; Scott, Carol; Stalker, James; Tyler-Smith, Chris; Gerstein, Mark B.; Balasubramanian, Suganthi; Chakravarti, Aravinda; Knoppers, Bartha M.; Abecasis, Gonçalo R.; Bustamante, Carlos D.; Gharani, Neda; Gibbs, Richard A.; Jorde, Lynn; Kaye, Jane S.; Kent, Alastair; Li, Taosha; McGuire, Amy L.; McVean, Gil A.; Ossorio, Pilar N.; Rotimi, Charles N.; Su, Yeyang; Toji, Lorraine H.; TylerSmith, Chris; Brooks, Lisa D.; Felsenfeld, Adam L.; McEwen, Jean E.; Abdallah, Assya; Juenger, Christopher R.; Clemm, Nicholas C.; Collins, Francis S.; Duncanson, Audrey; Green, Eric D.; Guyer, Mark S.; Peterson, Jane L.; Schafer, Alan J.; Abecasis, Gonçalo R.; Altshuler, David L.; Auton, Adam; Brooks, Lisa D.; Durbin, Richard M.; Gibbs, Richard A.; Hurles, Matt E.; McVean, Gil A.

    2011-01-01

    High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2–4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence. PMID:21730125

  20. Confounded by sequencing depth in association studies of rare alleles.

    PubMed

    Garner, Chad

    2011-05-01

    Next-generation DNA sequencing technologies are facilitating large-scale association studies of rare genetic variants. The depth of the sequence read coverage is an important experimental variable in the next-generation technologies and it is a major determinant of the quality of genotype calls generated from sequence data. When case and control samples are sequenced separately or in different proportions across batches, they are unlikely to be matched on sequencing read depth and a differential misclassification of genotypes can result, causing confounding and an increased false-positive rate. Data from Pilot Study 3 of the 1000 Genomes project was used to demonstrate that a difference between the mean sequencing read depth of case and control samples can result in false-positive association for rare and uncommon variants, even when the mean coverage depth exceeds 30× in both groups. The degree of the confounding and inflation in the false-positive rate depended on the extent to which the mean depth was different in the case and control groups. A logistic regression model was used to test for association between case-control status and the cumulative number of alleles in a collapsed set of rare and uncommon variants. Including each individual's mean sequence read depth across the variant sites in the logistic regression model nearly eliminated the confounding effect and the inflated false-positive rate. Furthermore, accounting for the potential error by modeling the probability of the heterozygote genotype calls in the regression analysis had a relatively minor but beneficial effect on the statistical results. PMID:21328616

  1. BIODEGRADATION AND GAS-EXCHANGE OF GASEOUS ALKANES IN MODEL ESTUARINE ECOSYSTEMS

    EPA Science Inventory

    Gas exchange-biodegradation experiments conducted in model estuarine ecosystems indicate that the ease of degradation of gaseious normal alkanes increases with chain length. The behavior of gaseous perhalogenated alkanes can be explained by gas exchange alone with no degradation....

  2. Hydromechanics and heat and mass exchange in weightlessness (Russian book): Table of contents

    NASA Technical Reports Server (NTRS)

    Avduyevskiy, V. S.; Poleshayev, V. I.

    1983-01-01

    The table of contents is given for a book on hydromechanics and heat and mass exchange in weightlessness. The book covers such subjects as hydromechanics, convection and heat and mass exchange, and technological experiments and complicated systems.

  3. Carriage of One or Two FMR1 Premutation Alleles Seems to Have No Effect on Illness Severity in a FXTAS Female with an Autozygous FMR1 Premutation Allele.

    PubMed

    Rodriguez-Revenga, Laia; Pagonabarraga, Javier; Gómez-Anson, Beatriz; López-Mourelo, Olga; Izquierdo, Silvia; Alvarez-Mora, Maria Isabel; Granell, Esther; Madrigal, Irene; Milà, Montserrat

    2016-10-01

    Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder that occurs in FMR1 premutation carriers. The prevalence of FMR1 premutation carriers in the general population is relatively high, and although rare, a premutation in both X chromosomes may occur in females inheriting a premutation allele from each of both parent carriers. Here, we report the first female with an autozygous (homozygous by descendent) FMR1 premutation allele, who fulfills neurological and radiological FXTAS findings/criteria. Molecular characterization included CGG repeat length, AGG interruption pattern, FMR1 messenger RNA (mRNA), fragile X mental retardation protein (FMRP) level quantification, and single-nucleotide polymorphism (SNP) microarray. Neuroradiological assessment of 3-T magnetic resonance imaging and neurological and cognitive/neuropsychological evaluations were performed. Neurological and neuroradiological examination of the female with the same FMR1 allele in the premutation range (77 CGGs) demonstrated FXTAS features. Further familial evaluation showed a similar neuropsychiatric profile, with impairments in cognitive flexibility and visuospatial function, mainly. A unique family with an autozygous FMR1 premutation female is presented. Neurological/cognitive and neuroradiological examinations revealed FXTAS-specific findings in the female with the autozygous FMR1 premutation allele. The consistent molecular and cognitive/psychiatric phenotype in family members suggests that carrying one or two FMR1 premutation alleles has no effect on illness severity. PMID:27315125

  4. Changes and Exchanges in Marginal Youth Transitions

    ERIC Educational Resources Information Center

    Bottrell, Dorothy; Armstrong, Derrick

    2007-01-01

    While some groups of young people may negotiate successful transitions to work, others are unable or unlikely to do so. The concept of "fair exchange" is pertinent to understanding youth transitions in their formative stages through educational experiences. Patterns of disrupted education challenge the education-work nexus not only because failure…

  5. Pion double charge exchange and hadron dynamics

    SciTech Connect

    Johnson, M.B.

    1991-01-01

    This paper will review theoretical results to show how pion double charge exchange is contributing to our understanding of hadron dynamics in nuclei. The exploitation of the nucleus as a filter is shown to be essential in facilitating the comparison between theory and experiment. 23 refs., 3 figs., 2 tabs.

  6. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.

    PubMed

    Chen, Jieming; Rozowsky, Joel; Galeev, Timur R; Harmanci, Arif; Kitchen, Robert; Bedford, Jason; Abyzov, Alexej; Kong, Yong; Regan, Lynne; Gerstein, Mark

    2016-01-01

    Large-scale sequencing in the 1000 Genomes Project has revealed multitudes of single nucleotide variants (SNVs). Here, we provide insights into the functional effect of these variants using allele-specific behaviour. This can be assessed for an individual by mapping ChIP-seq and RNA-seq reads to a personal genome, and then measuring 'allelic imbalances' between the numbers of reads mapped to the paternal and maternal chromosomes. We annotate variants associated with allele-specific binding and expression in 382 individuals by uniformly processing 1,263 functional genomics data sets, developing approaches to reduce the heterogeneity between data sets due to overdispersion and mapping bias. Since many allelic variants are rare, aggregation across multiple individuals is necessary to identify broadly applicable 'allelic elements'. We also found SNVs for which we can anticipate allelic imbalance from the disruption of a binding motif. Our results serve as an allele-specific annotation for the 1000 Genomes variant catalogue and are distributed as an online resource (alleledb.gersteinlab.org). PMID:27089393

  7. MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers

    PubMed Central

    Baek, In-Cheol; Jang, Jung-Pil; Choi, Eun-Jeong; Kim, Tai-Gyu

    2015-01-01

    Major histocompatibility complex (MHC) class I chain-related gene B (MICB) encodes a ligand for activating NKG2D that expressed in natural killer cells, γδ T cells, and αβ CD8+ T cells, which is associated with autoimmune diseases, cancer, and infectious diseases. Here, we have established a system for genotyping MICB alleles using allele-specific primer extension (ASPE) on microarrays. Thirty-six high quality, allele-specific extension primers were evaluated using strict and reliable cut-off values using mean fluorescence intensity (MFI), whereby an MFI >30,000 represented a positive signal and an MFI <10,000 represented a negative signal. Eight allele-specific extension primers were found to be false positives, five of which were improved by adjusting their length, and three of which were optimized by refractory modification. The MICB alleles (*002:01, *003, *005:02/*010, *005:03, *008, *009N, *018, and *024) present in the quality control panel could be exactly defined by 22 allele-specific extension primers. MICB genotypes that were identified by ASPE on microarrays were in full concordance with those identified by PCR-sequence-based typing. In conclusion, we have developed a method for genotyping MICB alleles using ASPE on microarrays; which can be applicable for large-scale single nucleotide polymorphism typing studies of population and disease associations. PMID:26569110

  8. Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer

    PubMed Central

    Halabi, Najeeb M.; Martinez, Alejandra; Al-Farsi, Halema; Mery, Eliane; Puydenus, Laurence; Pujol, Pascal; Khalak, Hanif G.; McLurcan, Cameron; Ferron, Gwenael; Querleu, Denis; Al-Azwani, Iman; Al-Dous, Eman; Mohamoud, Yasmin A.; Malek, Joel A.; Rafii, Arash

    2016-01-01

    Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy. However, tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression. We therefore developed a novel approach combining genome and transcriptome sequencing data from the same sample that corrects for sample heterogeneity and identifies significant preferentially expressed alleles. We applied this analysis to epithelial ovarian cancer samples consisting of matched primary ovary and peritoneum and lymph node metastasis. We find that preferentially expressed variant alleles include germline and somatic variants, are shared at a relatively high frequency between patients, and are in gene networks known to be involved in cancer processes. Analysis at a patient level identifies patient-specific preferentially expressed alleles in genes that are targets for known drugs. Analysis at a site level identifies patterns of site specific preferential allele expression with similar pathways being impacted in the primary and metastasis sites. We conclude that genes with preferentially expressed variant alleles can act as cancer drivers and that targeting those genes could lead to new therapeutic strategies. PMID:26735499

  9. Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer.

    PubMed

    Halabi, Najeeb M; Martinez, Alejandra; Al-Farsi, Halema; Mery, Eliane; Puydenus, Laurence; Pujol, Pascal; Khalak, Hanif G; McLurcan, Cameron; Ferron, Gwenael; Querleu, Denis; Al-Azwani, Iman; Al-Dous, Eman; Mohamoud, Yasmin A; Malek, Joel A; Rafii, Arash

    2016-01-01

    Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy. However, tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression. We therefore developed a novel approach combining genome and transcriptome sequencing data from the same sample that corrects for sample heterogeneity and identifies significant preferentially expressed alleles. We applied this analysis to epithelial ovarian cancer samples consisting of matched primary ovary and peritoneum and lymph node metastasis. We find that preferentially expressed variant alleles include germline and somatic variants, are shared at a relatively high frequency between patients, and are in gene networks known to be involved in cancer processes. Analysis at a patient level identifies patient-specific preferentially expressed alleles in genes that are targets for known drugs. Analysis at a site level identifies patterns of site specific preferential allele expression with similar pathways being impacted in the primary and metastasis sites. We conclude that genes with preferentially expressed variant alleles can act as cancer drivers and that targeting those genes could lead to new therapeutic strategies. PMID:26735499

  10. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

    PubMed Central

    Chen, Jieming; Rozowsky, Joel; Galeev, Timur R.; Harmanci, Arif; Kitchen, Robert; Bedford, Jason; Abyzov, Alexej; Kong, Yong; Regan, Lynne; Gerstein, Mark

    2016-01-01

    Large-scale sequencing in the 1000 Genomes Project has revealed multitudes of single nucleotide variants (SNVs). Here, we provide insights into the functional effect of these variants using allele-specific behaviour. This can be assessed for an individual by mapping ChIP-seq and RNA-seq reads to a personal genome, and then measuring ‘allelic imbalances' between the numbers of reads mapped to the paternal and maternal chromosomes. We annotate variants associated with allele-specific binding and expression in 382 individuals by uniformly processing 1,263 functional genomics data sets, developing approaches to reduce the heterogeneity between data sets due to overdispersion and mapping bias. Since many allelic variants are rare, aggregation across multiple individuals is necessary to identify broadly applicable ‘allelic elements'. We also found SNVs for which we can anticipate allelic imbalance from the disruption of a binding motif. Our results serve as an allele-specific annotation for the 1000 Genomes variant catalogue and are distributed as an online resource (alleledb.gersteinlab.org). PMID:27089393

  11. Quantifying the transcriptional output of single alleles in single living mammalian cells

    PubMed Central

    Yunger, Sharon; Rosenfeld, Liat; Garini, Yuval; Shav-Tal, Yaron

    2013-01-01

    Transcription kinetics of actively transcribing genes in vivo have generally been measured using tandem gene arrays. However, tandem arrays do not reflect the endogenous state of genome organization where genes appear as single alleles. We present here a robust technique for the quantification of mRNA synthesis from a single allele in real-time, in single living mammalian cells. The protocol describes how to generate cell clones harboring a tagged allele and how to detect in vivo transcription from this tagged allele at high spatial and temporal resolution throughout the cell cycle. Quantification of nascent mRNAs produced from the single tagged allele is performed using RNA fluorescence in situ hybridization (FISH) and live-cell imaging. Subsequent analyses and data modeling detailed in the protocol include measurements of: transcription rates of RNA polymerase II; determining the number of polymerases recruited to the tagged allele; and measuring the spacing between polymerases. Generating the cells containing the single tagged alleles should take up to a month; RNA FISH or live-cell imaging will require an additional week. PMID:23424748

  12. Allelic association of the D2 dopamine receptor gene with cocaine dependence.

    PubMed

    Noble, E P; Blum, K; Khalsa, M E; Ritchie, T; Montgomery, A; Wood, R C; Fitch, R J; Ozkaragoz, T; Sheridan, P J; Anglin, M D

    1993-10-01

    The objective of the present study was to examine allelic prevalence of the D2 dopamine receptor (DRD2) gene in male cocaine-dependent (CD) Caucasian (non-Hispanic) subjects and to determine the relationship of DRD2 alleles to family history and selected behavioral measures. The prevalence of the A1 allele in CD subjects (n = 53) was 50.9%. It was significantly higher than either the 16.0% prevalence (P < 10(-4)) in non-substance abusing controls (n = 100) or the 30.9% prevalence (P < 10(-2)) in population controls (n = 265) wherein substance abusers were not excluded. Similarly, a significantly higher prevalence (P < 10(-2)) of the B1 allele was found in CD subjects (n = 52) compared with non-substance abusing controls (n = 53); 38.5% vs. 13.2%. Logistic regression analysis of CD subjects identified potent routes of cocaine use and the interaction of early deviant behaviors and parental alcoholism as significant risk factors associated with the A1 allele. The cumulative number of these three risk factors in CD subjects was positively and significantly (P < 10(-3)) related to A1 allelic prevalence. The data showing a strong association of the minor alleles (A1 and B1) of the DRD2 with cocaine dependence suggest that a gene, located on the q22-q23 region of chromosome 11, confers susceptibility to this drug disorder. PMID:8261891

  13. Dynamic variation in allele-specific gene expression of Paraoxonase-1 in murine and human tissues

    PubMed Central

    Parker-Katiraee, Layla; Bousiaki, Eleni; Monk, David; Moore, Gudrun E.; Nakabayashi, Kazuhiko; Scherer, Stephen W.

    2008-01-01

    Differential allelic expression has been shown to be common in mice, humans and maize, and variability in the expression of polymorphic alleles has been associated with human disease. Here, we describe the differential expression pattern of Paraoxonase-1, a gene involved in lipid metabolism and implicated in the formation of atherosclerotic lesions. We measured the expression of the murine Paraoxonase-1 gene (Pon1) in livers at different stages of embryonic development using F1 hybrid crosses and quantified the transcriptional level of both parental alleles. Using human foetal tissues, we analysed the expression of the human orthologue (PON1) and found monoallelic or preferential allelic expression in 6/7 and 4/4 samples from liver and pancreas, respectively. We observed that Pon1 does not show a parent-of-origin preference in its allelic expression, but has dramatic variations in allele-specific expression occurring throughout development. This study has important repercussions in the analysis of haplotypes at disease loci, since it implies that the expression of polymorphic alleles can be unequal and dynamic. PMID:18678600

  14. Allele dependent silencing of COL1A2 using small interfering RNAs

    PubMed Central

    Lindahl, Katarina; Rubin, Carl-Johan; Kindmark, Andreas; Ljunggren, Östen

    2008-01-01

    Osteogenesis imperfecta (OI) is generally caused by a dominant mutation in Collagen I, encoded by the genes COL1A1 and COL1A2. To date there is no satisfactory therapy for OI, but inactivation of the mutant allele through small interfering RNAs (siRNA) is a promising approach, as siRNAs targeting each allele of a polymorphism could be used for allele-specific silencing irrespective of the location of the actual mutations. In this study we examined the allele dependent effects of several tiled siRNAs targeting a region surrounding an exonic COL1A2 T/C polymorphism (rs1800222) in heterozygous primary human bone cells. Relative abundances of COL1A2 alleles were determined by cDNA sequencing and overall COL1A2 abundance was analyzed by quantitative PCR. One of the siRNAs decreased overall COL1A2 abundance by 71% of which 75% was due to silencing of the targeted T-allele. In conclusion, allele-preferential silencing of Collagen type I genes may be a future therapeutic approach for OI. PMID:19015742

  15. Power decreases trust in social exchange

    PubMed Central

    Schilke, Oliver; Reimann, Martin; Cook, Karen S.

    2015-01-01

    How does lacking vs. possessing power in a social exchange affect people’s trust in their exchange partner? An answer to this question has broad implications for a number of exchange settings in which dependence plays an important role. Here, we report on a series of experiments in which we manipulated participants’ power position in terms of structural dependence and observed their trust perceptions and behaviors. Over a variety of different experimental paradigms and measures, we find that more powerful actors place less trust in others than less powerful actors do. Our results contradict predictions by rational actor models, which assume that low-power individuals are able to anticipate that a more powerful exchange partner will place little value on the relationship with them, thus tends to behave opportunistically, and consequently cannot be trusted. Conversely, our results support predictions by motivated cognition theory, which posits that low-power individuals want their exchange partner to be trustworthy and then act according to that desire. Mediation analyses show that, consistent with the motivated cognition account, having low power increases individuals’ hope and, in turn, their perceptions of their exchange partners’ benevolence, which ultimately leads them to trust. PMID:26438869

  16. Power decreases trust in social exchange.

    PubMed

    Schilke, Oliver; Reimann, Martin; Cook, Karen S

    2015-10-20

    How does lacking vs. possessing power in a social exchange affect people's trust in their exchange partner? An answer to this question has broad implications for a number of exchange settings in which dependence plays an important role. Here, we report on a series of experiments in which we manipulated participants' power position in terms of structural dependence and observed their trust perceptions and behaviors. Over a variety of different experimental paradigms and measures, we find that more powerful actors place less trust in others than less powerful actors do. Our results contradict predictions by rational actor models, which assume that low-power individuals are able to anticipate that a more powerful exchange partner will place little value on the relationship with them, thus tends to behave opportunistically, and consequently cannot be trusted. Conversely, our results support predictions by motivated cognition theory, which posits that low-power individuals want their exchange partner to be trustworthy and then act according to that desire. Mediation analyses show that, consistent with the motivated cognition account, having low power increases individuals' hope and, in turn, their perceptions of their exchange partners' benevolence, which ultimately leads them to trust. PMID:26438869

  17. Amyloid mediates the association of apolipoprotein E e4 allele to cognitive function in older people

    PubMed Central

    Bennett, D; Schneider, J; Wilson, R; Bienias, J; Berry-Kravis, E; Arnold, S

    2005-01-01

    Background: The neurobiological changes underlying the association of the apolipoprotein E (APOE) e4 allele with level of cognition are poorly understood. Objective: To test the hypothesis that amyloid load can account for (mediate) the association of the APOE e4 allele with level of cognition assessed proximate to death. Methods: There were 44 subjects with clinically diagnosed Alzheimer's disease and 50 without dementia, who had participated in the Religious Orders Study. They underwent determination of APOE allele status, had comprehensive cognitive testing in the last year of life, and brain autopsy at death. The percentage area of cortex occupied by amyloid beta and the density of tau positive neurofibrillary tangles were quantified from six brain regions and averaged to yield summary measures of amyloid load and neurofibrillary tangles. Multiple regression analyses were used to examine whether amyloid load could account for the effect of allele status on level of cognition, controlling for age, sex, and education. Results: Possession of at least one APOE e4 allele was associated with lower level of cognitive function proximate to death (p = 0.04). The effect of the e4 allele was reduced by nearly 60% and was no longer significant after controlling for the effect of amyloid load, whereas there was a robust inverse association between amyloid and cognition (p = 0.001). Because prior work had suggested that neurofibrillary tangles could account for the association of amyloid on cognition, we next examined whether amyloid could account for the effect of allele status on tangles. In a series of regression analyses, e4 was associated with density of tangles (p = 0.002), but the effect of the e4 allele was reduced by more than 50% and was no longer significant after controlling for the effect of amyloid load. Conclusion: These findings are consistent with a sequence of events whereby the e4 allele works through amyloid deposition and subsequent tangle formation to

  18. Extensive Allelic Diversity of MHC Class I in Wild Mallard Ducks.

    PubMed

    Fleming-Canepa, Ximena; Jensen, Shawna M; Mesa, Christine M; Diaz-Satizabal, Laura; Roth, Alexa J; Parks-Dely, Julie A; Moon, Debra A; Wong, Janet P; Evseev, Danyel; Gossen, Desolie A; Tetrault, David G; Magor, Katharine E

    2016-08-01

    MHC class I is critically involved in defense against viruses, and diversity from polygeny and polymorphism contributes to the breadth of the immune response and health of the population. In this article, we examine MHC class I diversity in wild mallard ducks, the natural host and reservoir of influenza A viruses. We previously showed domestic ducks predominantly use UAA, one of five MHC class I genes, but whether biased expression is also true for wild mallards is unknown. Using RT-PCR from blood, we examined expressed MHC class I alleles from 38 wild mallards (Anas platyrhynchos) and identified 61 unique alleles, typically 1 or 2 expressed alleles in each individual. To determine whether expressed alleles correspond to UAA adjacent to TAP2 as in domestic ducks, we cloned and sequenced genomic UAA-TAP2 fragments from all mallards, which matched transcripts recovered and allowed us to assign most alleles as UAA Allelic differences are primarily located in α1 and α2 domains in the residues known to interact with peptide in mammalian MHC class I, suggesting the diversity is functional. Most UAA alleles have unique residues in the cleft predicting distinct specificity; however, six alleles have an unusual conserved cleft with two cysteine residues. Residues that influence peptide-loading properties and tapasin involvement in chicken are fixed in duck alleles and suggest tapasin independence. Biased expression of one MHC class I gene may make viral escape within an individual easy, but high diversity in the population places continual pressure on the virus in the reservoir species. PMID:27342841

  19. Complex and multi-allelic copy number variation in human disease

    PubMed Central

    McCarroll, Steven A.

    2015-01-01

    Hundreds of copy number variants are complex and multi-allelic, in that they have many structural alleles and have rearranged multiple times in the ancestors who contributed chromosomes to current humans. Not only are the relationships of these multi-allelic CNVs (mCNVs) to phenotypes generally unknown, but many mCNVs have not yet been described at the basic levels—alleles, allele frequencies, structural features—that support genetic investigation. To date, most reported disease associations to these variants have been ascertained through candidate gene studies. However, only a few associations have reached the level of acceptance defined by durable replications in many cohorts. This likely stems from longstanding challenges in making precise molecular measurements of the alleles individuals have at these loci. However, approaches for mCNV analysis are improving quickly, and some of the unique characteristics of mCNVs may assist future association studies. Their various structural alleles are likely to have different magnitudes of effect, creating a natural allelic series of growing phenotypic impact and giving investigators a set of natural predictions and testable hypotheses about the extent to which each allele of an mCNV predisposes to a phenotype. Also, mCNVs’ low-to-modest correlation to individual single-nucleotide polymorphisms (SNPs) may make it easier to distinguish between mCNVs and nearby SNPs as the drivers of an association signal, and perhaps, make it possible to preliminarily screen candidate loci, or the entire genome, for the many mCNV–disease relationships that remain to be discovered. PMID:26163405

  20. Allelic variation in the squirrel monkey x-linked color vision gene: biogeographical and behavioral correlates.

    PubMed

    Cropp, Susan; Boinski, Sue; Li, Wen-Hsiung

    2002-06-01

    Most Neotropical primate species possess a polymorphic X-linked and a monomorphic autosomal color vision gene. Consequently, populations are composed of both dichromatics and trichromatics. Most theories on the maintenance of this genetic system revolve around possible advantages for foraging ecology. To examine the issue from a different angle, we compared the numbers and relative frequencies of alleles at the X-linked locus among three species of Saimiri representing a wide range of geographical and behavioral variation in the genus. Exons 3, 4, and 5 of the X-linked opsin gene were sequenced for a large number of X chromosomes for all three species. Several synonymous mutations were detected in exons 4 and 5 for the originally reported alleles but only a single nonsynonymous change was detected. Two alleles were found that appeared to be the result of recombination events. The low occurrence of recombinant alleles and absence of mutations in the amino acids critical for spectral tuning indicates that stabilizing selection acts to maintain the combinations of critical sites specific to each allele. Allele frequencies were approximately the same for all Saimiri species, with a slight but significant difference between S. boliviensis and S. oerstedii. No apparent correlation exists between allele frequencies and behavioral or biogeographical differences between species, casting doubt on the speculation that the spectral sensitivities of the alleles have been maintained because they are specifically well-tuned to Saimiri visual ecology. Rather, the spectral tuning peaks might have been maintained because they are as widely spaced as possible within the limited range of middlewave to longwave spectra useful to all primates. This arrangement creates a balance between maximizing the distance between spectral tuning peaks (allowing the color opponency of the visual system to distinguish between peaks) and maximizing the number of alleles within a limited range (yielding

  1. APOL1 Null Alleles from a Rural Village in India Do Not Correlate with Glomerulosclerosis

    PubMed Central

    Johnstone, Duncan B.; Shegokar, Vijay; Nihalani, Deepak; Rathore, Yogendra Singh; Mallik, Leena; Ashish; Zare, Vasant; Ikizler, H. Omer; Powar, Rajaram; Holzman, Lawrence B.

    2012-01-01

    Background Among African-Americans, genome wide association revealed a strong correlation between the G1 and G2 alleles of APOL1 (apolipoproteinL1, also called trypanolytic factor) and kidney diseases including focal and segmental glomerulosclerosis, HIV-associated nephropathy and hypertensive nephrosclerosis. In the prevailing hypothesis, heterozygous APOL1 G1 and G2 alleles increase resistance against Trypanosoma that cause African sleeping sickness, resulting in positive selection of these alleles, but when homozygous the G1 and G2 alleles predispose to glomerulosclerosis. While efforts are underway to screen patients for G1 and G2 alleles and to better understand “APOL1 glomerulopathy,” no data prove that these APOL1 sequence variants cause glomerulosclerosis. G1 and G2 correlate best with glomerulosclerosis as recessive alleles, which suggests a loss of function mutation for which proof of causality is commonly tested with homozygous null alleles. This test cannot be performed in rodents as the APOL gene cluster evolved only in primates. However, there is a homozygous APOL1 null human being who lives in a village in rural India. This individual and his family offer a unique opportunity to test causality between APOL1 null alleles and glomerulosclerosis. Methods and Findings We obtained clinical data, blood and urine from this APOL1 null patient and 50 related villagers. Based on measurements of blood pressure, BUN, creatinine, albuminuria, genotyping and immunoblotting, this APOL1 null individual does not have glomerulosclerosis, nor do his relatives who carry APOL1 null alleles. Conclusions This small study cannot provide definitive conclusions but the absence of glomerulosclerosis in this unique population is consistent with the possibility that African-American glomerulosclerosis is caused, not by loss of APOL1 function, but by other mechanisms including a subtle gain of function or by the “genetic hitchhiking” of deleterious mutations in a gene

  2. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.

    PubMed

    Reddy, Timothy E; Gertz, Jason; Pauli, Florencia; Kucera, Katerina S; Varley, Katherine E; Newberry, Kimberly M; Marinov, Georgi K; Mortazavi, Ali; Williams, Brian A; Song, Lingyun; Crawford, Gregory E; Wold, Barbara; Willard, Huntington F; Myers, Richard M

    2012-05-01

    A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this problem, we measured genome-wide differential allelic occupancy of 24 TFs and EP300 in a human lymphoblastoid cell line GM12878. Overall, 5% of human TF binding sites have an allelic imbalance in occupancy. At many sites, TFs clustered in TF-binding hubs on the same homolog in especially open chromatin. While genetic variation in core TF binding motifs generally resulted in large allelic differences in TF occupancy, most allelic differences in occupancy were subtle and associated with disruption of weak or noncanonical motifs. We also measured genome-wide differential allelic expression of genes with and without heterozygous exonic variants in the same cells. We found that genes with differential allelic expression were overall less expressed both in GM12878 cells and in unrelated human cell lines. Comparing TF occupancy with expression, we found strong association between allelic occupancy and expression within 100 bp of transcription start sites (TSSs), and weak association up to 100 kb from TSSs. Sites of differential allelic occupancy were significantly enriched for variants associated with disease, particularly autoimmune disease, suggesting that allelic differences in TF occupancy give functional insights into intergenic variants associated with disease. Our results have the potential to increase the power and interpretability of association studies by targeting functional intergenic variants in addition to protein coding sequences. PMID:22300769

  3. Dose effect of allele {epsilon}4 of apolipoprotein E on risk and age at onset of Pick disease

    SciTech Connect

    Farrer, L.A.; Abraham, C.; Volicer, L.

    1994-09-01

    Pick disease (PD) is a rare progressive dementing illness characterized by severe atrophy of the frontal and temporal lobes. Brains of PD patients lack neurofibrillary tangles which are characteristic findings of Alzheimer disease (AD), but display neuronal swelling and argyrophilic inclusions (i.e., Pick bodies) which contain phosphorylated neurofilaments, tau and complex lipids. Clinically, PD is often difficult to distinguish from AD. The fact that PD is often familial and the evidence suggesting that the {epsilon}4 allele of apoE is a risk factor for AD and multi-infarct dementia prompted us to study apoE isoforms in PD. ApoE genotypes were evaluated in an autopsy series of cases (19 AD, 15 PD, and 7 {open_quotes}controls{close_quotes} with other or no pathology). All subjects were unrelated except for 2 brothers who both had PD. Age at onset in the PD patients ranged from 41 to 59 years. The frequency of {epsilon}4 is significantly higher among AD subjects (47.4%) than in Pick cases (23.3%; P=0.4) or controls (7.1%; P=.008), but the 16% difference between PD and control subjects was not significant, perhaps due to small sample sizes. Linear regression analysis showed that the number of {epsilon}4 alleles was inversely related to age at onset of PD (P=.04) and accounted for 27% of the variation in age at onset. These results suggest that {epsilon}4 may be a susceptibility factor for dementia and not specifically AD. Preliminary experiments using an antibody against apoE suggest that Pick bodies may be immunoreactive with this antibody and that apoE binds to abnormal filaments. The association of the {epsilon}4 allele with dementias other than AD and the apoE staining results support a model postulating an interaction between the {epsilon}4 isoform and tau.

  4. Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping.

    PubMed

    Gautier, Mathieu; Foucaud, Julien; Gharbi, Karim; Cézard, Timothée; Galan, Maxime; Loiseau, Anne; Thomson, Marian; Pudlo, Pierre; Kerdelhué, Carole; Estoup, Arnaud

    2013-07-01

    Molecular markers produced by next-generation sequencing (NGS) technologies are revolutionizing genetic research. However, the costs of analysing large numbers of individual genomes remain prohibitive for most population genetics studies. Here, we present results based on mathematical derivations showing that, under many realistic experimental designs, NGS of DNA pools from diploid individuals allows to estimate the allele frequencies at single nucleotide polymorphisms (SNPs) with at least the same accuracy as individual-based analyses, for considerably lower library construction and sequencing efforts. These findings remain true when taking into account the possibility of substantially unequal contributions of each individual to the final pool of sequence reads. We propose the intuitive notion of effective pool size to account for unequal pooling and derive a Bayesian hierarchical model to estimate this parameter directly from the data. We provide a user-friendly application assessing the accuracy of allele frequency estimation from both pool- and individual-based NGS population data under various sampling, sequencing depth and experimental error designs. We illustrate our findings with theoretical examples and real data sets corresponding to SNP loci obtained using restriction site-associated DNA (RAD) sequencing in pool- and individual-based experiments carried out on the same population of the pine processionary moth (Thaumetopoea pityocampa). NGS of DNA pools might not be optimal for all types of studies but provides a cost-effective approach for estimating allele frequencies for very large numbers of SNPs. It thus allows comparison of genome-wide patterns of genetic variation for large numbers of individuals in multiple populations. PMID:23730833

  5. Using Ion Exchange Chromatography to Separate and Quantify Complex Ions

    ERIC Educational Resources Information Center

    Johnson, Brian J.

    2014-01-01

    Ion exchange chromatography is an important technique in the separation of charged species, particularly in biological, inorganic, and environmental samples. In this experiment, students are supplied with a mixture of two substitution-inert complex ions. They separate the complexes by ion exchange chromatography using a "flash"…

  6. Building Bridges. Meeting Institutional Needs by Collaboration Through Interinstitutional Exchanges.

    ERIC Educational Resources Information Center

    Mukenge, Ida Rousseau

    Discusses the rationale, experiences, and outcomes of the Interinstitutional Exchange Program (IEP), sponsored jointly by the Council of Independent Colleges (CIC) and the United Negro College Fund (UNCF). CIC made grants of up to $15,000 each to support exchanges of faculty and administrators between nine private historically black colleges and…

  7. Structured Exchange and Childhood Learning: Ghetto Children. Program Activity 12.

    ERIC Educational Resources Information Center

    Hamblin, Robert L.; Buckholdt, David

    Program descriptions are introduced by theories of the reasons for the apparent low IQ of many black ghetto children. The theories are the genetic, the stimulus deprivation, the expectation, and the learning-exchange theory. Five experiments with ghetto underachievers are described. The first was designed to use token exchange in a remedial class…

  8. How to buy the right heat exchanger

    SciTech Connect

    Crisi, G.S.

    1992-02-01

    Engineers are generally well schooled in the process aspects related to selecting, specifying and obtaining heat exchangers, and much literature on the subject is available. This paper reports that apart from this technical knowledge, however, an extensive amount of useful practical lore has accumulated on how to acquire exchangers effectively and without mishap. The discussion here relates mainly to heat-exchange devices, such as shell-and-tube, double-pipe and plate exchangers, that regularly accommodate process fluids on both the hot and cold sides. However, many of the same considerations apply to other heat-transfer devices used in the CPI, including air coolers, heating or cooling coils for vessels, and barometric condensers. Acquiring a heat exchanger generally consists of following these steps: Establish the process conditions; Make the thermal balance; Select the type of exchanger; Size the exchanger; Choose the materials of construction; Determine key construction details; Write the Data Sheet and the General Specification; Prepare the vendor list; Send the inquiries; Make the bid analysis; Check vendor drawings; Follow manufacture and testing. Selecting the type of exchanger entails process considerations, capacity, ease of maintenance, suitability for the site, cost, and perhaps other factors. Some can be resolved fairly readily. The first step in contacting suppliers is to assess their previous experience in equal or similar services. Whenever possible, visit the actual customer site and talk directly with the personnel who operate and maintain the equipment. When a visit is not possible, make at least a phone call. Also keep in mind the possibility of a quite different kind of pitfall during the selection step: your own subjective preferences.

  9. Clarifying the Relationship between Average Excesses and Average Effects of Allele Substitutions.

    PubMed

    Alvarez-Castro, José M; Yang, Rong-Cai

    2012-01-01

    Fisher's concepts of average effects and average excesses are at the core of the quantitative genetics theory. Their meaning and relationship have regularly been discussed and clarified. Here we develop a generalized set of one locus two-allele orthogonal contrasts for average excesses and average effects, based on the concept of the effective gene content of alleles. Our developments help understand the average excesses of alleles for the biallelic case. We dissect how average excesses relate to the average effects and to the decomposition of the genetic variance. PMID:22509178

  10. Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles | Office of Cancer Genomics

    Cancer.gov

    Cancer genome characterization efforts now provide an initial view of the somatic alterations in primary tumors. However, most point mutations occur at low frequency, and the function of these alleles remains undefined. We have developed a scalable systematic approach to interrogate the function of cancer-associated gene variants. We subjected 474 mutant alleles curated from 5,338 tumors to pooled in vivo tumor formation assays and gene expression profiling. We identified 12 transforming alleles, including two in genes (PIK3CB, POT1) that have not been shown to be tumorigenic.

  11. Heat exchanger restart evaluation

    SciTech Connect

    Morrison, J.M.; Hirst, C.W.; Lentz, T.F.

    1992-02-28

    On December 24, 1991, the K-Reactor was in the shutdown mode with full AC process water flow and full cooling water flow. Safety rod testing was being performed as part of the power ascension testing program. The results of cooling water samples indicated tritium concentrations higher than allowable. Further sampling and testing confirmed a Process Water System to Cooling Water System leak in heat exchanger 4A (HX 4A). The heat exchanger was isolated and the plant shutdown. Heat exchanger 4kA was removed from the plant and moved to C-Area prior to performing examinations and diagnostic testing. This included locating and identifying the leaking tube or tubes, eddy current examination of the leaking tube and a number of adjacent tubes, visually inspecting the leaking tube from both the inside as well as the area surrounding the failure mechanism. In addition ten other tubes that either exhibited eddy current indications or would represent a baseline condition were removed from heat exchanger 4A for metallurgical examination. Additional analysis and review of heat exchanger leakage history was performed to determine if there are any patterns which can be used for predictive purposes. Compensatory actions have been taken to improve the sensitivity and response time to any future events of this type. The results of these actions are summarized herein.

  12. Heat exchanger restart evaluation

    SciTech Connect

    Morrison, J.M.; Hirst, C.W.; Lentz, T.F.

    1992-03-18

    On December 24, 1991, the K-Reactor was in the shutdown mode with full AC process water flow and full cooling water flow. Safety rod testing was being performed as part of the power ascension testing program. The results of cooling water samples indicated tritium concentrations higher than allowable. Further sampling and testing confirmed a Process Water System to Cooling Water System leak in heat exchanger 4A (HX 4A). The heat exchanger was isolated and the plant shutdown. Heat exchanger 4A was removed from the plant and moved to C-Area prior to performing examinations and diagnostic testing. This included locating and identifying the leaking tube or tubes, eddy current examination of the leaking tube and a number of adjacent tubes, visually inspecting the leaking tube from both the inside as well as the area surrounding the identified tube. The leaking tube was removed and examined metallurgically to determine the failure mechanism. In addition ten other tubes that either exhibited eddy current indications or would represent a baseline condition were removed from heat exchanger 4A for metallurgical examination. Additional analysis and review of heat exchanger leakage history was performed to determine if there are any patterns which can be used for predictive purposes. Compensatory actions have been taken to improve the sensitivity and response time to any future events of this type. The results of these actions are summary herein.

  13. Heat exchanger restart evaluation

    SciTech Connect

    Morrison, J.M.; Hirst, C.W.; Lentz, T.F.

    1992-03-18

    On December 24, 1991, the K-Reactor was in the shutdown mode with full AC process water flow and full cooling water flow. Safety rod testing was being performed as part of the power ascension testing program. The results of cooling water samples indicated tritium concentrations higher than allowable. Further sampling and testing confirmed a Process Water System to Cooling Water System leak in heat exchanger 4A (HX 4A). The heat exchanger was isolated and the plant shutdown. Heat exchanger 4A was removed from the plant and moved to C-Area prior to performing examinations and diagnostic testing. This included locating and identifying the leaking tube or tubes, eddy current examination of the leaking tube and a number of adjacent tubes, visually inspecting the leaking tube from both the inside as well as the area surrounding the identified tube. The leaking tube was removed and examined metallurgically to determine the failure mechanism. In addition ten other tubes that either exhibited eddy current indications or would represent a baseline condition were removed from heat exchanger 4A for metallurgical examination. Additional analysis and review of heat exchanger leakage history was performed to determine if there are any patterns which can be used for predictive purposes. Compensatory actions have been taken to improve the sensitivity and response time to any future events of this type. The results of these actions are summarized.

  14. PCSK9 polymorphism in a Tunisian cohort: identification of a new allele, L8, and association of allele L10 with reduced coronary heart disease risk.

    PubMed

    Slimani, Afef; Hrira, Mohamed Yahia; Najah, Mohamed; Jomaa, Walid; Maatouk, Faouzi; Hamda, Khaldoun Ben; Abifadel, Marianne; Rabès, Jean-Pierre; Boileau, Catherine; Rouis, Mustapha; Slimane, Mohamed Naceur; Varret, Mathilde

    2015-02-01

    The c.61_63dupCTG (L10) allele of rs72555377 polymorphism in PCSK9 has been reported to be associated with low-density lipoprotein-cholesterol (LDL-C) levels and with a decreased risk of coronary artery disease (CAD). We investigated the effect of two known alleles for rs72555377, L10 and L11, on the risk of CAD in a Tunisian cohort (218 patients diagnosed by angiography and 125 control subjects). Two subgroups of patients were defined by their level of stenosis: ≥50% for CAD and <50% for no-CAD. The genotypes were obtained by the size measurement of fluorescent-labeled PCR products. We identified a novel allele for the rs72555377 polymorphism: an in-frame deletion, c.61_63delCTG (L8). The frequency of the L10 allele was significantly higher in the no-CAD subgroup than in the CAD subgroup (0.210 vs 0.114, p = 0.045), and than in the subgroup of CAD patients presenting a stenosis ≥50% in two or three major coronary arteries (0.210 vs 0.125, p = 0.028). Multiple regression analysis showed that the L10 allele was significantly associated with a reduced risk of CAD (p = 0.049, OR = 0.51[0.26-1.00]), and with its reduced severity (p = 0.045, OR = 0.44[0.20-0.98]). The L10 allele is associated with a reduced risk and severity of CAD, seemingly independently of its LDL-lowering effect, suggesting a direct effect of PCSK9 on atherogenesis. PMID:25239117

  15. Inborn errors of human STAT1: allelic heterogeneity governs the diversity of immunological and infectious phenotypes

    PubMed Central

    Boisson-Dupuis, Stephanie; Kong, Xiao-Fei; Okada, Satoshi; Cypowyj, Sophie; Puel, Anne; Abel, Laurent; Casanova, Jean-Laurent

    2012-01-01

    The genetic dissection of various human infectious diseases has led to the definition of inborn errors of human STAT1 immunity of four types, including (i) autosomal recessive (AR) complete STAT1 deficiency, (ii) AR partial STAT1 deficiency, (iii) autosomal dominant (AD) STAT1 deficiency, and (iv) AD gain of STAT1 activity. The two types of AR STAT1 defect give rise to a broad infectious phenotype with susceptibility to intramacrophagic bacteria (mostly mycobacteria) and viruses (herpes viruses at least), due principally to the impairment of IFN-γ-mediated and IFN-α/β-mediated immunity, respectively. Clinical outcome depends on the extent to which the STAT1 defect decreases responsiveness to these cytokines. AD STAT1 deficiency selectively predisposes individuals to mycobacterial disease, owing to the impairment of IFN-γ-mediated immunity, as IFN-α/β-mediated immunity is maintained. Finally, AD gain of STAT1 activity is associated with autoimmunity, probably owing to an enhancement of IFN-α/β-mediated immunity. More surprisingly, it is also associated with chronic mucocutaneous candidiasis, through as yet undetermined mechanisms involving an inhibition of the development of IL-17-producing T cells. Thus, germline mutations in human STAT1 define four distinct clinical disorders. Various combinations of viral, mycobacterial and fungal infections are therefore allelic at the human STAT1 locus. These experiments of Nature neatly highlight the clinical and immunological impact of the human genetic dissection of infectious phenotypes. PMID:22651901

  16. Evidence that putative ADHD low risk alleles at SNAP25 may increase the risk of schizophrenia.

    PubMed

    Carroll, L S; Kendall, K; O'Donovan, M C; Owen, M J; Williams, N M

    2009-10-01

    Synaptosomal Associated Protein 25 kDa (SNAP25) has been implicated in the pathogenesis of schizophrenia by numerous neuropathological studies and genetic variation at SNAP25 has been reported to be associated with ADHD. Expression levels of the putative schizophrenia susceptibility gene DTNBP1 has been shown to influence the levels of SNAP25 in vitro. We undertook directed mutation screening of SNAP25 in UK schizophrenic cases followed by direct association analysis of all variants identified and identified known exonic SNPs that showed evidence for association (rs3746544 P = 0.004 OR = 1.26, rs8636 P = 0.003 OR = 1.27), although these SNPs are highly correlated (r(2) > 0.99). We additionally genotyped a further 31 tag SNPs spanning the SNAP25 locus and identified several independent SNPs that were nominally associated with schizophrenia (strongest association at rs3787283, P = 0.006, OR = 1.25) however, due to the number of tests performed no SNP met experiment-wise significance (minimum permuted P-value = 0.1). Post hoc analysis revealed that the SNPs nominally associated with schizophrenia (rs3787283, rs3746544) were the same as those previously demonstrated to be associated with ADHD but with the opposite alleles, allowing the intriguing hypothesis that genetic variation at SNAP25 may be differentially associated with both schizophrenia and ADHD. PMID:19132710

  17. The HLA-DRB1 allele polymorphisms and nasopharyngeal carcinoma.

    PubMed

    Yang, Huimin; Yu, Kaihui; Zhang, Ruoheng; Li, Jiatong; Wei, Xiaomou; Zhang, Yuening; Zhang, Chengdong; Xiao, Feifan; Zhao, Dong; Lin, Xuandong; Wu, Huayu; Yang, Xiaoli

    2016-06-01

    Human leukocyte antigen (HLA)-DRB1 has been reported to influence individual's susceptibility to nasopharyngeal carcinoma (NPC) by many studies in recent years; however, these studies provided controversial results. The meta-analysis was thus conducted here to estimate the relationship between HLA-DRB1 polymorphisms and NPC. After an extensive review of journals from various databases (PubMed, the Web of Science, Embase, China National Knowledge Internet (CNKI), and Wanfang Database), 8 out of 69 case-control studies, including 778 cases and 1148 controls, were extracted. The results showed that 4 of 13 polymorphisms allele are statistically significantly associated with NPC, among them, HLA-DRB1*3, HLA-DRB1*9, and HLA-DRB1*10 may increase the risk of NPC while HLA-DRB1*01 has the opposite effect. The pooled odds ratio and 95 % confidence interval (CI) were 1.702 [95 % CI (1.047, 2.765)], 1.363 [95 % CI (1.029, 1.806)], 1.989 [95 % CI (1.042, 3.799)], and 0.461 [95 % CI (0.315, 0.676)], respectively. In a further ethnicity-based subgroup analysis, HLA-DRB1*08, HLA-DRB1*11, and HLA-DRB1*16 were found to be linked with NPC in Asian, Tunisian, and Caucasian, respectively. In Asian, HLA-DRB1*03, 08, and 10 may elevate the risk whereas HLA-DRB1*09 could lower it. In Tunisian, HLA-DRB1*01 and 11 are the protective factors while HLA-DRB1*03 is the only risk factor. In Caucasian, HLA-DRB1*01 and 03 increase the risk and HLA-DRB1*16 lowers it. The most frequent statistically associated gene is found to be HLA-DRB1*03 which has protective influence on Asian and Tunisian. In conclusion, HLA-DRB1*01, DRB1*03, DRB1*09, and DRB1*10 are related with NPC susceptibility, and the association of HLA-DRB1*08, DRB1*11, and DRB1*16 with NPC risk are significantly different in different ethnicities. PMID:27059731

  18. Type 2 Diabetes Risk Allele Loci in the Qatari Population

    PubMed Central

    Abi Khalil, Charbel; Fakhro, Khalid A.; Robay, Amal; Ramstetter, Monica D.; Al-Azwani, Iman K.; Malek, Joel A.; Zirie, Mahmoud; Jayyousi, Amin; Badii, Ramin; Al-Nabet Al-Marri, Ajayeb; Chiuchiolo, Maria J.; Al-Shakaki, Alya; Chidiac, Omar; Gharbiah, Maey; Bener, Abdulbari; Stadler, Dora; Hackett, Neil R.; Mezey, Jason G.; Crystal, Ronald G.

    2016-01-01

    Background The prevalence of type 2 diabetes (T2D) is increasing in the Middle East. However, the genetic risk factors for T2D in the Middle Eastern populations are not known, as the majority of studies of genetic risk for T2D are in Europeans and Asians. Methods All subjects were ≥3 generation Qataris. Cases with T2D (n = 1,124) and controls (n = 590) were randomly recruited and assigned to the 3 known Qatari genetic subpopulations [Bedouin (Q1), Persian/South Asian (Q2) and African (Q3)]. Subjects underwent genotyping for 37 single nucleotide polymorphisms (SNPs) in 29 genes known to be associated with T2D in Europeans and/or Asian populations, and an additional 27 tag SNPs related to these susceptibility loci. Pre-study power analysis suggested that with the known incidence of T2D in adult Qataris (22%), the study population size would be sufficient to detect significant differences if the SNPs were risk factors among Qataris, assuming that the odds ratio (OR) for T2D SNPs in Qatari’s is greater than or equal to the SNP with highest known OR in other populations. Results Haplotype analysis demonstrated that Qatari haplotypes in the region of known T2D risk alleles in Q1 and Q2 genetic subpopulations were similar to European haplotypes. After Benjamini-Hochberg adjustment for multiple testing, only two SNPs (rs7903146 and rs4506565), both associated with transcription factor 7-like 2 (TCF7L2), achieved statistical significance in the whole study population. When T2D subjects and control subjects were assigned to the known 3 Qatari subpopulations, and analyzed individually and with the Q1 and Q2 genetic subpopulations combined, one of these SNPs (rs4506565) was also significant in the admixed group. No other SNPs associated with T2D in all Qataris or individual genetic subpopulations. Conclusions With the caveats of the power analysis, the European/Asian T2D SNPs do not contribute significantly to the high prevalence of T2D in the Qatari population, suggesting

  19. No association between an allele at the D sub 2 dopamine receptor gene (DRD2) and alcoholism

    SciTech Connect

    Gelernter, J.; Krystal, J.; Kennedy, J.L. West Haven Dept. of Veterans Affairs Medical Center, CT ); O'Malley, S.; Risch, N.; Merikangas, K.; Kidd, K.K. ); Kranzler, H.R. )

    1991-10-02

    The author attempted to replicate a positive allelic association between the A1 allele of DRD2 (the D{sub 2} dopamine receptor locus) and alcoholism that has been reported. They compared allele frequencies at the previously described Taq I restriction fragment length polymorphism system of DRD2 in alcoholics and random population controls.

  20. Modular heat exchanger

    DOEpatents

    Culver, Donald W.

    1978-01-01

    A heat exchanger for use in nuclear reactors includes a heat exchange tube bundle formed from similar modules each having a hexagonal shroud containing a large number of thermally conductive tubes which are connected with inlet and outlet headers at opposite ends of each module, the respective headers being adapted for interconnection with suitable inlet and outlet manifold means. In order to adapt the heat exchanger for operation in a high temperature and high pressure environment and to provide access to all tube ports at opposite ends of the tube bundle, a spherical tube sheet is arranged in sealed relation across the chamber with an elongated duct extending outwardly therefrom to provide manifold means for interconnection with the opposite end of the tube bundle.