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Sample records for allelic exchange experiments

  1. 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

  2. Allelic exchange in Mycobacterium tuberculosis with long linear recombination substrates.

    PubMed Central

    Balasubramanian, V; Pavelka, M S; Bardarov, S S; Martin, J; Weisbrod, T R; McAdam, R A; Bloom, B R; Jacobs, W R

    1996-01-01

    Genetic studies of Mycobacterium tuberculosis have been greatly hampered by the inability to introduce specific chromosomal mutations. Whereas the ability to perform allelic exchanges has provided a useful method of gene disruption in other organisms, in the clinically important species of mycobacteria, such as M. tuberculosis and Mycobacterium bovis, similar approaches have thus far been unsuccessful. In this communication, we report the development of a shuttle mutagenesis strategy that involves the use of long linear recombination substrates to reproducibly obtain recombinants by allelic exchange in M. tuberculosis. Long linear recombination substrates, approximately 40 to 50 kb in length, were generated by constructing libraries in the excisable cosmid vector pYUB328. The cosmid vector could be readily excised from the recombinant cosmids by digestion with PacI, a restriction endonuclease for which there exist few, if any, sites in mycobacterial genomes. A cosmid containing the mycobacterial leuD gene was isolated, and a selectable marker conferring resistance to kanamycin was inserted into the leuD gene in the recombinant cosmid by interplasmid recombination in Escherichia coli. A long linear recombination substrate containing the insertionally mutated leuD gene was generated by PacI digestion. Electroporation of this recombination substrate containing the insertionally mutated leuD allele resulted in the generation of leucine auxotrophic mutants by homologous recombination in 6% of the kanamycin-resistant transformants for both the Erdman and H37Rv strains of M. tuberculosis. The ability to perform allelic exchanges provides an important approach for investigating the biology of this pathogen as well as developing new live-cell M. tuberculosis-based vaccines. PMID:8550428

  3. Genetic exchange of fimbrial alleles exemplifies the adaptive virulence strategy of Porphyromonas gingivalis.

    PubMed

    Kerr, Jennifer E; Abramian, Jared R; Dao, Doan-Hieu V; Rigney, Todd W; Fritz, Jamie; Pham, Tan; Gay, Isabel; Parthasarathy, Kavitha; Wang, Bing-yan; Zhang, Wenjian; Tribble, Gena D

    2014-01-01

    Porphyromonas gingivalis is a gram-negative anaerobic bacterium, a member of the human oral microbiome, and a proposed "keystone" pathogen in the development of chronic periodontitis, an inflammatory disease of the gingiva. P. gingivalis is a genetically diverse species, and is able to exchange chromosomal DNA between strains by natural competence and conjugation. In this study, we investigate the role of horizontal DNA transfer as an adaptive process to modify behavior, using the major fimbriae as our model system, due to their critical role in mediating interactions with the host environment. We show that P. gingivalis is able to exchange fimbrial allele types I and IV into four distinct strain backgrounds via natural competence. In all recombinants, we detected a complete exchange of the entire fimA allele, and the rate of exchange varies between the different strain backgrounds. In addition, gene exchange within other regions of the fimbrial genetic locus was identified. To measure the biological implications of these allele swaps we compared three genotypes of fimA in an isogenic background, strain ATCC 33277. We demonstrate that exchange of fimbrial allele type results in profound phenotypic changes, including the quantity of fimbriae elaborated, membrane blebbing, auto-aggregation and other virulence-associated phenotypes. Replacement of the type I allele with either the type III or IV allele resulted in increased invasion of gingival fibroblast cells relative to the isogenic parent strain. While genetic variability is known to impact host-microbiome interactions, this is the first study to quantitatively assess the adaptive effect of exchanging genes within the pan genome cloud. This is significant as it presents a potential mechanism by which opportunistic pathogens may acquire the traits necessary to modify host-microbial interactions.

  4. Genetic Exchange of Fimbrial Alleles Exemplifies the Adaptive Virulence Strategy of Porphyromonas gingivalis

    PubMed Central

    Kerr, Jennifer E.; Abramian, Jared R.; Dao, Doan-Hieu V.; Rigney, Todd W.; Fritz, Jamie; Pham, Tan; Gay, Isabel; Parthasarathy, Kavitha; Wang, Bing-yan; Zhang, Wenjian; Tribble, Gena D.

    2014-01-01

    Porphyromonas gingivalis is a gram–negative anaerobic bacterium, a member of the human oral microbiome, and a proposed “keystone” pathogen in the development of chronic periodontitis, an inflammatory disease of the gingiva. P. gingivalis is a genetically diverse species, and is able to exchange chromosomal DNA between strains by natural competence and conjugation. In this study, we investigate the role of horizontal DNA transfer as an adaptive process to modify behavior, using the major fimbriae as our model system, due to their critical role in mediating interactions with the host environment. We show that P. gingivalis is able to exchange fimbrial allele types I and IV into four distinct strain backgrounds via natural competence. In all recombinants, we detected a complete exchange of the entire fimA allele, and the rate of exchange varies between the different strain backgrounds. In addition, gene exchange within other regions of the fimbrial genetic locus was identified. To measure the biological implications of these allele swaps we compared three genotypes of fimA in an isogenic background, strain ATCC 33277. We demonstrate that exchange of fimbrial allele type results in profound phenotypic changes, including the quantity of fimbriae elaborated, membrane blebbing, auto-aggregation and other virulence-associated phenotypes. Replacement of the type I allele with either the type III or IV allele resulted in increased invasion of gingival fibroblast cells relative to the isogenic parent strain. While genetic variability is known to impact host-microbiome interactions, this is the first study to quantitatively assess the adaptive effect of exchanging genes within the pan genome cloud. This is significant as it presents a potential mechanism by which opportunistic pathogens may acquire the traits necessary to modify host-microbial interactions. PMID:24626479

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. Allelic variations of glut-1 deficiency syndrome: the chinese experience.

    PubMed

    Liu, Yanyan; Bao, Xinhua; Wang, Dong; Fu, Na; Zhang, Xiaoying; Cao, Guangna; Song, Fuying; Wang, Shuang; Zhang, Yuehua; Qin, Jiong; Yang, Hong; Engelstad, Kristin; De Vivo, Darryl C; Wu, Xiru

    2012-07-01

    Glucose transporter type 1 deficiency syndrome is characterized by infantile onset seizures, development delay, movement disorders, and acquired microcephaly. The phenotype includes allelic variants such as intermittent ataxia, choreoathetosis, dystonia, and alternating hemiplegia of childhood with or without epilepsy. Dystonias involve allelic variants of glucose transporter type 1 deficiency syndrome. Three Chinese patients presented with paroxysmal behavioral disturbance, weakness, ataxia (especially after fasting), and exercise intolerance. Electroencephalogram findings did not correlate with clinical manifestations. Cranial magnetic resonance imaging produced normal results or mild hypomyelination. Hypoglycorrhachia was evident in all cases. Cerebrospinal fluid glucose ranged from 1.63-2.45 mmol/L. Erythrocyte 3-O-methyl-d-glucose uptake was decreased to 58% in patient 1. Three SLC2A1 disease-causing mutations (761delA, P383H, and R400C) were observed. No patient tolerated ketogenic diets. Two patients responded to frequent meals with snacks. Cerebrospinal fluid evaluation constitutes the diagnostic testing permitting early treatment of glucose transporter type 1 deficiency syndrome. Early diagnosis and treatment improve prognoses.

  10. 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.

  11. Transformation and isolation of allelic exchange mutants of Chlamydia psittaci using recombinant DNA introduced by electroporation.

    PubMed

    Binet, Rachel; Maurelli, Anthony T

    2009-01-06

    To facilitate genetic investigations in the obligate intracellular pathogens Chlamydia, the ability to construct variants by homologous recombination was investigated in C. psittaci 6BC. The single rRNA operon was targeted with a synthetic 16S rRNA allele, harboring three nucleotide substitutions over 398 bp, which imparts resistance to kasugamycin (Ksm) and spectinomycin (Spc) and causes loss of one HpaI restriction site. A fourth, silent mutation was introduced 654 bp downstream in the beginning of the 23S rRNA gene. C. psittaci 6BC infectious particles were electroporated with various concentrations of circular or linearized plasmids containing different lengths of the rRNA region homologous to the chromosomal copy except for the four nucleotide substitutions. Ksm and Spc were added 18 h after inoculation onto confluent cell monolayers in the plaque assay. Resistant plaques were picked and expanded with selection 10 days later before collecting DNA for analysis by PCR, restriction mapping, sequencing, or Southern. Spontaneous resistance to Ksm and Spc was never observed in mock electroporated bacteria (frequency <6.2 x 10(-9)). Conversely, double resistance and replacement of the 16S rRNA gene were observed when C. psittaci was electroporated with the recombination substrates. Highest efficiency was obtained with 10 microg of circular vector prepared in a DNA methylase-deficient Escherichia coli (1.9 +/- 1.1 x 10(-6), n = 7). Coinheritance of the silent 23S rRNA mutation was seen in 46 of 67 recombinants analyzed, illustrating DNA exchange of up to 1,052 bp in length. These findings provide the first step toward genetic manipulation of Chlamydia.

  12. 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.

  13. Porphyromonas gingivalis Uses Specific Domain Rearrangements and Allelic Exchange to Generate Diversity in Surface Virulence Factors

    PubMed Central

    Dashper, Stuart G.; Mitchell, Helen L.; Seers, Christine A.; Gladman, Simon L.; Seemann, Torsten; Bulach, Dieter M.; Chandry, P. Scott; Cross, Keith J.; Cleal, Steven M.; Reynolds, Eric C.

    2017-01-01

    Porphyromonas gingivalis is a keystone pathogen of chronic periodontitis. The virulence of P. gingivalis is reported to be strain related and there are currently a number of strain typing schemes based on variation in capsular polysaccharide, the major and minor fimbriae and adhesin domains of Lys-gingipain (Kgp), amongst other surface proteins. P. gingivalis can exchange chromosomal DNA between strains by natural competence and conjugation. The aim of this study was to determine the genetic variability of P. gingivalis strains sourced from international locations over a 25-year period and to determine if variability in surface virulence factors has a phylogenetic basis. Whole genome sequencing was performed on 13 strains and comparison made to 10 previously sequenced strains. A single nucleotide polymorphism-based phylogenetic analysis demonstrated a shallow tri-lobed phylogeny. There was a high level of reticulation in the phylogenetic network, demonstrating extensive horizontal gene transfer between the strains. Two highly conserved variants of the catalytic domain of the major virulence factor the Kgp proteinase (KgpcatI and KgpcatII) were found. There were three variants of the fourth Kgp C-terminal cleaved adhesin domain. Specific variants of the cell surface proteins FimA, FimCDE, MfaI, RagAB, Tpr, and PrtT were also identified. The occurrence of all these variants in the P. gingivalis strains formed a mosaic that was not related to the SNP-based phylogeny. In conclusion P. gingivalis uses domain rearrangements and genetic exchange to generate diversity in specific surface virulence factors. PMID:28184216

  14. In-Frame and Unmarked Gene Deletions in Burkholderia cenocepacia via an Allelic Exchange System Compatible with Gateway Technology.

    PubMed

    Fazli, Mustafa; Harrison, Joe J; Gambino, Michela; Givskov, Michael; Tolker-Nielsen, Tim

    2015-06-01

    Burkholderia cenocepacia is an emerging opportunistic pathogen causing life-threatening infections in immunocompromised individuals and in patients with cystic fibrosis, which are often difficult, if not impossible, to treat. Understanding the genetic basis of virulence in this emerging pathogen is important for the development of novel treatment regimes. Generation of deletion mutations in genes predicted to encode virulence determinants is fundamental to investigating the mechanisms of pathogenesis. However, there is a lack of appropriate selectable and counterselectable markers for use in B. cenocepacia, making its genetic manipulation problematic. Here we describe a Gateway-compatible allelic exchange system based on the counterselectable pheS gene and the I-SceI homing endonuclease. This system provides efficiency in cloning homology regions of target genes and allows the generation of precise and unmarked gene deletions in B. cenocepacia. As a proof of concept, we demonstrate its utility by deleting the Bcam1349 gene, encoding a cyclic di-GMP (c-di-GMP)-responsive regulator protein important for biofilm formation.

  15. In-Frame and Unmarked Gene Deletions in Burkholderia cenocepacia via an Allelic Exchange System Compatible with Gateway Technology

    PubMed Central

    Fazli, Mustafa; Harrison, Joe J.; Gambino, Michela; Givskov, Michael

    2015-01-01

    Burkholderia cenocepacia is an emerging opportunistic pathogen causing life-threatening infections in immunocompromised individuals and in patients with cystic fibrosis, which are often difficult, if not impossible, to treat. Understanding the genetic basis of virulence in this emerging pathogen is important for the development of novel treatment regimes. Generation of deletion mutations in genes predicted to encode virulence determinants is fundamental to investigating the mechanisms of pathogenesis. However, there is a lack of appropriate selectable and counterselectable markers for use in B. cenocepacia, making its genetic manipulation problematic. Here we describe a Gateway-compatible allelic exchange system based on the counterselectable pheS gene and the I-SceI homing endonuclease. This system provides efficiency in cloning homology regions of target genes and allows the generation of precise and unmarked gene deletions in B. cenocepacia. As a proof of concept, we demonstrate its utility by deleting the Bcam1349 gene, encoding a cyclic di-GMP (c-di-GMP)-responsive regulator protein important for biofilm formation. PMID:25795676

  16. Hadron Spectroscopy in Double Pomeron Exchange Experiments

    SciTech Connect

    Albrow, Michael

    2016-11-15

    Central exclusive production in hadron-hadron collisions at high energies, for example p + p -> p + X + p, where the "+" represents a large rapidity gap, is a valuable process for spectroscopy of mesonic states X. At collider energies the gaps can be large enough to be dominated by pomeron exchange, and then the quantum numbers of the state X are restricted. Isoscalar JPC = 0++ and 2++ mesons are selected, and our understanding of these spectra is incomplete. In particular, soft pomeron exchanges favor gluon-dominated states such as glueballs, which are expected in QCD but not yet well established. I will review some published data.

  17. 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.

  18. 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)

  19. 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

  20. Suppressing magnetization exchange effects in stimulated-echo diffusion experiments.

    PubMed

    Pagès, Guilhem; Dvinskikh, Sergey V; Furó, István

    2013-09-01

    Exchange of nuclear magnetization between spin pools, either by chemical exchange or by cross-relaxation or both, has a significant influence on the signal attenuation in stimulated-echo-type pulsed field gradient experiments. Hence, in such cases the obtained molecular self-diffusion coefficients can carry a large systematic error. We propose a modified stimulated echo pulse sequence that contains T2-filters during the z-magnetization store period. We demonstrate, using a common theoretical description for chemical exchange and cross-relaxation, that these filters suppress the effects of exchange on the diffusional decay in that frequent case where one of the participating spin pools is immobile and exhibits a short T2. We demonstrate the performance of this experiment in an agarose/water gel. We posit that this new experiment has advantages over other approaches hitherto used, such as that consisting of measuring separately the magnetization exchange rate, if suitable by Goldman-Shen type experiments, and then correcting for exchange effects within the framework of a two-site exchange model. We also propose experiments based on selective decoupling and applicable in systems with no large T2 difference between the different spin pools.

  1. Controlling for P-value inflation in allele frequency change in experimental evolution and artificial selection experiments.

    PubMed

    Kemppainen, Petri; Rønning, Bernt; Kvalnes, Thomas; Hagen, Ingerid J; Ringsby, Thor Harald; Billing, Anna M; Pärn, Henrik; Lien, Sigbjørn; Husby, Arild; Saether, Bernt-Erik; Jensen, Henrik

    2016-11-04

    Experimental evolution studies can be used to explore genomic response to artificial and natural selection. In such studies, loci that display larger allele frequency change than expected by genetic drift alone are assumed to be directly or indirectly associated with traits under selection. However, such studies report surprisingly many loci under selection, suggesting that current tests for allele frequency change may be subject to P-value inflation and hence be anticonservative. One factor known from genomewide association (GWA) studies to cause P-value inflation is population stratification, such as relatedness among individuals. Here, we suggest that by treating presence of an individual in a population after selection as a binary response variable, existing GWA methods can be used to account for relatedness when estimating allele frequency change. We show that accounting for relatedness like this effectively reduces false-positives in tests for allele frequency change in simulated data with varying levels of population structure. However, once relatedness has been accounted for, the power to detect causal loci under selection is low. Finally, we demonstrate the presence of P-value inflation in allele frequency change in empirical data spanning multiple generations from an artificial selection experiment on tarsus length in two free-living populations of house sparrow and correct for this using genomic control. Our results indicate that since allele frequencies in large parts of the genome may change when selection acts on a heritable trait, such selection is likely to have considerable and immediate consequences for the eco-evolutionary dynamics of the affected populations.

  2. The GL Service: Web Service to Exchange GL String Encoded HLA & KIR Genotypes With Complete and Accurate Allele and Genotype Ambiguity

    PubMed Central

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

    2015-01-01

    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

  3. 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…

  4. 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

  5. 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%.

  6. 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.

  7. 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

  8. Lock-exchange experiments with an autocatalytic reaction front

    NASA Astrophysics Data System (ADS)

    Malham, I. Bou; Jarrige, N.; Martin, J.; Rakotomalala, N.; Talon, L.; Salin, D.

    2010-12-01

    A viscous lock-exchange gravity current corresponds to the reciprocal exchange of two fluids of different densities in a horizontal channel. The resulting front between the two fluids spreads as the square root of time, with a diffusion coefficient reflecting the buoyancy, viscosity, and geometrical configuration of the current. On the other hand, an autocatalytic reaction front between a reactant and a product may propagate as a solitary wave, namely, at a constant velocity and with a stationary concentration profile, resulting from the balance between molecular diffusion and chemical reaction. In most systems, the fluid left behind the front has a different density leading to a lock-exchange configuration. We revisit, with a chemical reaction, the classical situation of lock-exchange. We present an experimental analysis of buoyancy effects on the shape and the velocity of the iodate arsenous acid autocatalytic reaction fronts, propagating in horizontal rectangular channels and for a wide range of aspect ratios (1/3 to 20) and cylindrical tubes. We do observe stationary-shaped fronts, spanning the height of the cell and propagating along the cell axis. Our data support the contention that the front velocity and its extension are linked to each other and that their variations scale with a single variable involving the diffusion coefficient of the lock-exchange in the absence of chemical reaction. This analysis is supported by results obtained with lattice Bathnagar-Gross-Krook (BGK) simulations Jarrige et al. [Phys. Rev. E 81, 06631 (2010)], in other geometries (like in 2D simulations by Rongy et al. [J. Chem. Phys. 127, 114710 (2007)] and experiments in cylindrical tubes by Pojman et al. [J. Phys. Chem. 95, 1299 (1991)]), and for another chemical reaction Schuszter et al. [Phys. Rev. E 79, 016216 (2009)].

  9. 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.

  10. Identification and mutagenesis by allelic exchange of choE, encoding a cholesterol oxidase from the intracellular pathogen Rhodococcus equi.

    PubMed

    Navas, J; González-Zorn, B; Ladrón, N; Garrido, P; Vázquez-Boland, J A

    2001-08-01

    The virulence mechanisms of the facultative intracellular parasite Rhodococcus equi remain largely unknown. Among the candidate virulence factors of this pathogenic actinomycete is a secreted cholesterol oxidase, a putative membrane-damaging toxin. We identified and characterized the gene encoding this enzyme, the choE monocistron. Its protein product, ChoE, is homologous to other secreted cholesterol oxidases identified in Brevibacterium sterolicum and Streptomyces spp. ChoE also exhibits significant similarities to putative cholesterol oxidases encoded by Mycobacterium tuberculosis and Mycobacterium leprae. Genetic tools for use with R. equi are poorly developed. Here we describe the first targeted mutagenesis system available for this bacterium. It is based on a suicide plasmid, a selectable marker (the aacC4 apramycin resistance gene from Salmonella), and homologous recombination. The choE allele was disrupted by insertion of the aacC4 gene, cloned in pUC19 and introduced by electroporation in R. equi. choE recombinants were isolated at frequencies between 10(-2) and 10(-3). Twelve percent of the recombinants were double-crossover choE mutants. The choE mutation was associated with loss of cooperative (CAMP-like) hemolysis with sphingomyelinase-producing bacteria (Listeria ivanovii). Functional complementation was achieved by expression of choE from pVK173-T, a pAL5000 derivative conferring hygromycin resistance. Our data demonstrate that ChoE is an important cytolytic factor for R. equi. The highly efficient targeted mutagenesis procedure that we used to generate choE isogenic mutants will be a valuable tool for the molecular analysis of R. equi virulence.

  11. 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…

  12. Elimination of spin diffusion effects in saturation transfer experiments: application to hydrogen exchange in proteins.

    PubMed

    Jensen, Malene Ringkjøbing; Kristensen, Søren M; Led, Jens J

    2007-03-01

    The NMR saturation transfer experiment is widely used to characterize exchange processes in proteins that take place on the ms-s timescale. However, spin diffusion effects are inherently associated with the saturation transfer experiment and may overshadow the effect of the exchange processes of interest. As shown here, the effects from spin diffusion and exchange processes can be separated by varying the field strength of the saturation pulse, thereby allowing correct exchange rates to be obtained. The method is demonstrated using the hydrogen exchange process in the protein Escherichia coli thioredoxin as an example.

  13. Results from the OLYMPUS Two-Photon Exchange Experiment

    NASA Astrophysics Data System (ADS)

    O'Connor, Colton; Olympus Collaboration

    2017-01-01

    Measurements of the proton's electric-to-magnetic form factor ratio obtained by different methods disagree significantly in a way that depends on Q2. The OLYMPUS experiment was designed to empirically quantify two-photon exchange in lepton-proton scattering, an effect that, in some models, can fully account for this disagreement. This was achieved at the DORIS storage ring at DESY by measuring the ratio of the elastic cross-sections for positron-proton and electron-proton scattering with alternating 2.01 GeV lepton beams incident on an internal hydrogen gas target. Data were collected with an integrated luminosity of over 4.0 fb-1 using a large-acceptance toroidal spectrometer and multiple luminosity monitoring systems, allowing for precise results (<1% uncertainty) over the range of 0.6 <=Q2 <= 2.2 (GeV/ c)2. This work is supported by DOE Grant DE-FG02-94ER40818.

  14. A 3-cell deflecting RF cavity for emittance exchange experiment at ANL

    NASA Astrophysics Data System (ADS)

    Shi, Jiaru; Chen, Huaibi; Tang, Chuanxiang; Zheng, Shuxin; Huang, Wenhui; Power, John G.; Jing, Chunguang; Kim, Kwang-Je; Gai, Wei; Li, Derun

    2009-01-01

    An RF deflecting structure has been designed and fabricated for a transverse-to-longitudinal emittance exchange experiment at Argonne National Laboratory (ANL) [Y.-E. Sun, et al., Design study of a transverse-to-longitudinal emittance exchange proof-of-principle experiment, in: Proceedings of PAC-2007, Albuquerque, NM, USA, 2007, pp. 3441-3443 [1

  15. Characterization of an atomic hydrogen source for charge exchange experiments

    NASA Astrophysics Data System (ADS)

    Leutenegger, M. A.; Beiersdorfer, P.; Betancourt-Martinez, G. L.; Brown, G. V.; Hell, N.; Kelley, R. L.; Kilbourne, C. A.; Magee, E. W.; Porter, F. S.

    2016-11-01

    We characterized the dissociation fraction of a thermal dissociation atomic hydrogen source by injecting the mixed atomic and molecular output of the source into an electron beam ion trap containing highly charged ions and recording the x-ray spectrum generated by charge exchange using a high-resolution x-ray calorimeter spectrometer. We exploit the fact that the charge exchange state-selective capture cross sections are very different for atomic and molecular hydrogen incident on the same ions, enabling a clear spectroscopic diagnostic of the neutral species.

  16. 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.

  17. 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…

  18. 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…

  19. 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.

  20. 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.

  1. Sedimentary roles on hyporheic exchange in karst conduits at low Reynolds numbers by laboratory experiments

    NASA Astrophysics Data System (ADS)

    Wu, Yuexia; Hunkeler, Daniel

    2017-01-01

    The relative roles of the sediment grain size/permeability, conduit flow rate and conduit geometry/angle on the hyporheic exchange between a karst conduit and its underlying sediments under low Reynolds numbers (Re) were investigated by means of laboratory experiments and numerical simulations. Two laboratory analogues consisting of siphon structured glass tubes (with bend angles of 15 and 45°) were used for the experimental studies. Tracer experiments were performed in each analogue with sediments of variable grain size (0.45 mm, 0.4-0.7 mm, 1 mm) to characterize the transport properties of contaminants originating from the sediments. Numerical simulations were used to probe the exchange flow patterns and exchange flux magnitudes between the conduit and sediment. Tracer experiments demonstrated a zone of forward flow and a zone of reverse flow in the sediments that were independent of grain size, which were reproduced well by numerical simulations. The exchange flux ranged from 0.02% for fine grains to 2% for coarse grains under the experimental flow conditions. A linear relationship between the exchange flux and the conduit Re value, which was independent of the conduit geometry and sediment grain size, was established with numerical simulations. This study demonstrated that sediment grain size/permeability has no influence on the exchange flow patterns; however, relative to the conduit flow rate and conduit geometry/angle, sediment permeability has a much stronger influence on the exchange rate of hyporheic flow.

  2. 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.

  3. An Experiment with Official and Parallel Foreign Exchange Markets in a Developing Country.

    ERIC Educational Resources Information Center

    Hazlett, Denise; Ganje, Jeela

    1999-01-01

    Describes a classroom experiment that demonstrates under what conditions the parallel market rate approximates the free-market value of the domestic currency. Students act as foreign exchange traders in a developing country. Provides results of the experiment and discussion questions. (CMK)

  4. 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…

  5. 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…

  6. 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…

  7. 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…

  8. 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…

  9. 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.

  10. Application of geometric approximation to the CPMG experiment: Two- and three-site exchange.

    PubMed

    Chao, Fa-An; Byrd, R Andrew

    2017-02-04

    The Carr-Purcell-Meiboom-Gill (CPMG) experiment is one of the most classical and well-known relaxation dispersion experiments in NMR spectroscopy, and it has been successfully applied to characterize biologically relevant conformational dynamics in many cases. Although the data analysis of the CPMG experiment for the 2-site exchange model can be facilitated by analytical solutions, the data analysis in a more complex exchange model generally requires computationally-intensive numerical analysis. Recently, a powerful computational strategy, geometric approximation, has been proposed to provide approximate numerical solutions for the adiabatic relaxation dispersion experiments where analytical solutions are neither available nor feasible. Here, we demonstrate the general potential of geometric approximation by providing a data analysis solution of the CPMG experiment for both the traditional 2-site model and a linear 3-site exchange model. The approximate numerical solution deviates less than 0.5% from the numerical solution on average, and the new approach is computationally 60,000-fold more efficient than the numerical approach. Moreover, we find that accurate dynamic parameters can be determined in most cases, and, for a range of experimental conditions, the relaxation can be assumed to follow mono-exponential decay. The method is general and applicable to any CPMG RD experiment (e.g. N, C', C(α), H(α), etc.) The approach forms a foundation of building solution surfaces to analyze the CPMG experiment for different models of 3-site exchange. Thus, the geometric approximation is a general strategy to analyze relaxation dispersion data in any system (biological or chemical) if the appropriate library can be built in a physically meaningful domain.

  11. Application of geometric approximation to the CPMG experiment: Two- and three-site exchange

    NASA Astrophysics Data System (ADS)

    Chao, Fa-An; Byrd, R. Andrew

    2017-04-01

    The Carr-Purcell-Meiboom-Gill (CPMG) experiment is one of the most classical and well-known relaxation dispersion experiments in NMR spectroscopy, and it has been successfully applied to characterize biologically relevant conformational dynamics in many cases. Although the data analysis of the CPMG experiment for the 2-site exchange model can be facilitated by analytical solutions, the data analysis in a more complex exchange model generally requires computationally-intensive numerical analysis. Recently, a powerful computational strategy, geometric approximation, has been proposed to provide approximate numerical solutions for the adiabatic relaxation dispersion experiments where analytical solutions are neither available nor feasible. Here, we demonstrate the general potential of geometric approximation by providing a data analysis solution of the CPMG experiment for both the traditional 2-site model and a linear 3-site exchange model. The approximate numerical solution deviates less than 0.5% from the numerical solution on average, and the new approach is computationally 60,000-fold more efficient than the numerical approach. Moreover, we find that accurate dynamic parameters can be determined in most cases, and, for a range of experimental conditions, the relaxation can be assumed to follow mono-exponential decay. The method is general and applicable to any CPMG RD experiment (e.g. N, C‧, Cα, Hα, etc.) The approach forms a foundation of building solution surfaces to analyze the CPMG experiment for different models of 3-site exchange. Thus, the geometric approximation is a general strategy to analyze relaxation dispersion data in any system (biological or chemical) if the appropriate library can be built in a physically meaningful domain.

  12. Exchange rate regimes, saving glut and the Feldstein Horioka puzzle: The East Asian experience

    NASA Astrophysics Data System (ADS)

    Kaya-Bahçe, Seçil; Özmen, Erdal

    2008-04-01

    This paper investigates whether the recent experience of the emerging East Asian countries with current account surpluses is consistent with the “saving glut” hypothesis and the Feldstein and Horioka puzzle. The evidence suggests that the saving retention coefficients declined substantially in most of the countries after an endogenous break date coinciding with a major exchange rate regime change with the 1997-1998 crisis. Exchange rate flexibility appears to be enhancing financial integration. The results are consistent with an “investment slump” explanation rather than the “saving glut” postulation.

  13. 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.

  14. 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.

  15. 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.

  16. HeartMate II Left Ventricular Assist Device Pump Exchange: A Single-Institution Experience.

    PubMed

    Shaikh, Asad F; Joseph, Susan M; Lima, Brian; Hall, Shelley A; Malyala, Rajasekhar; Rafael, Aldo E; Gonzalez-Stawinski, Gonzalo V; Chamogeorgakis, Themistokles

    2016-11-30

    Background Left ventricular assist devices (LVADs) have revolutionized the treatment of patients with end-stage heart failure. These devices are replaced when pump complications arise if heart transplant is not possible. We present our experience with HeartMate II (HMII (Thoratec, Plesanton, California, United States)) LVAD pump exchange. Materials and Methods We retrospectively reviewed all cases that required pump exchange due to LVAD complication from November 2011 until June 2016 at a single high-volume institution. The indications, demographics, and outcome were extracted and analyzed. Results Of 250 total patients with implanted HMII LVADs, 16 (6%) required pump exchange during the study period. The initial indications for LVAD placement in these patients were bridge to transplantation (n = 6 [37.5%]) or destination therapy (n = 10 [62.5%]). Fifteen patients (93.8%) required pump exchange due to pump thrombosis and 1 (6.2%) due to refractory driveline infection. Nine patients (56.2%) underwent repeat median sternotomy while a left subcostal approach was used in the remaining seven patients. Fifteen patients (93.7%) survived until hospital discharge. During the follow-up period (median, 155 days), 11 patients remained alive and 4 of these underwent successful cardiac transplantation. Conclusion HMII LVAD pump exchange can be safely performed for driveline infection or pump thrombosis when heart transplantation is not an option.

  17. 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

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

    PubMed

    Hirvonen, J; Murtomäki, L; Kontturi, K

    1998-12-04

    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.

  19. General practice based teaching exchanges in Europe. Experiences from the EU Socrates programme 'primary health care'.

    PubMed

    van Weel, Chris; Mattsson, Bengt; Freeman, George K; de Meyere, Marc; von Fragstein, Martin

    2005-01-01

    This paper reviews the experience of international exchange of medical students for general practice. The experience is based on the EU Socrates programme 'Primary Health Care' that offers, since 1992, clinical attachments and research electives in primary care. This programme involves 11 university departments of general practice/primary care in eight countries: Austria - Vienna; Belgium - Gent; Germany Düsseldorf; Italy - Monza, Udine; Netherlands Nijmegen; Slovenia - Ljubljana; Sweden - Göteborg; and the UK - Edinburgh, Imperial College London and Nottingham. More than 150 students have taken part in the programme, most in the last four years. For clinical attachment communication to patients is essential, and students should be able to speak the language of the host university. A research elective in primary care is less demanding and requires students' ability to communicate in English. Despite marked differences in health care structure in the countries involved, it is quite possible to provide a valuable teaching environment in general practice, and the experience gained by students in the exchanges more than equals that what they would gain at home. The added value is in experiencing the influence of another health care system and of working in another academic primary care centre. A substantial number of research electives have been published in international peer reviewed scientific journals with the student as first (occasionally second) author and staff members of the student's host and home university as co-authors. A further benefit of the exchange programme lies in the transfer teaching innovations between universities.

  20. 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.

  1. 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.

  2. 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.

  3. Effect of Streambed Roughness and Topography on the Solute Transport and Hyporheic Exchanges: Laboratory Experiments

    NASA Astrophysics Data System (ADS)

    Chen, Xiaobing; Zhao, Jian; Chen, Li

    2013-04-01

    Hyporheic zones are critical for maintaining river ecosystem as they provide hyporheic and riparian organisms critical solutes, including nutrients and dissolved gases from bedforms to watershed scales. Among the hyporheic driving factors, the streambed topogaraphy is considered as a significant driving factor for hydraulic process in hyporheic zone that has been well documented in the past few decades. Previous research has implied that the rough streambed impact the flow resistance and continuously affect the hydraulic gradient between the river and the streambed. Recent research works focused more on the realistic pressure distribution along the bedform interface (eg. triangular-shaped sand dunes) on a macro level scale, while only few works related to the hyporheic exchanges induced by pore size scaled topography. How and to what extent that pore size scaled bedform would contribute to the total hyporheic discharge is still unclear. Indeed, the mesoscopic uneven topography can disturb the flow regime that near the water-sand interface, for example, it brings turbulent eddies and fluctuating pressure distribution along a rough gravel bed. In our study, a set of flume experiments were setup to examine the pore size roughness impacts on the solute transport and hyporheic exchanges in surface-subsurface system. Six kinds of riverbed sediments with median diameter range from 1.1 mm to 50.2 mm were chosen for comparative analyses. Also, three kinds of triangular shaped bedforms represented by the ratio α (=δ/?, δ is the amplitude and ? is the wavelength) with value of 0.125, 0.17 and 0.25 were considered as the macro-topography driver variation in our experiments. Our tests revealed that under a flat riverbed condition, the vertical diffusion is the main factor for the solute transport in hyporheic zone, however, the hyporheic exchange rate (represented by the decrease rate in concentration of surface water) is significantly enhanced as the growth of gravel grain

  4. Finnish physicians' experiences with computer-supported patient information exchange and communication in clinical work.

    PubMed

    Viitanen, Johanna; Nieminen, Marko; Hypponen, Hannele; Laaveri, Tinja

    2011-01-01

    Several researchers share the concern of healthcare information systems failing to support communication and collaboration in clinical practices. The objective of this paper is to investigate the current state of computer-supported patient information exchange and associated communication between clinicians. We report findings from a national survey on Finnish physicians? experiences with their currently used clinical information systems with regard to patient information documentation, retrieval, management and exchange-related tasks. The questionnaire study with 3929 physicians indicated the main concern being cross-organisational patient information delivery. In addition, physicians argued computer usage increasingly steals time and attention from caring activities and even disturbs physician?nurse collaboration. Problems in information management were particularly emphasised among those physicians working in hospitals and wards. The survey findings indicated that collaborative applications and mobile or wireless solutions have not been widely adapted in Finnish healthcare and suggested an urgent need for adopting appropriate information and communication technology applications to support information exchange and communication between physicians, and physicians and nurses.

  5. Fast time resolution charge-exchange measurements during the fishbone instability in the poloidal divertor experiment

    SciTech Connect

    Beiersdorfer, P.; Kaita, R.; Goldston, R.J.

    1984-01-01

    Measurements of fast ion losses due to the fishbone instability during high ..beta../sub T/q neutral beam heated discharges in the Poloidal Divertor Experiment have been made using two new vertical-viewing charge-exchange analyzers. The measurements show that the instability has an n=1 toroidal mode number, and that it ejects beam ions in a toroidally rotating beacon directed outward along a major radius. Observations of ejected ions with energies up to twice the beam injection energy at R approx. = R/sub 0/ + a indicate the presence of a non-..mu..-conserving acceleration mechanism.

  6. North Atlantic-Arctic Mediterranean exchanges in an ensemble hindcast experiment

    NASA Astrophysics Data System (ADS)

    Olsen, Steffen MalskæR.; Schmith, Torben

    2007-04-01

    An ensemble-hindcast approach is designed to simulate North Atlantic circulation changes during the period 1948-2005 using the Max Plank Institute Ocean Model forced by atmospheric reanalysis data. The experiment seeks to isolate oceanic changes related to the atmospheric forcing history by evaluating the role of initial conditions and masking internal model variability in the ensemble mean results. Characteristics of the complete North Atlantic-Arctic Mediterranean exchange system is described at key sections by time series of exchanges of volume, ice, heat, and liquid freshwater. Volume transports are divided into water masses by properties, and the constructed climatology of exchanges is shown to compare well with available observational estimates of individual branches. In response to the atmospheric forcing history, we find a modest but robust decline of the Atlantic meridional overturning circulation of 0.4 Sv/decade, in total 2-2.5 Sv since 1948. In contrast, overturning exchanges with the North Atlantic and Nordic Seas and with the Nordic Seas and Arctic Ocean show no sign of cessation. A marked increase in the freshwater storage of the Nordic Seas and in particular of the subpolar Atlantic accompany the model decline in Atlantic overturning. The characteristics of the modeled freshening bears similarities with observed patterns of change since the 1950s, but whereas the origin of observed freshening is uncertain, freshening in the model predominantly results from dynamic changes linked to prominent changes in atmospheric circulation. Moreover, documented increase in the drainage of major Arctic-rivers is found to have a negligible effect on the oceanic changes.

  7. From surfactant adsorption kinetics to asymmetric nanomembrane mechanics: pendant drop experiments with subphase exchange.

    PubMed

    Ferri, James K; Kotsmar, Csaba; Miller, Reinhard

    2010-12-15

    Adsorption equilibrium is the state in which the chemical potential of each species in the interface and bulk is the same. Dynamic phenomena at fluid-fluid interfaces in the presence of surface active species are often probed by perturbing an interface or adjoining bulk phase from the equilibrium state. Many methods designed for studying kinetics at fluid-fluid interfaces focus on removing the system from equilibrium through dilation or compression of the interface. This modifies the surface excess concentration Γ(i) and allows the species distribution in the bulk C(i) to respond. There are only a few methods available for studying fluid-fluid interfaces which seek to control C(i) and allow the interface to respond with changes to Γ(i). Subphase exchange in pendant drops can be achieved by the injection and withdrawal of liquid into a drop at constant volumetric flow rate R(E) during which the interfacial area and drop volume V(D) are controlled to be approximately constant. This can be accomplished by forming a pendant drop at the tip of two coaxial capillary tubes. Although evolution of the subphase concentration C(i)(t) is dictated by extrinsic factors such as R(E) and V(D), complete subphase exchange can always be attained when a sufficient amount of liquid is used. This provides a means to tailor driving forces for adsorption and desorption in fluid-fluid systems and in some cases, fabricate interfacial materials of well-defined composition templated at these interfaces. The coaxial capillary pendant drop (CCPD) method opens a wide variety of experimental possibilities. Experiments and theoretical frameworks are reviewed for the study of surfactant exchange kinetics, macromolecular adsorption equilibrium and dynamics, as well as the fabrication of a wide range of soft surface materials and the characterization of their mechanics. Future directions for new experiments are also discussed.

  8. 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.

  9. 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.

  10. 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.

  11. Improved TROSY-HNCA experiment with suppression of conformational exchange induced relaxation.

    PubMed

    Pervushin, K; Gallius, V; Ritter, C

    2001-10-01

    A general method for improving of the sensitivity of the TROSY-type triple resonance experiments in the presence of conformational exchange-induced (CSX) relaxation is proposed based on the use of CPMG-INEPT (Müller et al., J. Am. Chem. Soc., 1995, 117, 11043-11048) during the N-C polarization transfer periods. Significantly improved sensitivity is demonstrated for the majority of cross-peaks in the new [15N,1H]-TROSY-XY-HNCA experiment, measured with partially folded RNase AS-Protein, with negligible loss of sensitivity for resonances unaffected by CSX relaxation. In addition, a comparison of cross-peak amplitudes in [15N,1N]-TROSY-XY-HNCA and conventional [15N,1H]-TROSY-HNCA spectra provides a quick and sensitive estimation of the CSX relaxation contribution.

  12. 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.

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

    PubMed

    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⩾30s(-1)) while simultaneously eliminating signals originating from slower (∼5s(-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.

  14. 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.

  15. Investigation on the artificial exchange signals induced by the RIDER effect in CODEX experiments.

    PubMed

    Zhang, Rongchun; Chen, Tiehong; Sun, Pingchuan; Li, Baohui; Ding, Datong

    2012-01-01

    The CODEX (center-band only detection of exchange) NMR experiment is widely used for the detection of slow motions in organic solids, especially polymers. However, the RIDER (relaxation-induced dipolar exchange with recoupling) effect may result in artificial exchange signals in the CODEX pure exchange spectrum, which greatly limits the application of CODEX method. Herein, we investigate the distance range that the RIDER effect can reach by performing CODEX experiments on two typical organic solids, hexadecyltrimethylammonium bromide (CTAB) and semi-crystalline polyamide-6 (PA6) where there are no slow molecular motions at room temperature. Our experimental results demonstrate that generally two-bond distance is far enough to ignore the RIDER effect resulted from the dipolar interactions between (13)C and the fast relaxing heteronucleus (14)N. From the built-up curve of RIDER signals as a function of recoupling time and mixing time, it is clearly revealed that the RIDER effect can greatly affect the signal from (13)C directly bonded with (14)N. However, this RIDER effect accounts less than 3% of the reference intensity for signals from (13)C not directly bonded with (14)N if typical recoupling (~0.5 ms) and mixing times (~0.5 s) are used for the investigation of slow motions. When longer recoupling and mixing time are used, there are small RIDER signals even for the (13)C far away from the (14)N. These signals, to a large degree, result from the spin diffusion effect and/or the special microscopic molecule arrangement. However, they are so small compared to the reference signal (~5%) that they can be ignored. Finally, according to the simulation results, it is worth noting that the RIDER signal is still generally negligible compared to the signals due to slow motions if the chemical shift anisotropy reorientation during the mixing time is not too small(larger than 20°) under the condition of 4t(r) recoupling time at the magic-angle-spinning speed of 6.5 kHz.

  16. One year's experience using a rotating filter for therapeutic plasma exchange.

    PubMed

    Kaplan, A A; Halley, S E; Reardon, J; Sevigny, J

    1989-01-01

    The authors previously demonstrated the feasibility of using a rotating filter system for therapeutic plasma exchange. They now report on the technical details of a 1 year clinical experience. Seventeen patients underwent 188 treatments. Hemoaccess was provided by antecubital veins (147 Rx), femoral catheters (37 Rx), or an a-v fistula (3 Rx). Blood flows ranged from 75 to 100 ml/min. Net plasma removed per treatment was 3,231 +/- 53 ml (mean +/- SE, n = 188). Mean plasma removal rate per treatment was 40.2 +/- 0.6 ml/min; mean treatment time was 83 +/- 2 min. Platelet counts before and after treatment revealed a 15 +/- 4% decline (n = 46 Rx). Despite filtration fractions up to 86% there was no evidence of significant membrane plugging or hemolysis. For semiselective removal of cholesterol, the rotating filter was used in a cascade system with a secondary filter. Eighty percent of processed plasma was returned to the patient, but the treatment time was prolonged by 37% and the total cholesterol removed was 26% less when compared with the single pass system. The authors conclude that an inexpensive rotating filter can provide a highly efficient plasma exchange. The inherent efficiency of this system must be considered when evaluating its use with secondary filtration techniques.

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

    SciTech Connect

    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 was 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

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

    DOE PAGES

    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

  19. Turbulence and heat exchange inside the dome room of lidar station. Experiment and simulation

    NASA Astrophysics Data System (ADS)

    Nosov, V. V.; Lukin, V. P.; Nosov, E. V.; Torgaev, A. V.

    2016-10-01

    The structure of air turbulent motion inside the dome room - Primary Mirror (diameter 2.2 m) closed shaft at Siberian Lidar Station of V. E. Zuev Institute of Atmospheric Optics of Siberian Branch of the Russian Academy of Science has been experimentally and theoretically studied. Research is needed to forecast a laser radiation distortion. Results of experiments performed using the ultrasonic compact portable weather station are presented. The main heat exchange directions of air flows inside the shaft are determined. Theoretical results have been obtained by numerical solving of boundary value problem for Navier-Stokes equations. Solitary large vortices (coherent structures, topological solitons) are observed inside the shaft. Coherent decay of such vortices generates the coherent turbulence. It is determined that inside the primary mirror shaft one may expect the weakening of phase fluctuations of optical radiation, and thus improvement the lidar optical imaging. This increases the efficiency of Lidar Station.

  20. 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%.

  1. Social Networks and Externalities from Gift Exchange: Evidence from A Field Experiment.

    PubMed

    Currie, Janet; Lin, Wanchuan; Meng, Juanjuan

    2013-11-01

    This paper asks whether gift exchange generates externalities for people outside of the bilateral relationship between the gift giver and recipient, and whether the nature of this relationship is affected by social networks. We examine this question in the context of a field experiment in urban Chinese hospital outpatient clinics. We first show that when patients give a small gift, doctors reciprocate with better service and a fewer unnecessary prescriptions of antibiotics. We then show that gift giving creates externalities for third parties. If two patients, A and B are perceived as unrelated, B receives worse care when A gives a gift. However, if A identifies B as a friend, then both A and B benefit from A's gift giving. Hence, we show that gift giving can create positive or negative externalities, depending on the giver's social distance to the third party.

  2. 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.

  3. GEM luminosity monitors for the OLYMPUS experiment to determine the effect of two-photon exchange

    NASA Astrophysics Data System (ADS)

    Ates, Ozgur

    The OLYMPUS experiment at DESY acquired its data in two distinct periods between 2012-2013 to measure the ratio of positron-proton and electron-proton elastic scattering cross sections. In light of those measurements, OLYMPUS will be able to quantify the effect of two-photon exchange, which is widely considered to be responsible for the discrepancy between measurements of the proton electric to magnetic form factor ratio with the Rosenbluth separation and polarization transfer methods. In order to control the systematic uncertainties to the sub-percent level, the luminosities were monitored redundantly and with high precision. This was done by measuring the rates for symmetric Moller and Bhabha scattering and by measuring the ep-elastic count rates at forward angles and low momentum transfer with tracking telescopes based on GEM (Gas Electron Multiplier) and MWPC (Multi-Wire Proportional Chamber technology. A total of nine GEM detectors were constructed for the OLYMPUS experiment. Within the scope of this thesis, every single step of construction, testing and installation of the GEM OLYMPUS luminosity monitors are explained in the hardware part of this thesis. Moreover, based on the analysis of the data taken with the GEM luminosity monitors at the OLYMPUS experiment, individual GEM detector performance and preliminary results on the positron/electron luminosity ratio measured with elastic scattering at forward angles are discussed in the analysis part of the thesis.

  4. The shelf edge exchange processes experiment, SEEP-II: an introduction to hypotheses, results and conclusions

    NASA Astrophysics Data System (ADS)

    Biscaye, Pierre E.; Flagg, Charles N.; Falkowski, Paul G.

    The SEEP (Shelf Edge Exchange Processes)-II experiment was the second of two that took place in the Middle Atlantic Bight (MAB) of the eastern U.S. continental shelf and slope. The experiment included an array of 10 multi-instrumented moorings deployed for 15 months and 10 oceanographic cruises, all designed to address the problem of the fate of continental shelf particulate matter in general, and organic carbon in particular. This paper provides the setting and background for the SEEP Program, the SEEP-II experiment and an introduction to the 18 papers constituting the subject of this special volume. Because those papers lack one of a general nature on the physical oceanographic setting of the experiment, that aspect is treated in somewhat more detail here. The results of the experiment overwhelmingly show that the working hypothesis on which the SEEP Program was undertaken and sponsored by the Department of Energy is not valid. That is, there is not an export to the adjacent slope and open ocean of a large proportion of the particulate matter introduced to and biologically generated in the waters of the continental shelf; most of the biogenic particulate matter is recycled by consumption (bacterial and otherwise) and oxidation on the shelf, and only a small proportion (of order ≪5%) is exported to the adjacent slope. The small amount that is exported appears to be deposited preferentially in the sediments of an area of the slope centered at about 1000 m, and the export and sedimentation to that depocenter appears to increase from the northern to the southern MAB.

  5. Experimental search for two-hard-photon exchange in elastic ep experiments

    SciTech Connect

    Charles Perdrisat

    2012-09-01

    A remarkable change of paradigm was precipitated by the results, obtained in the last 12 years, of new measurements of the proton form factor ratio; the two form factors, G{sub Ep} and G{sub Mp}, are not in a constant ratio, as had been concluded from previous cross section experiments, and would be the case if charge and magnetization spatial distributions were the same. Rather, as the series of polarization measurements at JLab shows, the ratio {mu}{sub p}G{sub Ep}/G{sub Mp} decreases smoothly from 1 at Q{sup 2} = 0, to about 0.15 at Q{sup 2} = 8.5 GeV{sup 2}, with Q{sup 2} the negative of the four-momentum transfer squared. The interesting question is then: how can the results using two methods both related through the Born approximation, be found to lead to a different form factor ratio? The short answer is that cross sections require large radiative corrections, which tend to mask G{sub Ep} for increasing Q{sup 2}, whereas recoil polarization experiments measure the ratio of two components of the recoil polarization, which tends to cancel the effect of radiative corrections. Radiative corrections to the cross section of ep scattering have a long history. They may just not be accurate enough when the ratio G{sub Ep}/G{sub Mp} {approx} 0.05 and {tau} = Q{sup 2}/4m{sub p}{sup 2} {approx} 2.5, as is the case for the largest Q{sup 2} for which we have double-polarization data, 8.5 GeV{sup 2}. For this Q{sup 2} and with the Born cross section given by d{sigma} {approx} G{sub Ep}{sup 2} + ({tau}/{var_epsilon})G{sub Mp}{sup 2}, with {var_epsilon} the kinematic factor, the contribution to the cross section of G{sub Ep} becomes smaller than 0.1%, i.e. non-measurable in cross section experiments. The other hypothesis, is that the radiative corrections are incomplete, and that the exchange of two hard photons is the source of the discrepancy; the idea has been pursued in numerous works, but to this day there is no direct, experimental evidence that two

  6. 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

  7. Facial convective heat exchange coefficients in cold and windy environments estimated from human experiments.

    PubMed

    Ben Shabat, Yael; Shitzer, Avraham

    2012-07-01

    Facial heat exchange convection coefficients were estimated from experimental data in cold and windy ambient conditions applicable to wind chill calculations. Measured facial temperature datasets, that were made available to this study, originated from 3 separate studies involving 18 male and 6 female subjects. Most of these data were for a -10°C ambient environment and wind speeds in the range of 0.2 to 6 m s(-1). Additional single experiments were for -5°C, 0°C and 10°C environments and wind speeds in the same range. Convection coefficients were estimated for all these conditions by means of a numerical facial heat exchange model, applying properties of biological tissues and a typical facial diameter of 0.18 m. Estimation was performed by adjusting the guessed convection coefficients in the computed facial temperatures, while comparing them to measured data, to obtain a satisfactory fit (r(2) > 0.98, in most cases). In one of the studies, heat flux meters were additionally used. Convection coefficients derived from these meters closely approached the estimated values for only the male subjects. They differed significantly, by about 50%, when compared to the estimated female subjects' data. Regression analysis was performed for just the -10°C ambient temperature, and the range of experimental wind speeds, due to the limited availability of data for other ambient temperatures. The regressed equation was assumed in the form of the equation underlying the "new" wind chill chart. Regressed convection coefficients, which closely duplicated the measured data, were consistently higher than those calculated by this equation, except for one single case. The estimated and currently used convection coefficients are shown to diverge exponentially from each other, as wind speed increases. This finding casts considerable doubts on the validity of the convection coefficients that are used in the computation of the "new" wind chill chart and their applicability to humans in

  8. 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

  9. Single and Multiresponse Adaptive Design of Experiments with Application to Design Optimization of Novel Heat Exchangers

    DTIC Science & Technology

    2009-01-01

    performance evaluation method for air- cooled heat exchangers in which conventional 3D Computational Fluid Dynamics (CFD) simulation is replaced with a 2D...parts to this research thrust. First, is a new multi-level performance evaluation method for air- cooled heat exchangers in which conventional 3D...performance of a novel air- cooled heat exchanger such as tube-fin or microchannels . The novel aspect generally refers to a new fin design or a tube

  10. 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…

  11. Spin Exchange Optical Pumping of 129Xe for the Neutron Electron Dipole Moment Experiment at TRIUMF

    NASA Astrophysics Data System (ADS)

    Miller, Eric; Hayamizu, Tomohiro; Wienands, Joshua; Altiere, Emily; Jones, David; Madison, Kirk; Momose, Takamasa; Lang, Michael; Bidinosti, Chris; Martin, Jeffery

    2016-09-01

    Spin polarized noble gases have been a field of study for several decades and are of particular interest with respect to magnetic sensing. Using the Spin Exchange Optical Pumping technique, one can use the angular momentum of circularly polarized NIR photons to spin polarize Rb atoms, which then collide with Xe to polarize the ground state Zeeman sublevels of Xe many orders of magnitude above typical thermal Boltzmann distributions. The resulting polarized gas, with its magnetic dipole moment, is a useful probe of magnetic fields. We plan to use two spin polarized species, 129Xe and 199Hg, as dual co-magnetometers for the neutron EDM experiment at TRIUMF. They will be used to correct the neutron precession frequency for drifts due to magnetic field instability and geometric phase effects. For 129Xe, we aim to probe the populations of the ground state Zeeman sublevels using UV two-photon transitions. The respective populations depend on how much polarization we can produce using the SEOP technique. We will present technical details of our apparatus including results from a parameter space search, investigating how mode of preparation (batch or continuous flow), temperature, flow rate, and laser power affect 129Xe polarization as measured by low field NMR.

  12. Therapeutic Plasma Exchange in Neurologic Diseases: An Experience with 91 Patients in Seven Years

    PubMed Central

    KARACA, Sibel; KOZANOĞLU, İlknur; KARAKURUM GÖKSEL, Başak; KARATAŞ, Mehmet; TAN, Meliha; YERDELEN, V. Deniz; GİRAY, Semih; ARLIER, Zülfikar

    2014-01-01

    Introduction In this study, we report the results of our experience of therapeutic plasma exchange (TPE) for neuroimmunologic disorders performed at our hospital over a seven-year period. Methods We retrospectively reviewed the medical records of 91 patients (53 male, 38 female) who had been treated at our center with TPE. Results 60 patients with Guillain-Barrè syndrome (GBS), 23 with myasthenia gravis (MG), 4 with chronic inflammatory demyelinating polyneuropathy (CIDP) and 1 patient each with polymyositis, septic encephalopathy, acute disseminated encephalomyelitis (ADEM) and Opsoclonus-Myoclonus syndrome (OMS) received TPE. 26.7% of GBS patient’s made complete recovery, 61.7% had partial recovery and 11.7% patients died due to respiratory failure. Despite our best efforts and effective TPE treatments, 13.4% of MG patients deceased, however, 78% had full recovery. Three patients with CIDP were discharged with full and 1 patient with partial recovery. The patient with ADEM had partial recovery with TPE at first, but deceased 2 months later due to pneumonia-related respiratory insufficiency. While, patient with polymyositis had slight-partial recovery, we obtained full recovery with TPE in septic encephalopathy and OMS patients. The side effects and complications of treatments with TPE, which included hypotension, hypocalcaemia and anemia, were mild and manageable. Conclusion The improvement rates were encouraging and we concluded that significant benefit can be achieved with TPE for the treatment of neuroimmunological disorders.

  13. Language and Culture Exchange in Foreign Language Learning: An Experiment and Recommendations

    ERIC Educational Resources Information Center

    Lockley, Thomas; Yoshida, Chiharu

    2016-01-01

    This study attempts to build on the little work that has been done so far on empirically and systematically researching what language and culture exchange (LCE) in the classroom between students of different foreign languages means to those students. It describes the context and method used to build such an exchange and after reviewing relevant…

  14. The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments.

    PubMed

    Chandak, Mahesh S; Nakamura, Takashi; Takenaka, Toshio; Chaudhuri, Tapan K; Yagi-Utsumi, Maho; Chen, Jin; Kato, Koichi; Kuwajima, Kunihiro

    2013-04-01

    Dimethylsulfoxide (DMSO)-quenched hydrogen/deuterium (H/D)-exchange is a powerful method to characterize the H/D-exchange behaviors of proteins and protein assemblies, and it is potentially useful for investigating non-protected fast-exchanging amide protons in the unfolded state. However, the method has not been used for studies on fully unfolded proteins in a concentrated denaturant or protein solutions at high salt concentrations. In all of the current DMSO-quenched H/D-exchange studies of proteins so far reported, lyophilization was used to remove D2 O from the protein solution, and the lyophilized protein was dissolved in the DMSO solution to quench the H/D exchange reactions and to measure the amide proton signals by two-dimensional nuclear magnetic resonance (2D NMR) spectra. The denaturants or salts remaining after lyophilization thus prevent the measurement of good NMR spectra. In this article, we report that the use of spin desalting columns is a very effective alternative to lyophilization for the medium exchange from the D2 O buffer to the DMSO solution. We show that the medium exchange by a spin desalting column takes only about 10 min in contrast to an overnight length of time required for lyophilization, and that the use of spin desalting columns has made it possible to monitor the H/D-exchange behavior of a fully unfolded protein in a concentrated denaturant. We report the results of unfolded ubiquitin in 6.0M guanidinium chloride.

  15. Effect of cation exchange on major cation chemistry in the large scale redox experiment at Aespoe

    SciTech Connect

    Viani, B.E.; Bruton, C.J.

    1994-10-01

    Predicting the chemical changes that result from excavating a repository below the groundwater table in granitic terrain is a major focus of the SKB geochemistry program. The modeling study presented here demonstrates that cation exchange can play a major role in controlling the fluid chemistry that results when groundwaters of differing composition mix due to flow induced by excavation of the HRL tunnel. The major goal of this study was to assess whether an equilibrium cation exchange model could explain the composition of groundwater sampled from boreholes in the HRL tunnel. Given the consistency of the cation exchange hypothesis with observations, geochemical modeling was used to assess whether the quantity of exchanger necessary to match model results and observation was physically reasonable. The impact of mineral dissolution and precipitation on fluid chemistry was also evaluated. Finally, the compositions of exchanger phases expected to be in equilibrium with various Aespoe groundwaters were predicted.

  16. 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

  17. The implicit cognition of reciprocal exchange: automatic retrieval of positive and negative experiences with partners in a prisoner's dilemma game.

    PubMed

    Bell, Raoul; Koranyi, Nicolas; Buchner, Axel; Rothermund, Klaus

    2016-03-02

    Models of reciprocity imply that cheater detection is an important prerequisite for successful social exchange. Considering the fundamental role of memory in reciprocal exchange, these theories lead to the prediction that memory for cheaters should be preferentially enhanced. Here, we examine whether information of a partner's previous behaviour in an interaction is automatically retrieved when encountering the face of a partner who previously cheated or cooperated. In two studies, participants played a sequential prisoner's dilemma game with cheaters and cooperative partners. Alternating with the game blocks, participants were asked to classify the smiling or angry facial expressions of cooperators and cheaters. Both experiments revealed congruence effects, reflecting faster identification of the smiles of cooperators (Experiments 1 and 2) and faster identification of the angry facial expressions of cheaters (Experiment 2). Our study provides evidence for the automatic retrieval of the partner's behaviour in the game, regardless of whether partners cheated or cooperated, and thus provides further evidence against the cheater detection hypothesis.

  18. 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

  19. 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

  20. Understanding the Decisions and Values of Stakeholders in Health Information Exchanges: Experiences From Massachusetts

    PubMed Central

    Simon, Steven R.; Volk, Lynn A.; Tripathi, Micky; Bates, David

    2009-01-01

    Objectives. We studied how health information exchange systems are established by examining the decisions (and thus, indirectly, the values) of key stakeholders (health care providers) participating in a health information exchange pilot project in 3 Massachusetts communities. Our aim was to understand how these kinds of information exchanges can be made viable. Methods. We used semistructured interviews to assess health care providers' decision-making processes in selecting technical architectures and vendors for the pilot projects to uncover their needs, expectations, and motivations. Results. Our interviews indicated that, after extensive evaluations, health care providers in all 3 communities eventually selected a hybrid architecture that included a central data repository. However, the reasons for selecting this architecture varied considerably among the 3 communities, reflecting their particular values. Plans to create a community patient portal also differed across communities. Conclusions. Our findings suggest that, to become established, health information exchange efforts must foster trust, appeal to strategic interests of the medical community as a whole, and meet stakeholder expectations of benefits from quality measurements and population health interventions. If health information exchange organizations cannot address these factors, sustainability will remain precarious. PMID:19299671

  1. 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…

  2. 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…

  3. Experiments with an ion-neutral hybrid trap: cold charge-exchange collisions

    NASA Astrophysics Data System (ADS)

    Smith, W. W.; Goodman, D. S.; Sivarajah, I.; Wells, J. E.; Banerjee, S.; Côté, R.; Michels, H. H.; Mongtomery, J. A.; Narducci, F. A.

    2014-01-01

    Due to their large trap depths (˜1 eV or 10,000 K), versatility, and ease of construction, Paul traps have important uses in high-resolution spectroscopy, plasma physics, and precision measurements of fundamental constants. An ion-neutral hybrid trap consisting of two separate but spatially concentric traps [a magneto-optic trap (MOT) for the neutral species and a mass-selective linear Paul trap for the ionic species] is an ideal apparatus for sympathetic cooling. However, over the past few years, hybrid traps have proven most useful in measuring elastic and charge-exchange rate constants of ion-neutral collisions over a wide temperature range from kilo-Kelvin to nano-Kelvin. We report some initially surprising results from a hybrid trap system in our laboratory where we have loaded the Paul trap with Ca+ ions in the presence of a Na MOT (localized dense gas of cold Na atoms). We find a strong loss of Ca+ ions with MOT exposure, attributed to an exothermic, non-resonant ion-neutral charge-exchange process with an activation barrier, which leads to the formation of Na+ ions. We propose a detailed mechanism for this process. We obtain an estimated measure of the rate constant for this charge exchange of ˜2 × 10-11 cm3/s, much less than the Langevin rate, which suggests that the Langevin assumption of unit efficiency in the reaction region is not correct in this case.

  4. 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

  5. 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.

  6. 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

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

    PubMed

    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

    2014-02-11

    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.

  8. Leveraging health information exchange to support public health situational awareness: the indiana experience.

    PubMed

    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.

  9. Effects of ultrafiltration, dialysis, and temperature on gas exchange during hemodiafiltration: a laboratory experiment.

    PubMed

    Ruzicka, J; Novak, I; Rokyta, R; Matejovic, M; Hadravsky, M; Nalos, M; Sramek, V

    2001-12-01

    To study gas exchange in the filter during continuous venovenous hemodiafiltration (CVVHDF), an air-tight heated mixing chamber with adjustable CO2 supply was constructed and connected to a CVVHDF monitor. Bicarbonate-free crystalloid (Part 1) and packed red blood cell (Part 2) solutions were circulated at 150 ml x min(-1). Gas exchange expressed as pre-postfilter difference in CO2 and O2 contents was measured at different CVVHDF settings and temperatures of circulating and dialysis solutions. Ultrafiltration was most efficacious for CO2 removal (at 1,000 ml x h(-1) ultrafiltration CO2 losses reached 13% of prefilter CO2 content). Addition of dialysis (1,000 ml x h(-1)) increased CO2 loss to 17% and at maximal parameters (filtration 3,000 ml x h(-1), dialysis 2,500 ml x h(-1)), the loss of CO2 amounted to 35% of prefilter content. Temperature changes of circulating and/or dialysis fluids had no significant impact on CO2 losses. The O2 exchange during CVVHDF was negligible. Currently used CVVHDF is only marginally effective in CO2 removal. Higher volume ultrafiltration combined with dialysis can be expected to reach clinical significance.

  10. Isotope exchange between natural and anthropogenic Pb in the coastal waters of Singapore: exchange experiment, Kd model, and implications for the interpretation of coastal 210Pb data

    NASA Astrophysics Data System (ADS)

    Boyle, E. A.; Chen, M.; Zurbrick, C.; Carrasco, G. G.

    2015-12-01

    Observations from annually-banded corals and seawater samples show that marine lead (Pb) in the coastal waters of Singapore has an isotopic composition that does not match that of the anthropogenic aerosols in this region, unlike what is seen in most parts of the open ocean. The 206Pb/207Pb composition of Singaporean marine Pb is 1.18-1.20 whereas the local aerosols are 1.14-1.16. In order to explore this discrepancy further, we collected a large volume water from the Johor River estuary (flowing from Malaysia to the northern border of Singapore), added a distinct isotope spike (NBS981, 206Pb/207Pb =1.093) to an unfiltered sample, and followed the dissolved isotope composition of the mixture during the following two months. The initial dissolved Pb concentration was 18.3 pmol/kg with 206Pb/207Pb of 1.200. "Total dissolvable" Pb released after acidification of the in the unfiltered sample was 373 pmol/kg with 206Pb/207Pb of 1.199, indicating that there is a large particulate Pb reservoir with an isotopic composition comparable to regional crustal natural Pb. The isotope spike should have brought the dissolved 206Pb/207Pb to 1.162, but less than a day after isotope spiking, the dissolved Pb had risen to 1.181 and continued a slow increase to 1.197 over the next two months. This experiment demonstrates that Johor estuary particulate matter contains a large reservoir of exchangeable Pb that will modify the isotopic composition of deposited aeolian aerosol anthropogenic Pb. We have modeled the evolution of Pb and Pb isotopes in this experiment with a single Kd -type model that assumes that there are two or three different Pb reservoirs with different exchange time constants. This observation has implications for isotope equilibrium between high Pb/210Pb continental particles and low Pb/210Pb ocean waters - what is merely isotope equilibration may appear to be 210Pb scavenging.

  11. Sodium concentration measurement during hemodialysis through ion-exchange resin and conductivity measure approach: in vitro experiments.

    PubMed

    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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. SirX: a selective inversion recovery experiment on X-nuclei for the determination of the exchange rate of slow chemical exchanges between two sites.

    PubMed

    Xie, Xiulan; Bönisch, Friedrich

    2015-10-01

    Nuclear magnetic resonance spectroscopy has proven to be powerful for the study of dynamic processes. A new pulse sequence, SirX, is designed to provide boundary conditions that simplify the McConnell equations. Both an initial rate approximation and a whole curve fitting to the time course of magnetization can be used to calculate the exchange rate. These methods were used to study the exchange kinetics of N,N-dimethylacetamide. As compared with the well-established exchange spectroscopy suitable to studies of slow exchange, SirX has the advantage of being less time consuming and capable of providing more reliable kinetic data. Furthermore, by setting the observation on X-nuclei with larger chemical shift dispersion as compared with an observation on (1)H resonance, SirX extends the upper limit of a reliable determination of exchange rates.

  18. An Overview of the Regional Experiments for Land-atmosphere Exchanges 2012 (REFLEX 2012) Campaign

    NASA Astrophysics Data System (ADS)

    Timmermans, Wim J.; 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)

    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.

  19. Experience with NuResin, a mobile ion exchange resin reprocessing system

    SciTech Connect

    Palazzi, K.R.; Bell, M.J.; Concklin, J.R.

    1995-12-31

    Ion exchange resin used in condensate polishing, steam generator blowdown, and radwaste systems is a major contributor to the volume of low-level waste (LLW) at operating nuclear plants. Plant regeneration systems for resins use large quantities of demineralized water for cleaning, separating, and regenerating resins. These systems generate a tremendous volume of LLW from boiling water reactors (BWRs) and those pressurized water reactors (PWRs) that have experienced steam generator tube leaks. At essentially all BWRs and those PWRs that replace rather than regenerate condensate polishing resin, the LLW volume contribution from the resin alone is significant. This report describes a process for the treatment of resins with the objective of returning the resin to service.

  20. A loudspeaker-driven system for rapid and multiple solution exchanges in patch-clamp experiments.

    PubMed

    Méry, P F; Lechêne, P; Fischmeister, R

    1992-04-01

    A new and inexpensive system allowing rapid and synchronized changes of solutions around a membrane patch or a cell under voltage-clamp conditions is described. Four plastic capillary tubings (OD 640 microns; ID 430 microns) were glued together horizontally and attached to a coil of a commercially available loudspeaker. Servo-control of the position of the coil allowed the mouth of any of the capillaries to be positioned near the pipette tip within 6 ms. A high flow speed of the test solution was crucial to achieve rapid solution exchange. At a flow speed of 5 cm/s, complete exchange of the external environment of a frog ventricular cell was achieved within 20-30 ms. The time course of solution change was found to be 3-5 times faster at the tip of an open patch pipette. To preserve the physical integrity of the cell, the cell was usually perfused by a control capillary at a slow velocity (0.2-0.4 cm/s) and test solutions flowing out of adjacent capillaries at high velocity (4-5 cm/s) were applied to the cell only for short periods. Determination of the three-dimensional contamination profile around the mouth of the control capillary allowed the optimal conditions for the use of the system to be established and possible sources of contamination to be avoided between adjacent capillaries with unmatched flow speeds. Successive and multiple changes in external solutions could be easily synchronized with voltage-clamp depolarizations to examine the time course of the effect of drugs on voltage-operated ion channels.(ABSTRACT TRUNCATED AT 250 WORDS)

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. Hydrogen peroxide in the marine atmospheric boundary layer during the Atlantic Stratocumulus Transition Experiment/Marine Aerosol and Gas Exchange experiment in the eastern subtropical North Atlantic

    NASA Astrophysics Data System (ADS)

    Martin, Daniel; Tsivou, Maria; Bonsang, Bernard; Abonnel, Christian; Carsey, Thomas; Springer-Young, Margie; Pszenny, Alex; Suhre, Karsten

    1997-03-01

    Gas phase H2O2 was measured in surface air on the NOAA ship Malcolm Baldrige from June 8 to 27, 1992 (Julian days 160-179), during the Atlantic Stratocumulus Transition Experiment/Marine Aerosol and Gas Exchange experiment in the eastern subtropical North Atlantic region. Average H2O2 mixing ratios observed were 0.63±0.28 ppbv, ranging between detection limit and 1.5 ppbv. For the entire experiment, only weak or no correlation was found between H2O2 mixing ratio and meteorological parameters (pressure, temperature, humidity, or UV radiation flux) as well as with tracers of continental air masses (CO, black carbon, radon). The average daily H2O2 cycle for the entire period exhibits a maximum of 0.8±0.3 ppbv near sunset and a minimum of 0.4±0.2 ppbv 4-5 hours after sunrise. Several clear H2O2 diurnal variations have been observed, from which a first-order removal rate of about 1×10-5 s-1 for H2O2 can be inferred from nighttime measurements. This rate compares well with those deduced from measurements taken at Cape Grim (Tasmania, 41°S) and during the Soviet-American Gas and Aerosol III experiment (equatorial Pacific Ocean).

  6. Allele Mining Strategies: Principles and Utilisation for Blast Resistance Genes in Rice (Oryza sativa L.).

    PubMed

    Ashkani, Sadegh; Yusop, Mohd Rafii; Shabanimofrad, Mahmoodreza; Azady, Amin; Ghasemzadeh, Ali; Azizi, Parisa; Latif, Mohammad Abdul

    2015-01-01

    Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.

  7. Experiences and Coping Strategies of Host Families in International Youth Exchange

    ERIC Educational Resources Information Center

    Weidemann, Arne; Bluml, Frances

    2009-01-01

    Twenty narrative interviews were conducted with German host parents between 2006 and 2007 about their experiences with a one-year stay of a guest student in their family. The study took place within the context of a student research project as part of the research-oriented MA course "Intercultural Communication-Intercultural Competence"…

  8. 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.…

  9. Thermal and Mechanical Non-Equilibrium Effects on Turbulent Flows: Fundamental Studies of Energy Exchanges Through Direct Numerical Simulations, Molecular Simulations and Experiments

    DTIC Science & Technology

    2016-02-26

    AFRL-AFOSR-VA-TR-2016-0104 Thermal and mechanical non-equilibrium effects on turbulent flows:fundamental studies of energy exchanges through direct ...flows: fundamental studies of energy exchanges through direct numerical simulations, molecular simulations and experiments 5a.  CONTRACT NUMBER 5b...control of basic fluid dynamic processes is of direct relevance to AFOSR scientific objectives especially for turbulence flows. The very limited

  10. 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.

  11. A Prospective Screening of HLA-B*57.01 Allelic Variant for Preventing the Hypersensivity Reaction to Abacavir: Experience from the Laboratory of Molecular Biology of the Infectious Diseases Division at the University Hospital of Salerno.

    PubMed

    Senatore, C; Charlier, B; Truono, A; Punzi, R; D'Aniello, F; Boffa, N; Izzo, V; Conti, V; Russomanno, G; Manzo, V; Filippelli, A; Mazzeo, M

    2015-01-01

    Abacavir is a nucleoside reverse transcriptase inhibitor largely used as part of the antiretroviral therapy in Human Immunodeficiency Virus (HIV)-infected patients. Some individuals (2-9%) who start an abacavir treatment show an immunologic reaction indicated as hypersensitivity reaction syndrome (HSR) that is often responsible for therapy discontinuation and could represent a life-threatening event. Some studies demonstrated a correlation between this adverse reaction and the class I of the major histocompatibility complex (MHC) allele, HLA-B*57.01, in several populations, including Caucasians. Nowadays, International HIV treatment guidelines recommend the HLA-B*57.01 genotyping before abacavir administration to reduce the incidence of HSR. Both male and female HIV-infected patients were enrolled at the Infectious Diseases Division at the University Hospital of Salerno, and admitted to a prospective HLAB*57.01 screening. Genetic analysis was carried out through two sequential Real-Time PCR reactions in which Sybr-Green was used. Out of 248 patients, 215 were Italians from Southern Italy and 33 were coming from several non-EU members countries. All were genotyped: 6 Italians (2.8%) and 1 of the non-EU group (3%) were identified as HLAB*57.01 carriers. In this paper we present our experience in the field of abacavir pharmacogenetic and confirm the importance of Real Time PCR as a valid and cost-effective HLA-B*57.01 typing methodology.

  12. 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

  13. 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.

  14. Reference layer exchange in spin transfer torque experiment using magnetic-coated nanometric point contacts

    NASA Astrophysics Data System (ADS)

    Cunha, R. O.; Baptista, D. L.; Heinemann, M.; Kuhn, M. F.; Schmidt, J. E.; Pereira, L. G.

    2012-09-01

    We investigate the importance of using nanotips on a point contact spin-transfer torque (STT) experiment. A systematic analysis comparing the STT in a magnetic thin film in current-perpendicular-to-plane (CPP) geometry sample for magnetic coated and uncoated tungsten nanotips is shown. The STT effect presents a reverse resistance to current behavior when using a magnetic coating layer on the nanotips. We demonstrate that the magnetic layer on the tip may assume the role of a polarizer layer. This effect opens up the possibility of exploiting simpler architectures in STT-based devices, such as STT-random access memory (STT-RAM).

  15. The Impact of Na—H+ Exchange on Long-Term Borosilicate Glass Corrosion: Experiments and Field Observations

    SciTech Connect

    Icenhower, Jonathan P; Pierce, Eric M; McGrail, B Peter

    2009-05-01

    New insights from laboratory experiments coupled with field observations indicate that pore water solutions that eventually breach containment materials in disposal systems will interact with sodium-excess borosilicate waste glass in an unexpected way. Because many glass waste forms are relatively sodium-rich, they are especially vulnerable to Na+—H+ exchange (ion exchange or simply, IEX). Although the kinetics of this process has been previously investigated for early-stage glass reactions, the implications of IEX for long-term dissolution resistance have not yet been realized. Non-radioactive glass with major- and minor-element chemical compositions similar to Hanford high-Na waste glass were subjected to dissolution experiments to quantify the rates of matrix dissolution and IEX rates. Single-Pass Flow-Through (SPFT) tests quantified the IEX rate at 40°C pH = 8 and silica saturation and showed a dependence upon the fraction of excess sodium in the glass. The equation for the rate (in moles of sodium released per meter squared per second) dependence on excess sodium is: log10rate[mol/(m2∙s)] = 0.63R + (-11.0); r2 = 0.86 where R = molar Na+/(M3+). Further, rates of Na release are slower by ≥30% in D2O-based solutions compared to those in H2O. These results are the hallmark of IEX reactions. Our results are compared against those from a lysimeter field experiment consisting of glasses buried in Hanford sand and to dissolution experiments conducted with a Pressurized Unsaturated Flow (PUF) apparatus. These longer-term tests indicate an initial decrease in dissolution rate by a factor of 10×, and then a constant steady-state rate thereafter. Thus, these data show that IEX reactions are important at near-saturation conditions and effectively prevent dissolution rates from falling below a minimum value. In sum, IEX modifies the long-term behavior of glass dissolution and models cannot assume that dissolution of Na-rich borosilicate glass will decrease by a

  16. 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.

  17. 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)

  18. Choreography of Ig allelic exclusion.

    PubMed

    Cedar, Howard; Bergman, Yehudit

    2008-06-01

    Allelic exclusion guarantees that each B or T cell only produces a single antigen receptor, and in this way contributes to immune diversity. This process is actually initiated in the early embryo when the immune receptor loci become asynchronously replicating in a stochastic manner with one early and one late allele in each cell. This distinct differential replication timing feature then serves an instructive mark that directs a series of allele-specific epigenetic events in the immune system, including programmed histone modification, nuclear localization and DNA demethylation that ultimately bring about preferred rearrangement on a single allele, and this decision is temporally stabilized by feedback mechanisms that inhibit recombination on the second allele. In principle, these same molecular components are also used for controlling monoallelic expression at other genomic loci, such as those carrying interleukins and olfactory receptor genes that require the choice of one gene out of a large array. Thus, allelic exclusion appears to represent a general epigenetic phenomenon that is modeled on the same basis as X chromosome inactivation.

  19. Laboratory Measurements of Oxygen Gas Release from Basaltic Minerals Exposed to UV- Radiation: Implications for the Viking Gas Exchange Experiments

    NASA Astrophysics Data System (ADS)

    Hurowitz, J. A.; Yen, A. S.

    2007-12-01

    The biology experiments onboard the Viking Landers determined that the Martian soils at Chryse and Utopia Planitia contain an unknown chemical compound of a highly oxidizing nature. The Gas Exchange Experiments (GEx) demonstrated that the humidification of a 1-cc Martian soil sample resulted in the production of as much as 790 nanomoles of oxygen gas. Yen et al. (2000) have provided experimental evidence that superoxide radicals can be generated on plagioclase feldspar (labradorite) grain surfaces by exposure to ultraviolet (UV) light in the presence of oxygen gas. Adsorbed superoxide radicals are thought to react readily with water vapor, and produce oxygen gas in quantities sufficient to explain the Viking GEx results. Direct evidence for the formation of oxygen gas, however, was not provided in the experiments of Yen et al (2000). Accordingly, the motivation of this study is to determine whether superoxide radicals adsorbed on labradorite surfaces are capable of producing oxygen gas upon exposure to water vapor. We have constructed an experimental apparatus that is capable of monitoring oxygen gas release from basaltic mineral powders that have been exposed to UV-radiation under Martian atmospheric pressure conditions. The apparatus consists of a stainless-steel vacuum chamber with a UV- transparent window where sample radiation exposures are performed. The vacuum chamber has multiple valved ports for injection of gases and water vapor. The vacuum chamber is connected via a precision leak valve to a quadrupole mass spectrometer, which measures changes in the composition of the headspace gases over our mineral samples. We will report on the results of our experiments, which are aimed at detecting and quantifying oxygen gas release from UV-exposed basaltic mineral samples using this new experimental facility. These results will further constrain whether superoxide ions adsorbed on mineral surfaces provide a viable explanation for the Viking GEx results, which have

  20. Polymorphism of Mhc-DRB alleles in Cercopithecus aethiops (green monkey): generation and functionality.

    PubMed

    Rosal-Sánchez, M; Paz-Artal, E; Moreno-Pelayo, M A; Martínez-Quiles, N; Martínez-Laso, J; Martín-Villa, J M; Arnaiz-Villena, A

    1998-05-01

    DRB genes have been studied for the first time in green monkeys (Cercopithecus aethiops). Eleven new DRB alleles (exon 2, exon 3) have been obtained and sequenced from cDNA. A limited number of lineages have been identified: DRB1*03 (4 alleles), DRB1*07 (3 alleles), DRB5 (1 allele), DRB*w6 (1 allele), and DRB*w7 (2 alleles). The existence of Ceae-DRB1 duplications is supported by the finding of 3 DRB1 alleles in 3 different individuals. Ceae-DRB1*0701 may be non-functional because it bears serine at position 82, which hinders molecule surface expression in mice; the allele is only found in Ceae-DRB duplicated haplotypes. Base changes in cDNA Ceae-DRB alleles are consistent with the generation of polymorphism by point mutations or short segment exchanges between alleles. The eleven green monkey DRB alleles meet the requirements for functionality as antigen-presenting molecules (perhaps, excluding DRB1*0701), since: 1) they have been isolated from cDNA and do not present deletions, insertions or stop codons: 2) structural motifs necessary for a correct folding of the molecule, for the formation of DR/DR dimers and for CD4 interactions are conserved, and 3) the number of non-synonymous substitutions is higher than the number of synonymous substitutions in the peptide binding region (PBR), while the contrary holds true for the non-PBR region.

  1. Aerosol size distribution and aerosol water content measurements during Atlantic Stratocumulus Transition Experiment/Marine Aerosol and Gas Exchange

    NASA Astrophysics Data System (ADS)

    Kim, Y.; Sievering, H.; Boatman, J.; Wellman, D.; Pszenny, A.

    1995-11-01

    Aerosol size distribution data measured during the June 1992 Marine Aerosol and Gas Exchange experiment are analyzed to investigate the characteristics of fine marine aerosol particles measured over the North Atlantic near the Azores Islands. Measured aerosol size distribution data were corrected using the corrected size calibration data based on the optical properties of particles being measured. The corrected size distribution data were then approximated with either one or two lognormal size distributions, depending on air mass conditions. Under clean air mass conditions <3 μm diameter aerosol size distributions typically exhibited two modes, consisting of an accumulation mode and the small end of the sea-salt particle mode. However, under the influence of continental polluted air masses, the aerosol size distribution was dominated by <1 μm diameter particles in a single mode with an increased aerosol concentration. Aerosol water content of accumulation mode marine aerosols was estimated from differences between several series of ambient and dried aerosol size distributions. The average aerosol water fraction was 0.31, which is in good agreement with an empirical aerosol growth model estimate. The average rate of SO4= production in the accumulation mode aerosol water by H2O2 oxidation was estimated to be <7×10-10 mol L-1 s-1, which is an insignificant contributor to the observed non-sea-salt SO4= in the accumulation mode.

  2. Further characterization of the genotoxicity of formaldehyde in vitro by the sister chromatid exchange test and co-cultivation experiments.

    PubMed

    Neuss, Simone; Speit, Günter

    2008-09-01

    The induction of sister chromatid exchanges (SCE) was used to further characterize the genotoxic action of formaldehyde (FA) on cultured mammalian cells. FA induced SCE in V79 Chinese hamster cells and A549 human lung cells in a concentration-related manner. Addition of 5-bromodeoxyuridine (BrdUrd) for the differentiation of sister chromatids to visualize SCE 4 h after the FA treatment led to a clearly reduced induction of SCE in agreement with the repair kinetics of FA-induced DNA-protein cross-links. When A549 cells were treated with FA for 1 h and then co-cultivated with V79 cells in the presence of BrdUrd, a clear induction of SCE was measured in V79 cells. When the same experiment was performed including washing and change of medium after the FA treatment, no induction of SCE was measured in V79 cells. These results indicate that reactive FA remains in the cell culture medium for a longer time period despite the high reactivity of FA with macromolecules. However, FA that has entered a cell is not released and does not damage other cells. Possible implications for the mutagenicity of FA in vivo will be discussed.

  3. 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

  4. Therapeutic plasma exchange for renal-related conditions in the elderly: ten years experience in one center.

    PubMed

    Hayes, John S; Balogun, Rasheed A; Chang, Jamison; Abdel-Rahman, Emaad M

    2012-01-01

    The elderly people, 65 years old and above, are growing in number. The structural and functional changes associated with aging place the elderly at risk when challenged by extracorporeal therapies, such as therapeutic plasma exchange (TPE). We retrospectively analyzed data on all patients who underwent TPE for renal indications at our institution between January 1, 2000 and June 30, 2010 and compared renal indications and mortality associated with the use of TPE in older versus younger patients. During this period, 621 patients underwent 4722 sessions of TPE. Of them, 191 patients were elderly (30.7%) and they underwent 1289 sessions (27.3%) of TPE. A total of 104 patients (16.7%) underwent 593 sessions of TPE because of renal-related indications: 26 patients in the elderly group and 78 in the younger. Side effects of dyspnea and hypotension were documented in only two patients, both in the elderly cohort. The main indication for TPE in the elderly was glomerulonephritis (GN) as compared with renal allograft rejection in the younger cohort, with a trend toward more death in the elderly (p = 0.07). The multivariable regression model which included age as a category, serum albumin, and initial serum creatinine were unable to predict mortality in this group of patients. In our experience, the main renal indications for TPE in elderly are different from those for younger patients, with GN being the most common renal indication in the elderly. The TPE used for renal indications in the elderly is relatively safe. Trends toward death in the elderly may be multifactorial and not necessarily related to TPE.

  5. Plasma-exchange as a "rescue therapy" for dermato/polymyositis in acute phase. Experience in three young patients.

    PubMed

    Cozzi, Franco; Marson, Piero; Pigatto, Erika; Tison, Tiziana; Polito, Pamela; Galozzi, Paola; De Silvestro, Giustina; Punzi, Leonardo

    2015-12-01

    There are few data in the literature supporting the efficacy of plasma-exchange in dermato/polymyositis. The authors report three cases of patients with acute disease phase showing severe pharyngo-esophageal muscle weakness unresponsive to conventional therapy (corticosteroids and immunosuppressant agents) who were treated with plasma-exchange. As the patients were at high risk of "aspiration pneumonia", tracheostomy and PEG tubes were placed. The patients underwent a series of plasma-exchange for a mean of 15 weeks, during which time they progressively recovered muscle strength, their serum muscle enzyme values returned to normal levels, and MRI showed resolution of muscle edema. The tracheostomy and PEG tubes could be removed. Our findings suggest that plasma-exchange in association with immunosuppressant agents could play a relevant role in the management of dermato/polymyositis in acute phase.

  6. 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.

  7. 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.

  8. 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

    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.

  9. Identification and functional characterization of three novel alleles for the serotonin transporter-linked polymorphic region.

    PubMed

    Ehli, E A; Hu, Y; Lengyel-Nelson, T; Hudziak, J J; Davies, G E

    2012-02-01

    A promoter polymorphism in the serotonin transporter gene (5-HTTLPR) has been reported to confer relative risk for phenotypes (depression/anxiety) and endophenotypes (amygdala reactivity). In this report, we identify and characterize three rare 5-HTTLPR alleles not previously described in the human literature. The three novel alleles were identified while genotyping 5-HTTLPR in a family-based attention deficit hyperactivity disorder clinical population. Two of the novel alleles are longer than the common 16-repeat long (L) allele (17 and 18 repeats) and the third is significantly smaller than the 14-repeat short (S) allele (11 repeats). The sequence and genetic architecture of each novel allele is described in detail. We report a significant decrease in the expression between the XL₁₇ (17r) allele and the L(A) (16r) allele. The XS₁₁ (11r) allele showed similar expression with the S (14r) allele. A 1.8-fold increase in expression was observed with the L(A)(16r) allele compared with the L(G) (16r) allele, which replicates results from earlier 5-HTTLPR expression experiments. In addition, transcription factor binding site (TFBS) analysis was performed using MatInspector (Genomatix) that showed the presence or absence of different putative TFBSs between the novel alleles and the common L (16r) and S (14r) alleles. The identification of rare variants and elucidation of their functional impact could potentially lead to understanding the contribution that the rare variant may have on the inheritance/susceptibility of multifactorial common diseases.

  10. 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...

  11. 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.

  12. The Iġnik Sikumi Field Experiment, Alaska North Slope: Design, operations, and implications for CO2−CH4 exchange in gas hydrate reservoirs

    USGS Publications Warehouse

    Boswell, Ray; Schoderbek, David; Collett, Timothy S.; Ohtsuki, Satoshi; White, Mark; Anderson, Brian J.

    2017-01-01

    The Iġnik Sikumi Gas Hydrate Exchange Field Experiment was conducted by ConocoPhillips in partnership with the U.S. Department of Energy, the Japan Oil, Gas and Metals National Corporation, and the U.S. Geological Survey within the Prudhoe Bay Unit on the Alaska North Slope during 2011 and 2012. The primary goals of the program were to (1) determine the feasibility of gas injection into hydrate-bearing sand reservoirs and (2) observe reservoir response upon subsequent flowback in order to assess the potential for CO2 exchange for CH4 in naturally occurring gas hydrate reservoirs. Initial modeling determined that no feasible means of injection of pure CO2 was likely, given the presence of free water in the reservoir. Laboratory and numerical modeling studies indicated that the injection of a mixture of CO2 and N2 offered the best potential for gas injection and exchange. The test featured the following primary operational phases: (1) injection of a gaseous phase mixture of CO2, N2, and chemical tracers; (2) flowback conducted at downhole pressures above the stability threshold for native CH4 hydrate; and (3) an extended (30-days) flowback at pressures near, and then below, the stability threshold of native CH4 hydrate. The test findings indicate that the formation of a range of mixed-gas hydrates resulted in a net exchange of CO2 for CH4 in the reservoir, although the complexity of the subsurface environment renders the nature, extent, and efficiency of the exchange reaction uncertain. The next steps in the evaluation of exchange technology should feature multiple well applications; however, such field test programs will require extensive preparatory experimental and numerical modeling studies and will likely be a secondary priority to further field testing of production through depressurization. Additional insights gained from the field program include the following: (1) gas hydrate destabilization is self-limiting, dispelling any notion of the potential for

  13. 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.

  14. 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

  15. Archiving and Exchange of a Computerized Marine Seismic Database: The ROSE (Rivera Ocean Seismic Experiment) Data Archive System

    DTIC Science & Technology

    1983-12-01

    The participating institutions provided their data to the facility where the data were catalogued and distributed. This report describes in detail ...distributed. This report describes in detail the processes and computer programs used to catalog, store and distribute the ROSE seismic data. The...of the Data Base 1 II. The Rose Storage and Exchange Format 2 A. The Tape Header File 2 B. File Header Record and Data Structure 6 C. Shot

  16. Improving exchange with consumers within mental health organizations: Recognizing mental ill health experience as a 'sneaky, special degree'.

    PubMed

    Scholz, Brett; Bocking, Julia; Happell, Brenda

    2017-02-01

    Stigmatizing views towards consumers may be held even by those working within mental health organizations. Contemporary mental health policies require organizations to work collaboratively with consumers in producing and delivering services. Using social exchange theory, which emphasises mutual exchange to maximise benefits in partnership, the current study explores the perspectives of those working within organizations that have some level of consumer leadership. Interviews were conducted with 14 participants from a range of mental health organizations. Data were transcribed, and analyzed using thematic analytic and discursive psychological techniques. Findings suggest stigma is still prevalent even in organizations that have consumers in leadership positions, and consumers are often perceived as less able to work in mental health organizations than non-consumers. Several discourses challenged such a view - showing how consumers bring value to mental health organizations through their expertise in the mental health system, and their ability to provide safety and support to other consumers. Through a social exchange theory lens, the authors call for organizations to challenge stigma and promote the value that consumers can bring to maximize mutual benefits.

  17. 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.

  18. 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

  19. 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

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

    PubMed

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

    2015-01-01

    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.

  1. 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.

  2. 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…

  3. Forensic animal DNA typing: Allele nomenclature and standardization of 14 feline STR markers.

    PubMed

    Schury, N; Schleenbecker, U; Hellmann, A P

    2014-09-01

    Since the domestic cat (Felis catus) has become one of the most popular pets and owners usually develop a close relationship to their cats, it is necessary to take traces of cats into account for forensic casework. For this purpose feline short tandem (STR) repeat markers have been investigated in several earlier studies, but no detailed description of sequence data, allelic variations or a repeat-based nomenclature is available. The aim of the study was to provide a suggestion for the allele nomenclature of 14 cat STR markers according to the recommendations of the International Society for Forensic Genetics (ISFG) for human DNA typing and to present a standardized system for a secure DNA typing of samples. Samples of 122 unrelated cats from a local animal shelter and private owners in Germany were used to generate a population database with allele frequencies and to analyze the tandemly repeated sequence variations within the alleles of each STR marker. These markers could be grouped into two STR classes: simple repeat STRs and complex STRs (some with the supplement highly complex), consisting of di- and tetranucleotide repeat motifs. After analyzing the repeat structure and elaborating a repeat based nomenclature, allelic ladders of common and rarely occurring alleles for each marker were designed to enable accurate typing of alleles that differ in fragment length and to facilitate data exchange.

  4. 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.

  5. A novel measurement of allele discrimination for assessment of allele-specific silencing by RNA interference.

    PubMed

    Takahashi, Masaki; Hohjoh, Hirohiko

    2014-11-01

    Allele-specific silencing by RNA interference (ASP-RNAi) is an atypical RNAi that is capable of discriminating target alleles from non-target alleles, and may be therapeutically useful for specific inhibition of disease-causing alleles without affecting their corresponding normal alleles. However, it is difficult to design and select small interfering RNA (siRNAs) that confer ASP-RNAi. A major problem is that there are few appropriate measures in determining optimal allele-specific siRNAs. Here we show two novel formulas for calculating a new measure of allele-discrimination, named "ASP-score". The formulas and ASP-score allow for an unbiased determination of optimal siRNAs, and may contribute to characterizing such allele-specific siRNAs.

  6. Isotope exchange experiments on TEXTOR and TORE SUPRA using Ion Cyclotron Wall Conditioning and Glow Discharge Conditioning

    NASA Astrophysics Data System (ADS)

    Wauters, T.; Douai, D.; Lyssoivan, A.; Philipps, V.; Brémond, S.; Freisinger, M.; Kreter, A.; Lombard, G.; Marchuk, O.; Mollard, P.; Paul, M. K.; Pegourié, B.; Reimer, H.; Sergienko, G.; Tsitrone, E.; Vervier, M.; Van Wassenhove, G.; Wünderlich, D.; Van Schoor, M.; Van Oost, G.

    2011-08-01

    This contribution reports on isotope exchange studies with both Ion Cyclotron Wall Conditioning (ICWC) and Glow Discharge Conditioning (GDC) in TEXTOR and TORE SUPRA. The discharges have been carried out in H2, D2 (ICWC and GDC) and He/H2 mixtures (ICWC). The higher reionization probability in ICWC compared to GDC, following from the 3 to 4 orders of magnitude higher electron density, leads to a lower pumping efficiency of wall desorbed species. GDC has in this analysis (5-10) times higher removal rates of wall desorbed species than ICWC, although the wall release rate is 10 times higher in ICWC. Also the measured high retention during ICWC can be understood as an effect of the high reionization probability. The use of short RF pulses (∼1 s) followed by a larger pumping time significantly improves the ratio of implanted over recovered particles, without severely lowering the total amount of removed particles.

  7. Allelic selection of human IL-2 gene.

    PubMed

    Matesanz, F; Delgado, C; Fresno, M; Alcina, A

    2000-12-01

    The allelic expression of mouse IL-2 cannot be definitely extrapolated to what might happen in humans. Therefore, we investigated the regulation of allelic expression of the IL-2 gene in non-genetically manipulated human T lymphocytes by following natural allelic polymorphisms. We found a phenotypically silent punctual change in the human IL-2 at position 114 after the first nucleotide of the initiation codon, which represents a dimorphic polymorphism at the first exon of the IL-2 gene. This allowed the study by single-cell PCR of the regulation of the human IL-2 allelic expression in heterozygous CD4(+) T cells, which was found to be tightly controlled monoallelically. These findings may be used as a suitable marker for monitoring the IL-2 allelic contribution to effector activities and in immune responses against different infections or in pathological situations.

  8. HIV risk behaviours of current sex workers attending syringe exchange: the experiences of women in five US cities.

    PubMed

    Paone, D; Cooper, H; Alperen, J; Shi, Q; Des Jarlais, D C

    1999-06-01

    Existing research indicates that sex workers who inject drugs are vulnerable to HIV infection through both risky sexual and drug use practices. This study is the first attempt to learn whether this increased risk persists among current sex workers who participate in syringe exchange programmes (SEPs). With data from interviews with randomly selected participants in five US cities, we compared the demographic characteristics, sexual risk behaviours, drug use practices, emotional and physical health, and SEP utilization patterns of currently active female sex workers who attend SEPs with female SEP participants who do not engage in sex work. Data indicate that women enrolled in SEPs who were currently trading sex typically reported greater HIV risk than women non-sex workers. Current sex workers reported higher levels of risk for every drug risk variable examined in bivariate analysis. They were more likely than other women to inject with a syringe previously used by someone else, to inject daily and to attend shooting galleries; they were less likely to use a condom with their primary partners and to report higher levels of psychological distress than their counterparts. The relationship between sex work status and risky injection practices persisted when potential confounders were controlled for in multivariate analysis. SEPs can serve a pivotal role in providing sex workers with services and referrals which would help them reduce risk behaviours.

  9. Elevated CO(2) and temperature alter net ecosystem C exchange in a young Douglas fir mesocosm experiment.

    PubMed

    Tingey, David T; Lee, E Henry; Phillips, Donald L; Rygiewicz, Paul T; Waschmann, Ronald S; Johnson, Mark G; Olszyk, David M

    2007-11-01

    We investigated the effects of elevated CO(2) (EC) [ambient CO(2) (AC) + 190 ppm] and elevated temperature (ET) [ambient temperature (AT) + 3.6 degrees C] on net ecosystem exchange (NEE) of seedling Douglas fir (Pseudotsuga menziesii) mesocosms. As the study utilized seedlings in reconstructed soil-litter-plant systems, we anticipated greater C losses through ecosystem respiration (R(e)) than gains through gross photosynthesis (GPP), i.e. negative NEE. We hypothesized that: (1) EC would increase GPP more than R(e), resulting in NEE being less negative; and (2) ET would increase R(e) more than GPP, resulting in NEE being more negative. We also evaluated effects of CO(2) and temperature on light inhibition of dark respiration. Consistent with our hypothesis, NEE was a smaller C source in EC, not because EC increased photosynthesis but rather because of decreased respiration resulting in less C loss. Consistent with our hypothesis, NEE was more negative in ET because R(e) increased more than GPP. The light level that inhibited respiration varied seasonally with little difference among CO(2) and temperature treatments. In contrast, the degree of light inhibition of respiration was greater in AC than EC. In our system, respiration was the primary control on NEE, as EC and ET caused greater changes in respiration than photosynthesis.

  10. 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

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

    PubMed

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

    2016-05-09

    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.

  12. 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

  13. 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.

  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. Nucleotide variation and identification of novel blast resistance alleles of Pib by allele mining strategy.

    PubMed

    Ramkumar, G; Madhav, M S; Devi, S J S Rama; Prasad, M S; Babu, V Ravindra

    2015-04-01

    Pib is one of significant rice blast resistant genes, which provides resistance to wide range of isolates of rice blast pathogen, Magnaporthe oryzae. Identification and isolation of novel and beneficial alleles help in crop enhancement. Allele mining is one of the best strategies for dissecting the allelic variations at candidate gene and identification of novel alleles. Hence, in the present study, Pib was analyzed by allele mining strategy, and coding and non-coding (upstream and intron) regions were examined to identify novel Pib alleles. Allelic sequences comparison revealed that nucleotide polymorphisms at coding regions affected the amino acid sequences, while the polymorphism at upstream (non-coding) region affected the motifs arrangements. Pib alleles from resistant landraces, Sercher and Krengosa showed better resistance than Pib donor variety, might be due to acquired mutations, especially at LRR region. The evolutionary distance, Ka/Ks and phylogenetic analyzes also supported these results. Transcription factor binding motif analysis revealed that Pib (Sr) had a unique motif (DPBFCOREDCDC3), while five different motifs differentiated the resistance and susceptible Pib alleles. As the Pib is an inducible gene, the identified differential motifs helps to understand the Pib expression mechanism. The identified novel Pib resistant alleles, which showed high resistance to the rice blast, can be used directly in blast resistance breeding program as alternative Pib resistant sources.

  17. Comparison of HLA allelic imputation programs.

    PubMed

    Karnes, Jason H; Shaffer, Christian M; Bastarache, Lisa; Gaudieri, Silvana; Glazer, Andrew M; Steiner, Heidi E; Mosley, Jonathan D; Mallal, Simon; Denny, Joshua C; Phillips, Elizabeth J; Roden, Dan M

    2017-01-01

    Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS) data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository. We performed four-digit HLA sequencing for HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1 using long-read 454 FLX sequencing. All samples were genotyped using both the Illumina HumanExome BeadChip platform and a GWAS platform. Call rates and concordance rates were compared by platform, frequency of allele, and race/ethnicity. Overall concordance rates were similar between programs in European Americans (EA) (0.975 [SNP2HLA]; 0.939 [HLA*IMP:02]; 0.976 [HIBAG]). SNP2HLA provided a significant advantage in terms of call rate and the number of alleles imputed. Concordance rates were lower overall for African Americans (AAs). These observations were consistent when accuracy was compared across HLA loci. All imputation programs performed similarly for low frequency HLA alleles. Higher concordance rates were observed when HLA alleles were imputed from GWAS platforms versus the HumanExome BeadChip, suggesting that high genomic coverage is preferred as input for HLA allelic imputation. These findings provide guidance on the best use of HLA imputation methods and elucidate their limitations.

  18. Comparison of HLA allelic imputation programs

    PubMed Central

    Shaffer, Christian M.; Bastarache, Lisa; Gaudieri, Silvana; Glazer, Andrew M.; Steiner, Heidi E.; Mosley, Jonathan D.; Mallal, Simon; Denny, Joshua C.; Phillips, Elizabeth J.; Roden, Dan M.

    2017-01-01

    Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS) data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository. We performed four-digit HLA sequencing for HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1 using long-read 454 FLX sequencing. All samples were genotyped using both the Illumina HumanExome BeadChip platform and a GWAS platform. Call rates and concordance rates were compared by platform, frequency of allele, and race/ethnicity. Overall concordance rates were similar between programs in European Americans (EA) (0.975 [SNP2HLA]; 0.939 [HLA*IMP:02]; 0.976 [HIBAG]). SNP2HLA provided a significant advantage in terms of call rate and the number of alleles imputed. Concordance rates were lower overall for African Americans (AAs). These observations were consistent when accuracy was compared across HLA loci. All imputation programs performed similarly for low frequency HLA alleles. Higher concordance rates were observed when HLA alleles were imputed from GWAS platforms versus the HumanExome BeadChip, suggesting that high genomic coverage is preferred as input for HLA allelic imputation. These findings provide guidance on the best use of HLA imputation methods and elucidate their limitations. PMID:28207879

  19. Overview of the CoOP experiments: Physical and chemical measurements parameterizing air-sea heat exchange

    NASA Astrophysics Data System (ADS)

    Bock, Erik John; Bearer Edson, James; Frew, Nelson M.; Hara, Tetsu; Haussecker, Horst; Jähne, Bernd; McGillis, Wade R.; McKenna, Sean P.; Nelson, Robert K.; Schimpf, Uwe; Uz, Mete

    Experiments performed in the Pacific and Atlantic Oceans in 1995 and 1997 attempted to measure the short time-scale and small spatial scale variability in the air-sea gas transfer rate. Along with these measurements, physical and chemical parameters known from previous laboratory studies to influence transfer rates were also characterized. These parameters include the atmospheric forcing, the capillary and capillary-gravity wave state, the surface chemical enrichment, and the level of near-surface turbulence. In this contribution we describe the methodologies employed for the measurement campaigns and summarize some general observations resulting from them. Other contributions from the coauthors describe in more detail the specific conclusions derived from the Coastal Ocean Processes (CoOP) field program.

  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. Ten novel HLA-DRB1 alleles and one novel DRB3 allele.

    PubMed

    Lazaro, A M; Steiner, N K; Moraes, M E; Moraes, J R; Ng, J; Hartzman, R J; Hurley, C K

    2005-10-01

    Ten novel HLA-DRB1 and one DRB3 alleles are described. Eight of the variants are single-nucleotide substitutions, four resulting in an amino acid change (DRB1*1145, *1148, *0828 and *1514) and four with silent substitutions (DRB1*040504, *130103, *160502 and DRB3*020204). Two alleles differ by two nucleotide changes altering one (DRB1*1447 and *1361) amino acid and one allele alters three nucleotides and two amino acids.

  2. Abnormal segregation of alleles in CEPH pedigree DNAs arising from allele loss in lymphoblastoid DNA

    SciTech Connect

    Royle, N.J.; Armour, J.A.L.; Crosier, M.; Jeffreys, A.J. )

    1993-01-01

    Somatic events that result in the reduction to hemior homozygosity at all loci affected by the event have been identified in lymphoblastoid DNA from mothers of two CEPH families. Using suitably informative probes, the allele deficiencies were detected by the abnormal transmission of alleles from grandparents to grandchildren, with the apparent absence of the alleles from the parent. Undetected somatic deficiencies in family DNAs could result in misscoring of recombination events and consequently introduce errors into linkage analysis. 15 refs., 2 figs.

  3. Ten Novel HLA-DRB1 Alleles and One Novel DRB3 Allele

    DTIC Science & Technology

    2006-05-31

    BRIEF COMMUNICATION Ten novel HLA-DRB1 alleles and one novel DRB3 allele A. M. Lazaro1, N. K. Steiner1, M. E. Moraes2, J. R. Moraes2, J. Ng1, R. J...accepted for publication 31 May 2005 doi: 10.1111/j.1399-0039.2005.00459.x Abstract Ten novel HLA-DRB1 and one DRB3 alleles are described. Eight of the...substitutions (DRB1*040504, *130103, *160502 and DRB3 *020204). Two alleles differ by two nucleotide changes altering one (DRB1*1447 and *1361) amino acid and

  4. Pitfalls in the Measurement of Metabolite Concentrations Using the One-Pulse Experiment in in Vivo NMR: Commentary on ``On Neglecting Chemical Exchange Effects When Correcting in Vivo 31P MRS Data for Partial Saturation''

    NASA Astrophysics Data System (ADS)

    Spencer, Richard G. S.; Fishbein, Kenneth W.; Galban, Craig J.

    2001-04-01

    In an article in a previous issue of the Journal of Magnetic Resonance, Ouwerkerk and Bottomley (J. Magn. Reson.148, pp. 425-435, 2001) show that even in the presence of chemical exchange, the dependence of saturation factors on repetition time in the one-pulse experiment is approximately monoexponential. They conclude from this fact that the effect of chemical exchange on the use of saturation factors when correcting for partial saturation is negligible. We take issue with this conclusion and demonstrate that because saturation factors in the presence of chemical exchange are strongly dependent upon all of the chemical parameters of the system, that is, upon all T1's and M0's of resonances in the exchange network and upon the reaction rates themselves, it is problematic to apply saturation factor corrections in situations in which any of these parameters may change. The error criterion we establish reflects actual errors in quantitation, rather than departures from monoexponentiality.

  5. 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

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

    PubMed

    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.

  7. Long repetition time experiments for measurement of concentrations in systems with chemical exchange and undergoing temporal variation-comparison of methods with and without correction for saturation

    NASA Astrophysics Data System (ADS)

    Galbán, Craig J.; Spencer, Richard G. S.

    2003-02-01

    The purpose of this paper is to compare two methods for quantifying metabolite concentrations using the one-pulse experiment for a sample undergoing chemical exchange and subject to an intervention or other temporal variation. The methods, LATR-C (Long Acquisition TR (interpulse delay); Corrected for partial saturation) and LATR-NC (Long Acquisition TR; Not Corrected), are compared in terms of signal-to-noise ratio, SNR, per unit time and quantitation errors. Parameters relevant to the isolated perfused rat heart are used as a specific application, although the results are general. We assume throughout that spin-lattice relaxation times, T1, do not change. For a given flip angle, θ, TR's are calculated which result in maximal SNR per unit time under 10%, 5%, and 1% constraints on quantitation errors. Additional simulations were performed to demonstrate explicitly the dependence of the quantitation errors on TR for a fixed θ. We find (i) if the allowed error is large, and when both metabolite concentrations and rate constants vary, LATR-C permits use of shorter TR, and hence yields greater SNR per unit time, than LATR-NC; (ii) for small allowed error, the two methods give similar TR's and SNR per unit time, so that the simpler LATR-NC experiment may be preferred; (iii) large values of θ result in similar constrained TR's and hence SNR per unit time for the two methods; (iv) the ratio of concentrations of metabolites with similar T1 exhibit similar errors for the two methods.

  8. 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.

  9. Field study on effects of a heat exchanger on broiler performance, energy use, and calculated carbon dioxide emission at commercial broiler farms, and the experiences of farmers using a heat exchanger.

    PubMed

    Bokkers, E A M; van Zanten, H H E; van den Brand, H

    2010-12-01

    In broiler houses, ventilation removes moisture and maintains ambient temperature and air quality. During cold weather conditions, ventilation can result in undesirable heat loss from the house. Extra input of energy for heating the building is needed then, resulting in extra CO(2) emissions when fossil fuels are used for this purpose. In such a situation, an air-to-air heat exchanger (HE) might be valuable because it recovers heat by prewarming fresh supply air with warm inside air. The aim of this study was to analyze effects of on-farm use of an HE on broiler performance, energy use, and CO(2) emission by comparing production cycles with and without an HE, and to inventory the experiences of farmers using an HE. Data were collected of production cycles finished with (102) or without (149) an HE on 25 farms. Data on mortality, feed intake, water intake, and BW gain were obtained to analyze broiler performance. When available, gas and electricity use were obtained to analyze energy use and to calculate CO(2) emission. Farmers were interviewed about their experiences regarding the HE. The use of an HE tended to increase daily weight gain (56 vs. 55, SEM 0.3 g/d; P = 0.07), but did not affect other performance variables. Based on 13 farms, gas use was reduced by 38% (P < 0.01) after installing an HE. Based on 3 farms only, an HE did not affect electricity use, total energy use, or calculated CO(2) emission. It appeared that farmers were satisfied with the HE because they experienced an increase in job satisfaction, an improvement of climate conditions and litter quality in the broiler house, and a more uniform temperature and broiler distribution in the house. We concluded that the use of an HE reduced gas use and has the ability to improve broiler weight gain but had no effect on other broiler performance variables. Effects on CO(2) emission were unclear. Farmers appeared to be positive about using an HE, because it improved broiler house climate and job

  10. Allele-specific DNA methylation: beyond imprinting.

    PubMed

    Tycko, Benjamin

    2010-10-15

    Allele-specific DNA methylation (ASM) and allele-specific gene expression (ASE) have long been studied in genomic imprinting and X chromosome inactivation. But these types of allelic asymmetries, along with allele-specific transcription factor binding (ASTF), have turned out to be far more pervasive-affecting many non-imprinted autosomal genes in normal human tissues. ASM, ASE and ASTF have now been mapped genome-wide by microarray-based methods and NextGen sequencing. Multiple studies agree that all three types of allelic asymmetries, as well as the related phenomena of expression and methylation quantitative trait loci, are mostly accounted for by cis-acting regulatory polymorphisms. The precise mechanisms by which this occurs are not yet understood, but there are some testable hypotheses and already a few direct clues. Future challenges include achieving higher resolution maps to locate the epicenters of cis-regulated ASM, using this information to test mechanistic models, and applying genome-wide maps of ASE/ASM/ASTF to pinpoint functional regulatory polymorphisms influencing disease susceptibility.

  11. A "successful allele" at Campylobacter jejuni contingency locus Cj0170 regulates motility; "successful alleles" at locus Cj0045 are strongly associated with mouse colonization.

    PubMed

    Artymovich, Katherine; Kim, Joo-Sung; Linz, John E; Hall, David F; Kelley, Lauren E; Kalbach, Harrison L; Kathariou, Sophia; Gaymer, Jean; Paschke, Brenda

    2013-06-01

    Campylobacter jejuni is an important foodborne pathogen of humans and its primary reservoir is the gastrointestinal (GI) tract of chickens. Our previous studies demonstrated that phase variation to specific "successful alleles" at C. jejuni contingency loci Cj0045 (successful alleles carry 9G or 10G homopolymeric tracts) and Cj0170 (successful allele carries a 10G homopolymeric tract) in C. jejuni populations is strongly associated with colonization and enteritis in C57BL/6 IL-10 deficient mice. In the current study, we strengthened the association between locus Cj0170, Cj0045, and mouse colonization. We generated 8 independent strains derived from C. jejuni 11168 strain KanR4 that carried a Cj0170 gene disruption and these were all non motile. Two randomly chosen strains with the Cj0170 gene disruption (DM0170-2 and DM0170-6) were gavaged into mice. DM0170-2 and DM0170-6 failed to colonize mice while the control strain that carried a "successful"Cj0170 10G allele was motile and did colonize mice. In parallel studies, when we inoculated C. jejuni strain 33292 into mice, the "unsuccessful"Cj0045 11G allele experienced phase variation to "successful" 9G and 10G alleles in 2 independent experiments prior to d4 post inoculation in mice while the "successful" 9G allele in the control strain remained stable through d21 post inoculation or shifted to other successful alleles. These data confirm that locus Cj0170 regulates motility in C. jejuni strain KanR4 and is a virulence factor in the mouse model. The data also support a possible role of locus Cj0045 as a virulence factor in strain 33292 in infection of mice.

  12. AlleleSeq: analysis of allele-specific expression and binding in a network framework.

    PubMed

    Rozowsky, Joel; Abyzov, Alexej; Wang, Jing; Alves, Pedro; Raha, Debasish; Harmanci, Arif; Leng, Jing; Bjornson, Robert; Kong, Yong; Kitabayashi, Naoki; Bhardwaj, Nitin; Rubin, Mark; Snyder, Michael; Gerstein, Mark

    2011-08-02

    To study allele-specific expression (ASE) and binding (ASB), that is, differences between the maternally and paternally derived alleles, we have developed a computational pipeline (AlleleSeq). Our pipeline initially constructs a diploid personal genome sequence (and corresponding personalized gene annotation) using genomic sequence variants (SNPs, indels, and structural variants), and then identifies allele-specific events with significant differences in the number of mapped reads between maternal and paternal alleles. There are many technical challenges in the construction and alignment of reads to a personal diploid genome sequence that we address, for example, bias of reads mapping to the reference allele. We have applied AlleleSeq to variation data for NA12878 from the 1000 Genomes Project as well as matched, deeply sequenced RNA-Seq and ChIP-Seq data sets generated for this purpose. In addition to observing fairly widespread allele-specific behavior within individual functional genomic data sets (including results consistent with X-chromosome inactivation), we can study the interaction between ASE and ASB. Furthermore, we investigate the coordination between ASE and ASB from multiple transcription factors events using a regulatory network framework. Correlation analyses and network motifs show mostly coordinated ASB and ASE.

  13. 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.

  14. Forensic Loci Allele Database (FLAD): Automatically generated, permanent identifiers for sequenced forensic alleles.

    PubMed

    Van Neste, Christophe; Van Criekinge, Wim; Deforce, Dieter; Van Nieuwerburgh, Filip

    2016-01-01

    It is difficult to predict if and when massively parallel sequencing of forensic STR loci will replace capillary electrophoresis as the new standard technology in forensic genetics. The main benefits of sequencing are increased multiplexing scales and SNP detection. There is not yet a consensus on how sequenced profiles should be reported. We present the Forensic Loci Allele Database (FLAD) service, made freely available on http://forensic.ugent.be/FLAD/. It offers permanent identifiers for sequenced forensic alleles (STR or SNP) and their microvariants for use in forensic allele nomenclature. Analogous to Genbank, its aim is to provide permanent identifiers for forensically relevant allele sequences. Researchers that are developing forensic sequencing kits or are performing population studies, can register on http://forensic.ugent.be/FLAD/ and add loci and allele sequences with a short and simple application interface (API).

  15. Transformation of QTL genotypic effects to allelic effects

    PubMed Central

    Nagamine, Yoshitaka

    2005-01-01

    The genotypic and allelic effect models are equivalent in terms of QTL detection in a simple additive model, but the QTL allelic model has the advantage of providing direct information for marker-assisted selection. However, the allelic matrix is four times as large as the genotypic IBD matrix, causing computational problems, especially in genome scans examining multiple positions. Transformation from genotypic to allelic effects, after estimating the genotypic effects with a smaller IBD matrix, can solve this problem. Although the validity of transformation from genotypic to allelic effects has been disputed, this work proves that transformation can successfully yield unique allelic effects when genotypic and allelic IBD matrixes exist. PMID:16093016

  16. Common Kibra alleles are associated with human memory performance.

    PubMed

    Papassotiropoulos, Andreas; Stephan, Dietrich A; Huentelman, Matthew J; Hoerndli, Frederic J; Craig, David W; Pearson, John V; Huynh, Kim-Dung; Brunner, Fabienne; Corneveaux, Jason; Osborne, David; Wollmer, M Axel; Aerni, Amanda; Coluccia, Daniel; Hänggi, Jürgen; Mondadori, Christian R A; Buchmann, Andreas; Reiman, Eric M; Caselli, Richard J; Henke, Katharina; de Quervain, Dominique J-F

    2006-10-20

    Human memory is a polygenic trait. We performed a genome-wide screen to identify memory-related gene variants. A genomic locus encoding the brain protein KIBRA was significantly associated with memory performance in three independent, cognitively normal cohorts from Switzerland and the United States. Gene expression studies showed that KIBRA was expressed in memory-related brain structures. Functional magnetic resonance imaging detected KIBRA allele-dependent differences in hippocampal activations during memory retrieval. Evidence from these experiments suggests a role for KIBRA in human memory.

  17. Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles.

    PubMed

    Brunner, Susanne; Hurni, Severine; Streckeisen, Philipp; Mayr, Gabriele; Albrecht, Mario; Yahiaoui, Nabila; Keller, Beat

    2010-11-01

    Some plant resistance genes occur as allelic series, with each member conferring specific resistance against a subset of pathogen races. In wheat, there are 17 alleles of the Pm3 gene. They encode nucleotide-binding (NB-ARC) and leucine-rich-repeat (LRR) domain proteins, which mediate resistance to distinct race spectra of powdery mildew. It is not known if specificities from different alleles can be combined to create resistance genes with broader specificity. Here, we used an approach based on avirulence analysis of pathogen populations to characterize the molecular basis of Pm3 recognition spectra. A large survey of mildew races for avirulence on the Pm3 alleles revealed that Pm3a has a resistance spectrum that completely contains that of Pm3f, but also extends towards additional races. The same is true for the Pm3b and Pm3c gene pair. The molecular analysis of these allelic pairs revealed a role of the NB-ARC protein domain in the efficiency of effector-dependent resistance. Analysis of the wild-type and chimeric Pm3 alleles identified single residues in the C-terminal LRR motifs as the main determinant of allele specificity. Variable residues of the N-terminal LRRs are necessary, but not sufficient, to confer resistance specificity. Based on these data, we constructed a chimeric Pm3 gene by intragenic allele pyramiding of Pm3d and Pm3e that showed the combined resistance specificity and, thus, a broader recognition spectrum compared with the parental alleles. Our findings support a model of stepwise evolution of Pm3 recognition specificities.

  18. Estimating the probability of allelic drop-out of STR alleles in forensic genetics.

    PubMed

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt; Morling, Niels

    2009-09-01

    In crime cases with available DNA evidence, the amount of DNA is often sparse due to the setting of the crime. In such cases, allelic drop-out of one or more true alleles in STR typing is possible. We present a statistical model for estimating the per locus and overall probability of allelic drop-out using the results of all STR loci in the case sample as reference. The methodology of logistic regression is appropriate for this analysis, and we demonstrate how to incorporate this in a forensic genetic framework.

  19. Exchange Network

    EPA Pesticide Factsheets

    The Environmental Information Exchange Network (EIEN) is an Internet-based system used by state, tribal and territorial partners to securely share environmental and health information with one another and EPA.

  20. Gas exchange

    MedlinePlus Videos and Cool Tools

    ... during exhalation. Gas exchange is the delivery of oxygen from the lungs to the bloodstream, and the ... share a membrane with the capillaries in which oxygen and carbon dioxide move freely between the respiratory ...

  1. 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)

  2. High-Throughput Genotyping with TaqMan Allelic Discrimination and Allele-Specific Genotyping Assays.

    PubMed

    Heissl, Angelika; Arbeithuber, Barbara; Tiemann-Boege, Irene

    2017-01-01

    Real-time PCR-based genotyping methods, such as TaqMan allelic discrimination assays and allele-specific genotyping, are particularly useful when screening a handful of single nucleotide polymorphisms in hundreds of samples; either derived from different individuals, tissues, or pre-amplified DNA. Although real-time PCR-based methods such as TaqMan are well-established, alternative methods, like allele-specific genotyping, are powerful alternatives, especially for genotyping short tandem repeat (STR) length polymorphisms. Here, we describe all relevant aspects when developing an assay for a new SNP or STR using either TaqMan or allele-specific genotyping, respectively, such as primer and probe design, optimization of reaction conditions, the experimental procedure for typing hundreds of samples, and finally the data evaluation. Our goal is to provide a guideline for developing genotyping assays using these two approaches that render reliable and reproducible genotype calls involving minimal optimization.

  3. 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…

  4. HLA-B alleles of the Cayapa of Ecuador: new B39 and B15 alleles.

    PubMed

    Garber, T L; Butler, L M; Trachtenberg, E A; Erlich, H A; Rickards, O; De Stefano, G; Watkins, D I

    1995-01-01

    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.

  5. 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

  6. Initial invasion of gametophytic self-incompatibility alleles in the absence of tight linkage between pollen and pistil S alleles.

    PubMed

    Sakai, Satoki; Wakoh, Haluka

    2014-08-01

    In homomorphic self-incompatibility (SI) systems of plants, the loci controlling the pollen and pistil types are tightly linked, and this prevents the generation of compatible combinations of alleles expressing pollen and pistil types, which would result in self-fertilization. We modeled the initial invasion of the first pollen and pistil alleles in gametophytic SI to determine whether these alleles can stably coexist in a population without tight linkage. We assume pollen and pistil loci each carry an incompatibility allele S and an allele without an incompatibility function N. We assume that pollen with an S allele are incompatible with pistils carrying S alleles, whereas other crosses are compatible. Ovules in pistils carrying an S allele suffer viability costs because recognition consumes resources. We found that the cost of carrying a pistil S allele allows pollen and pistil S alleles to coexist in a stable equilibrium if linkage is partial. This occurs because parents that carry pistil S alleles but are homozygous for pollen N alleles cannot avoid self-fertilization; however, they suffer viability costs. Hence, pollen N alleles are selected again. When pollen and pistil S alleles can coexist in a polymorphic equilibrium, selection will favor tighter linkage.

  7. Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection

    PubMed Central

    Chesler, Elissa J.; Gatti, Daniel M.; Morgan, Andrew P.; Strobel, Marge; Trepanier, Laura; Oberbeck, Denesa; McWeeney, Shannon; Hitzemann, Robert; Ferris, Martin; McMullan, Rachel; Clayshultle, Amelia; Bell, Timothy A.; Manuel de Villena, Fernando Pardo; Churchill, Gary A.

    2016-01-01

    Multi-parent populations (MPPs) capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO) mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility. PMID:27694113

  8. Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection.

    PubMed

    Chesler, Elissa J; Gatti, Daniel M; Morgan, Andrew P; Strobel, Marge; Trepanier, Laura; Oberbeck, Denesa; McWeeney, Shannon; Hitzemann, Robert; Ferris, Martin; McMullan, Rachel; Clayshultle, Amelia; Bell, Timothy A; Manuel de Villena, Fernando Pardo; Churchill, Gary A

    2016-12-07

    Multi-parent populations (MPPs) capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO) mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility.

  9. 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.

  10. Allelic variation contributes to bacterial host specificity

    DOE PAGES

    Yue, Min; Han, Xiangan; Masi, Leon De; ...

    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

  11. 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...

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins.

    PubMed

    Remington, David L

    2015-12-01

    Perspectives on the role of large-effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular-based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular-based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome-wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology.

  17. 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.

  18. Update on allele nomenclature for human cytochromes P450 and the Human Cytochrome P450 Allele (CYP-allele) Nomenclature Database.

    PubMed

    Sim, Sarah C; Ingelman-Sundberg, Magnus

    2013-01-01

    Interindividual variability in xenobiotic metabolism and drug response is extensive and genetic factors play an important role in this variation. A majority of clinically used drugs are substrates for the cytochrome P450 (CYP) enzyme system and interindividual variability in expression and function of these enzymes is a major factor for explaining individual susceptibility for adverse drug reactions and drug response. Because of the existence of many polymorphic CYP genes, for many of which the number of allelic variants is continually increasing, a universal and official nomenclature system is important. Since 1999, all functionally relevant polymorphic CYP alleles are named and published on the Human Cytochrome P450 Allele (CYP-allele) Nomenclature Web site (http://www.cypalleles.ki.se). Currently, the database covers nomenclature of more than 660 alleles in a total of 30 genes that includes 29 CYPs as well as the cytochrome P450 oxidoreductase (POR) gene. On the CYP-allele Web site, each gene has its own Webpage, which lists the alleles with their nucleotide changes, their functional consequences, and links to publications identifying or characterizing the alleles. CYP2D6, CYP2C9, CYP2C19, and CYP3A4 are the most important CYPs in terms of drug metabolism, which is also reflected in their corresponding highest number of Webpage hits at the CYP-allele Web site.The main advantage of the CYP-allele database is that it offers a rapid online publication of CYP-alleles and their effects and provides an overview of peer-reviewed data to the scientific community. Here, we provide an update of the CYP-allele database and the associated nomenclature.

  19. 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

  20. Biased gene conversion skews allele frequencies in human populations, increasing the disease burden of recessive alleles.

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-02

    Gene conversion results in the nonreciprocal transfer of genetic information between two recombining sequences, and there is evidence that this process is biased toward G and C alleles. However, the strength of GC-biased gene conversion (gBGC) in human populations and its effects on hereditary disease have yet to be assessed on a genomic scale. Using high-coverage whole-genome sequences of African hunter-gatherers, agricultural populations, and primate outgroups, we quantified the effects of GC-biased gene conversion on population genomic data sets. We find that genetic distances (FST and population branch statistics) are modified by gBGC. In addition, the site frequency spectrum is left-shifted when ancestral alleles are favored by gBGC and right-shifted when derived alleles are favored by gBGC. Allele frequency shifts due to gBGC mimic the effects of natural selection. As expected, these effects are strongest in high-recombination regions of the human genome. By comparing the relative rates of fixation of unbiased and biased sites, the strength of gene conversion was estimated to be on the order of Nb ≈ 0.05 to 0.09. We also find that derived alleles favored by gBGC are much more likely to be homozygous than derived alleles at unbiased SNPs (+42.2% to 62.8%). This results in a curse of the converted, whereby gBGC causes substantial increases in hereditary disease risks. Taken together, our findings reveal that GC-biased gene conversion has important population genetic and public health implications.

  1. An Experience of the Transfer of Appropriate Technology from Fiji to Kenya; The 1987 ISIS-WICCE Exchange Programme on Women and Appropriate Technology.

    ERIC Educational Resources Information Center

    Bolabola, Cema

    1987-01-01

    The author describes the 1987 exchange program "Women and Appropriate Technology." The program concentrated on appropriate technology in relation to rural women. She also describes a pilot appropriate technology project carried out in Kenya that involved the construction of three community buildings (a laundry and two bathrooms). (CH)

  2. Separation of Anisotropy and Exchange Broadening Using 15N CSA- 15N- 1H Dipole-Dipole Relaxation Cross-Correlation Experiments

    NASA Astrophysics Data System (ADS)

    Renner, Christian; Holak, Tad A.

    2000-08-01

    Based on the measurement of cross-correlation rates between 15N CSA and 15N-1H dipole-dipole relaxation we propose a procedure for separating exchange contributions to transverse relaxation rates (R2 = 1/T2) from effects caused by anisotropic rotational diffusion of the protein molecule. This approach determines the influence of anisotropy and chemical exchange processes independently and therefore circumvents difficulties associated with the currently standard use of T1/T2 ratios to determine the rotational diffusion tensor. We find from computer simulations that, in the presence of even small amounts of internal flexibility, fitting T1/T2 ratios tends to underestimate the anisotropy of overall tumbling. An additional problem exists when the N-H bond vector directions are not distributed homogeneously over the surface of a unit sphere, such as in helix bundles or β-sheets. Such a case was found in segment 4 of the gelation factor (ABP 120), an F-actin cross-linking protein, in which the diffusion tensor cannot be calculated from T1/T2 ratios. The 15N CSA tensor of the residues for this β-sheet protein was found to vary even within secondary structure elements. The use of a common value for the whole protein molecule therefore might be an oversimplification. Using our approach it is immediately apparent that no exchange broadening exists for segment 4 although strongly reduced T2 relaxation times for several residues could be mistaken as indications for exchange processes.

  3. 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

  4. 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)

  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. Identification of a novel DRB1 allele through intergenic recombination between HLA-DRB1 and HLA-DRB3∗02 in a Chinese family.

    PubMed

    Huang, Weijin; Liu, Xiangjun; Li, Erwei; Zhao, Chenyan; Liu, Qiang; Liang, Zhenglun; Wang, Youchun; Lu, Fengmin

    2013-12-01

    In this study, a novel DRB1 allele was revealed by routine HLA-SBT typing noted for its extensive mismatches to any known DRB1 alleles within the exon 2. Sequences containing the exons 2, 3 of HLA-DRB1, their surrounding introns, and the full-length cDNA of DRB1 were analyzed to determine a possible recombination event. Interestingly, the sequences of entire exon 2 were characterized as DRB3(∗)02:02:01:01/02; while exon 3 were characterized as DRB1(∗)14 like alleles. Further analysis of the sequences using Simplot software suggested that an intergenic recombinant event (i.e. exchange of sequence between non-allelic genes) may have occurred between DRB3(∗)02 allele and DRB1(∗)14 like allele, and the recombination sites are located at intron 1 and the boundary of exon 2 and intron 2 of DRB1. There are 5 CGGGG sequences flanking each side of exon 2 could serve as potential recombination site. Moreover, the full-length cDNA of the novel allele has been identified. The exon 1 and exon 3 to exon 6 share the same sequence as DRB1(∗)14 like alleles. At the mRNA level, the new allele has no significant difference when compared with the other DRB1 allele. This novel recombinant allele is also found to be paternally inherited. In conclusion, this is the first report of a DRB1 and DRB3 intergenic recombination event involving whole exon 2, which generate a new DRB1(∗)14:141.

  7. A pseudodeficiency allele (D152N) of the human beta-glucuronidase gene.

    PubMed

    Vervoort, R; Islam, M R; Sly, W; Chabas, A; Wevers, R; de Jong, J; Liebaers, I; Lissens, W

    1995-10-01

    We present evidence that a 480G-->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 480G-->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-->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-->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.

  8. Specificity and promiscuity among naturally processed peptides bound to HLA-DR alleles

    PubMed Central

    1993-01-01

    Naturally processed peptides were acid extracted from immunoaffinity- purified HLA-DR2, DR3, DR4, DR7, and DR8. Using the complementary techniques of mass spectrometry and Edman microsequencing, > 200 unique peptide masses were identified from each allele, ranging from 1,200 to 4,000 daltons (10-34 residues in length), and a total of 201 peptide sequences were obtained. These peptides were derived from 66 different source proteins and represented sets nested at both the amino- and carboxy-terminal ends with an average length of 15-18 amino acids. Strikingly, most of the peptides (> 85%) were derived from endogenous proteins that intersect the endocytic/class II pathway, even though class II molecules are thought to function mainly in the presentation of exogenous foreign peptide antigens. The predominant endogenous peptides were derived from major histocompatibility complex-related molecules. A few peptides derived from exogenous bovine serum proteins were also bound to every allele. Four prominent promiscuous self- peptide sets (capable of binding to multiple HLA-DR alleles) as well as 84 allele-specific peptide sets were identified. Binding experiments confirmed that the promiscuous peptides have high affinity for the binding groove of all HLA-DR alleles examined. A potential physiologic role for these endogenous self-peptides as immunomodulators of the cellular immune response is discussed. PMID:8315383

  9. Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency.

    PubMed

    Kiezun, Adam; Pulit, Sara L; Francioli, Laurent C; van Dijk, Freerk; Swertz, Morris; Boomsma, Dorret I; van Duijn, Cornelia M; Slagboom, P Eline; van Ommen, G J B; Wijmenga, Cisca; de Bakker, Paul I W; Sunyaev, Shamil R

    2013-01-01

    Large-scale population sequencing studies provide a complete picture of human genetic variation within the studied populations. A key challenge is to identify, among the myriad alleles, those variants that have an effect on molecular function, phenotypes, and reproductive fitness. Most non-neutral variation consists of deleterious alleles segregating at low population frequency due to incessant mutation. To date, studies characterizing selection against deleterious alleles have been based on allele frequency (testing for a relative excess of rare alleles) or ratio of polymorphism to divergence (testing for a relative increase in the number of polymorphic alleles). Here, starting from Maruyama's theoretical prediction (Maruyama T (1974), Am J Hum Genet USA 6:669-673) that a (slightly) deleterious allele is, on average, younger than a neutral allele segregating at the same frequency, we devised an approach to characterize selection based on allelic age. Unlike existing methods, it compares sets of neutral and deleterious sequence variants at the same allele frequency. When applied to human sequence data from the Genome of the Netherlands Project, our approach distinguishes low-frequency coding non-synonymous variants from synonymous and non-coding variants at the same allele frequency and discriminates between sets of variants independently predicted to be benign or damaging for protein structure and function. The results confirm the abundance of slightly deleterious coding variation in humans.

  10. Microarrays for high-throughput genotyping of MICA alleles using allele-specific primer extension.

    PubMed

    Baek, I C; Jang, J-P; Choi, H-B; Choi, E-J; Ko, W-Y; Kim, T-G

    2013-10-01

    The role of major histocompatibility complex (MHC) class I chain-related gene A (MICA), a ligand of NKG2D, has been defined in human diseases by its allele associations with various autoimmune diseases, hematopoietic stem cell transplantation (HSCT) and cancer. This study describes a practical system to develop MICA genotyping by allele-specific primer extension (ASPE) on microarrays. From the results of 20 control primers, strict and reliable cut-off values of more than 30,000 mean fluorescence intensity (MFI) as positive and less than 3000 MFI as negative, were applied to select high-quality specific extension primers. Among 55 allele-specific primers, 44 primers could be initially selected as optimal primer. Through adjusting the length, six primers were improved. The other failed five primers were corrected by refractory modification. MICA genotypes by ASPE on microarrays showed the same results as those by nucleotide sequencing. On the basis of these results, ASPE on microarrays may provide high-throughput genotyping for MICA alleles for population studies, disease-gene associations and HSCT.

  11. Self-incompatibility of Prunus tenella and evidence that reproductively isolated species of Prunus have different SFB alleles coupled with an identical S-RNase allele.

    PubMed

    Surbanovski, Nada; Tobutt, Kenneth R; Konstantinović, Miroslav; Maksimović, Vesna; Sargent, Daniel J; Stevanović, Vladimir; Bosković, Radovan I

    2007-05-01

    Many species of Prunus display an S-RNase-based gametophytic self-incompatibility (SI), controlled by a single highly polymorphic multigene complex termed the S-locus. This comprises tightly linked stylar- and pollen-expressed genes that determine the specificity of the SI response. We investigated SI of Prunus tenella, a wild species found in small, isolated populations on the Balkan peninsula, initially by pollination experiments and identifying stylar-expressed RNase alleles. Nine P. tenella S-RNase alleles (S(1)-S(9)) were cloned; their sequence analysis showed a very high ratio of non-synonymous to synonymous nucleotide substitutions (K(a)/K(s)) and revealed that S-RNase alleles of P. tenella, unlike those of Prunus dulcis, show positive selection in all regions except the conserved regions and that between C2 and RHV. Remarkably, S(8)-RNase, was found to be identical to S(1)-RNase from Prunus avium, a species that does not interbreed with P. tenella and, except for just one amino acid, to S(11) of P. dulcis. However, the corresponding introns and S-RNase-SFB intergenic regions showed considerable differences. Moreover, protein sequences of the pollen-expressed SFB alleles were not identical, harbouring 12 amino-acid replacements between those of P. tenella SFB(8) and P. avium SFB(1). Implications of this finding for hypotheses about the evolution of new S-specificities are discussed.

  12. 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.

  13. Diurnal and annual exchanges of mass and energy between an aspen-hazelnut forest and the atmosphere: Testing the mathematical model Ecosys with data from the BOREAS experiment

    NASA Astrophysics Data System (ADS)

    Grant, R. F.; Black, T. A.; den Hartog, G.; Berry, J. A.; Neumann, H. H.; Blanken, P. D.; Yang, P. C.; Russell, C.; Nalder, I. A.

    1999-11-01

    There is much uncertainty about the net carbon (C) exchange of boreal forest ecosystems, although this exchange may be an important part of global C dynamics. To resolve this uncertainty, net C exchange has been measured at several sites in the boreal forest of Canada as part of the Boreal Ecosystem-Atmosphere Study (BOREAS). One of these sites is the Southern Old Aspen site at which diurnal CO2 and energy (radiation, latent, and sensible heat) fluxes were measured during 1994 using eddy correlation techniques at different positions within a mixed 70 year old aspen-hazelnut forest. These measurements were used to test a complex ecosystem model "ecosys" in which mass and energy exchanges between terrestrial ecosystems and the atmosphere are simulated hourly under diverse conditions of soil, management, and climate. These simulations explained between 70% and 80% of diurnal variation in ecosystem CO2 and energy fluxes measured during three 1 week intervals in late April, early June, and mid-July. Total annual CO2 fluxes indicated that during 1994, aspen was a net sink of 540 (modeled) versus 670 (measured) g C m-2 yr-1, while hazelnut plus soil were a net source of 472 (modeled) versus 540 (measured) g C m-2 yr-1. The aspen-hazelnut forest at the BOREAS site was therefore estimated to be a net sink of about 68 (modeled) versus 130 (measured) g C m-2 yr-1 during 1994. Long-term simulations indicated that this sink may be larger during cooler years and smaller during warmer years because C fixation in the model was less sensitive to temperature than respiration. These simulations also indicated that the magnitude of this sink declines with forest age because respiration increases with respect to fixation as standing phytomass grows. Confidence in the predictive capabilities of ecosystem models at decadal or centennial timescales is improved by well-constrained tests of these models at hourly timescales.

  14. Use of allele scores as instrumental variables for Mendelian randomization

    PubMed Central

    Burgess, Stephen; Thompson, Simon G

    2013-01-01

    Background An allele score is a single variable summarizing multiple genetic variants associated with a risk factor. It is calculated as the total number of risk factor-increasing alleles for an individual (unweighted score), or the sum of weights for each allele corresponding to estimated genetic effect sizes (weighted score). An allele score can be used in a Mendelian randomization analysis to estimate the causal effect of the risk factor on an outcome. Methods Data were simulated to investigate the use of allele scores in Mendelian randomization where conventional instrumental variable techniques using multiple genetic variants demonstrate ‘weak instrument’ bias. The robustness of estimates using the allele score to misspecification (for example non-linearity, effect modification) and to violations of the instrumental variable assumptions was assessed. Results Causal estimates using a correctly specified allele score were unbiased with appropriate coverage levels. The estimates were generally robust to misspecification of the allele score, but not to instrumental variable violations, even if the majority of variants in the allele score were valid instruments. Using a weighted rather than an unweighted allele score increased power, but the increase was small when genetic variants had similar effect sizes. Naive use of the data under analysis to choose which variants to include in an allele score, or for deriving weights, resulted in substantial biases. Conclusions Allele scores enable valid causal estimates with large numbers of genetic variants. The stringency of criteria for genetic variants in Mendelian randomization should be maintained for all variants in an allele score. PMID:24062299

  15. 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

  16. 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.

  17. Identification of a novel HLA-A allele, A*3120.

    PubMed

    Chang, Y; Pascual, C J; Alonzo, P; Chamizo, A

    2009-03-01

    A novel human leukocyte antigen (HLA)-A allele, HLA-A*3120, was first identified in a National Marrow Donor Program (NMDP) donor. The A*3120 allele resulted from a single nucleotide substitution (T to G) at codon 92 of exon 3 of A*310102. The substitution caused an amino acid change (serine to alanine). This novel allele was also seen in two other unrelated NMDP donors.

  18. An American Exchange Teacher in England

    ERIC Educational Resources Information Center

    Bradley, James V.

    1976-01-01

    Gives an American exchange teacher's descriptions of British education and experiences while teaching biology there as well as presenting the experiences of the British teacher who had replaced him in America. (LS)

  19. 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.

  20. Novel HLA-A and HLA-B alleles.

    PubMed

    Hurley, C K; Steiner, N; Kosman, C; Mitton, W; Koester, R; Bei, M; Bush, J; McCormack, J; Hahn, A; Henson, V; Hoyer, R; Wade, J A; Hartzman, R J; Ng, J

    1998-07-01

    Nine novel HLA-A and HLA-B alleles are described: A*2609, A*6803, A*6806, B*1539, B*1540, B*2712, B*4103, B*5109, and B*5603. Most appear to have arisen by gene conversion events. B*5603 appears to have arisen by a reciprocal recombination event joining exon 2 of a B*55/ *56 allele with exon 3 of a B*15 allele. Serologically, the antigen encoded by this allele types with broad B22- and Bw6-specific alloantisera. Also unique, the antigen encoded by B*2712 does not react with B27-specific alloantisera but does react with Bw6-specific alloantisera.

  1. 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

    2014-04-22

    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.

  2. 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.

  3. Analyses of Allele-Specific Gene Expression in Highly Divergent Mouse Crosses Identifies Pervasive Allelic Imbalance

    PubMed Central

    Crowley, James J; Zhabotynsky, Vasyl; Sun, Wei; Huang, Shunping; Pakatci, Isa Kemal; Kim, Yunjung; Wang, Jeremy R; Morgan, Andrew P; Calaway, John D; Aylor, David L; Yun, Zaining; Bell, Timothy A; Buus, Ryan J; Calaway, Mark E; Didion, John P; Gooch, Terry J; Hansen, Stephanie D; Robinson, Nashiya N; Shaw, Ginger D; Spence, Jason S; Quackenbush, Corey R; Barrick, Cordelia J; Nonneman, Randal J.; Kim, Kyungsu; Xenakis, James; Xie, Yuying; Valdar, William; Lenarcic, Alan B; Wang, Wei; Welsh, Catherine E; Fu, Chen-Ping; Zhang, Zhaojun; Holt, James; Guo, Zhishan; Threadgill, David W; Tarantino, Lisa M; Miller, Darla R; Zou, Fei; McMillan, Leonard; Sullivan, Patrick F; de Villena, Fernando Pardo-Manuel

    2015-01-01

    Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Since regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in this process. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. These effects influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. We also observe two types of parent-of-origin effects, including classical imprinting and a novel, global allelic imbalance in favor of the paternal allele. We conclude that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals. PMID:25730764

  4. 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.

  5. 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} .

  6. 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.

  7. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots

    PubMed Central

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

    2015-01-01

    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

  8. 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.

  9. 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.

  10. Controls on carbon and energy exchange by a black spruce-moss ecosystem: Testing the mathematical model Ecosys with data from the BOREAS Experiment

    NASA Astrophysics Data System (ADS)

    Grant, R. F.; Jarvis, P. G.; Massheder, J. M.; Hale, S. E.; Moncrieff, J. B.; Rayment, M.; Scott, S. L.; Berry, J. A.

    2001-03-01

    Stomatal limitations to mass and energy exchange over boreal black spruce forests may be caused by low needle N concentrations that limit CO2 fixation rates. These low concentrations may be caused by low N uptake rates from cold boreal soils with high soil C:N ratios and by low N deposition rates from boreal atmospheres. A mathematical model of terrestrial ecosystems ecosys was used to examine the likelihood that slow N cycling could account for the low rates of mass and energy exchange measured over a 115-year old boreal spruce/moss forest as part of the Boreal Ecosystem-Atmosphere Study (BOREAS). In the model, net N mineralization was slowed by the high C:N ratios measured in the forest floor and by high lignin contents in spruce litterfall. Slow mineralization caused low N uptake rates and hence high C:N ratios in spruce and moss leaves that reduced specific activities and areal densities of rubisco and chlorophyll. Consequent low CO2 fixation rates caused low stomatal conductances and transpiration rates which in turn caused high soil water contents. Wet soils, in conjunction with large accumulations of surface detritus generated by slow litter mineralization, caused low soil temperatures that further slowed mineralization rates. Model outputs for ecosystem N status were corroborated by low needle N concentrations (< 10 mg g-1), stomatal conductances (< 0.05 mol m-2 s-1) and CO2 fixation rates (< 6 μmol m-2 s-1), and by high canopy Bowen ratios (1.5-2.0) and low canopy net CO2 exchange rates (< 10 μmol m-2 s-1) measured over the black spruce/moss forest at the BOREAS site. Modeled C accumulation rates of 60 (wood) + 10 (soil) = 70 g C m-2 yr-1 were consistent with estimates from aggregated CO2 fluxes measured over the spruce canopy and from allometric equations developed for black spruce in Canadian boreal forests. Model projections under IS92a climate change indicate that rates of wood C accumulation would rise and those of soil C accumulation would decline

  11. Sequence of Three Bronze Alleles of Maize and Correlation with the Genetic Fine Structure

    PubMed Central

    Ralston, E. J.; English, J. J.; Dooner, H. K.

    1988-01-01

    The genomic sequences of three bronze alleles from Zea mays, Bz-McC, Bz-W22 and bz-R, are presented together with their flanking sequences. The bronze locus encodes UDPglucose flavonoid glucosyl-transferase (UFGT), an anthocyanin biosynthetic enzyme. The wild-type alleles Bz-McC and Bz-W22 condition purple phenotypes in the seed and plant, while bz-R conditions a bronze color. A full length cDNA corresponding to the Bz-McC allele was cloned and sequenced. Primer extension and RNase protection experiments were used to verify the 5' end of the bronze transcript. The Bz-McC allele has a 1416-bp coding region, a 100-bp intron and an approximately 83-bp 5' leader. Upstream of the message initiation site the sequences CTAACT and AATAAA occupy the positions where the eukaryotic consensus CCAAT and TATA boxes are normally found. The alleles Bz-McC and bz-R each have different large insertions with characteristics of transposable elements in their 5' flanking regions. The bz-R allele is distinguished by a 340-bp deletion starting within the intron and including 285 bp of the second exon. The Bz-McC and Bz-W22 isoalleles are known to differ in two genetically defined locations. The uts and uqv sites from the Bz-McC allele condition, respectively, lowered thermostability for the UFGT enzyme and increased amount of UFGT activity when compared with the corresponding sites in the Bz-W22 allele. The uts site maps to a region of the gene encoding two adjacent amino acid differences, either or both of which might alter the thermostability of the UFGT enzyme. The difference in UFGT levels conditioned by the uqv site is shown here to be correlated with variation in the bronze mRNA level. A likely cause of this decreased bronze mRNA level in Bz-W22 is a 6-bp duplication near the sequence CTAACT located 74 bp upstream of the bronze message iniation site. This region is therefore tentatively identified as the uqv site. PMID:3396861

  12. Observations Suggesting Allelism of the Achondroplasia and Hypochondroplasia Genes

    PubMed Central

    McKusick, Victor A.; Kelly, Thaddeus E.; Dorst, John P.

    1973-01-01

    It is argued that there are at least two alleles at the achondroplasia locus: one responsible for classic achondroplasia and one responsible for hypochondroplasia. Homozygosity for the achondroplasia gene produces a lethal skeletal dysplasia; homozygosity for hypochondroplasia has not been described. We report here a child considered to be a genetic compound for the achondroplasia and hypochondroplasia alleles. Images PMID:4697848

  13. 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

  14. 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,…

  15. Assortative mating can impede or facilitate fixation of underdominant alleles.

    PubMed

    Newberry, Mitchell G; McCandlish, David M; Plotkin, Joshua B

    2016-12-01

    Underdominant mutations have fixed between divergent species, yet classical models suggest that rare underdominant alleles are purged quickly except in small or subdivided populations. We predict that underdominant alleles that also influence mate choice, such as those affecting coloration patterns visible to mates and predators alike, can fix more readily. We analyze a mechanistic model of positive assortative mating in which individuals have n chances to sample compatible mates. This one-parameter model naturally spans random mating (n=1) and complete assortment (n→∞), yet it produces sexual selection whose strength depends non-monotonically on n. This sexual selection interacts with viability selection to either inhibit or facilitate fixation. As mating opportunities increase, underdominant alleles fix as frequently as neutral mutations, even though sexual selection and underdominance independently each suppress rare alleles. This mechanism allows underdominant alleles to fix in large populations and illustrates how life history can affect evolutionary change.

  16. Estimating Relatedness in the Presence of Null Alleles.

    PubMed

    Huang, Kang; Ritland, Kermit; Dunn, Derek W; Qi, Xiaoguang; Guo, Songtao; Li, Baoguo

    2016-01-01

    Studies of genetics and ecology often require estimates of relatedness coefficients based on genetic marker data. However, with the presence of null alleles, an observed genotype can represent one of several possible true genotypes. This results in biased estimates of relatedness. As the numbers of marker loci are often limited, loci with null alleles cannot be abandoned without substantial loss of statistical power. Here, we show how loci with null alleles can be incorporated into six estimators of relatedness (two novel). We evaluate the performance of various estimators before and after correction for null alleles. If the frequency of a null allele is <0.1, some estimators can be used directly without adjustment; if it is >0.5, the potency of estimation is too low and such a locus should be excluded. We make available a software package entitled PolyRelatedness v1.6, which enables researchers to optimize these estimators to best fit a particular data set.

  17. 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.

  18. Frequency of FCGR3B Alleles in Thai Blood Donors

    PubMed Central

    Kaset, Chollanot; Leetrakool, Nipapan; Intharanut, Kamphon

    2013-01-01

    Background Human neutrophil antigens (HNAs) are involved in autoimmune and alloimmune neutropenia and transfusion-related acute lung injury. The HNA-1 system is important in immunogenetics, and allele frequencies have been described in different populations. This study investigated the frequency of FCGR3B alleles encoding HNA-1a, HNA-1b, and HNA-1c among Thai blood donors and compared these frequencies with those previously reported for other populations. Methods Eight hundred DNA samples obtained from unrelated healthy blood donors at the National Blood Centre, Thai Red Cross Society, Bangkok, and the Blood Bank, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand, were included. Samples were simultaneously typed for each FCGR3B allele using an in-house polymerase chain reaction with sequence-specific primer (PCR-SSP) technique. Results The frequencies of FCGR3B*1, FCGR3B*2, and FCGR3B*3 alleles in central Thai blood donors were 0.548, 0.452, and 0.004, respectively; only FCGR3B*1 and FCGR3B*2 alleles were found in northern Thai blood donors (0.68 and 0.32, respectively). Compared with other Asian populations, central Thais had higher frequencies of the FCGR3B*2 allele (P<0.001), while the frequencies of the FCGR3B*1 and FCGR3B*2 alleles in northern Thais were similar to those previously reported in Taiwanese and Japanese populations. In contrast, the frequencies of the FCGR3B*1 and FCGR3B*2 alleles in the northern Thai population were statistically different from those observed in central Thai, Korean, German, and Turkish populations. Conclusions FCGR3B allele frequencies were significantly different between central and northern Thai blood donors. Our in-house PCR-SSP method is a simple, cost-effective, and convenient method for FCGR3B allele detection. PMID:24205492

  19. Microsatellite null alleles and estimation of population differentiation.

    PubMed

    Chapuis, Marie-Pierre; Estoup, Arnaud

    2007-03-01

    Microsatellite null alleles are commonly encountered in population genetics studies, yet little is known about their impact on the estimation of population differentiation. Computer simulations based on the coalescent were used to investigate the evolutionary dynamics of null alleles, their impact on F(ST) and genetic distances, and the efficiency of estimators of null allele frequency. Further, we explored how the existing method for correcting genotype data for null alleles performed in estimating F(ST) and genetic distances, and we compared this method with a new method proposed here (for F(ST) only). Null alleles were likely to be encountered in populations with a large effective size, with an unusually high mutation rate in the flanking regions, and that have diverged from the population from which the cloned allele state was drawn and the primers designed. When populations were significantly differentiated, F(ST) and genetic distances were overestimated in the presence of null alleles. Frequency of null alleles was estimated precisely with the algorithm presented in Dempster et al. (1977). The conventional method for correcting genotype data for null alleles did not provide an accurate estimate of F(ST) and genetic distances. However, the use of the genetic distance of Cavalli-Sforza and Edwards (1967) corrected by the conventional method gave better estimates than those obtained without correction. F(ST) estimation from corrected genotype frequencies performed well when restricted to visible allele sizes. Both the proposed method and the traditional correction method have been implemented in a program that is available free of charge at http://www.montpellier.inra.fr/URLB/. We used 2 published microsatellite data sets based on original and redesigned pairs of primers to empirically confirm our simulation results.

  20. 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.

  1. Allele-Specific Reduction of the Mutant Huntingtin Allele Using Transcription Activator-Like Effectors in Human Huntington's Disease Fibroblasts.

    PubMed

    Fink, Kyle D; Deng, Peter; Gutierrez, Josh; Anderson, Joseph S; Torrest, Audrey; Komarla, Anvita; Kalomoiris, Stefanos; Cary, Whitney; Anderson, Johnathon D; Gruenloh, William; Duffy, Alexandra; Tempkin, Teresa; Annett, Geralyn; Wheelock, Vicki; Segal, David J; Nolta, Jan A

    2016-01-01

    Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by an abnormal expansion of CAG repeats. Although pathogenesis has been attributed to this polyglutamine expansion, the underlying mechanisms through which the huntingtin protein functions have yet to be elucidated. It has been suggested that postnatal reduction of mutant huntingtin through protein interference or conditional gene knockout could prove to be an effective therapy for patients suffering from HD. For allele-specific targeting, transcription activator-like effectors (TALE) were designed to target single-nucleotide polymorphisms (SNP) in the mutant allele and packaged into a vector backbone containing KRAB to promote transcriptional repression of the disease-associated allele. Additional TALEs were packaged into a vector backbone containing heterodimeric FokI and were designed to be used as nucleases (TALEN) to cause a CAG-collapse in the mutant allele. Human HD fibroblasts were treated with each TALE-SNP or TALEN. Allele-expression was measured using a SNP-genotyping assay and mutant protein aggregation was quantified with Western blots for anti-ubiquitin. The TALE-SNP and TALEN significantly reduced mutant allele expression (p < 0.05) when compared to control transfections while not affecting expression of the nondisease allele. This study demonstrates the potential of allele-specific gene modification using TALE proteins, and provides a foundation for targeted treatment for individuals suffering from Huntington's or other genetically linked diseases.

  2. Allele-specific H3K79 Di- versus trimethylation distinguishes opposite parental alleles at imprinted regions.

    PubMed

    Singh, Purnima; Han, Li; Rivas, Guillermo E; Lee, Dong-Hoon; Nicholson, Thomas B; Larson, Garrett P; Chen, Taiping; Szabó, Piroska E

    2010-06-01

    Imprinted gene expression corresponds to parental allele-specific DNA CpG methylation and chromatin composition. Histone tail covalent modifications have been extensively studied, but it is not known whether modifications in the histone globular domains can also discriminate between the parental alleles. Using multiplex chromatin immunoprecipitation-single nucleotide primer extension (ChIP-SNuPE) assays, we measured the allele-specific enrichment of H3K79 methylation and H4K91 acetylation along the H19/Igf2 imprinted domain. Whereas H3K79me1, H3K79me2, and H4K91ac displayed a paternal-specific enrichment at the paternally expressed Igf2 locus, H3K79me3 was paternally biased at the maternally expressed H19 locus, including the paternally methylated imprinting control region (ICR). We found that these allele-specific differences depended on CTCF binding in the maternal ICR allele. We analyzed an additional 11 differentially methylated regions (DMRs) and found that, in general, H3K79me3 was associated with the CpG-methylated alleles, whereas H3K79me1, H3K79me2, and H4K91ac enrichment was specific to the unmethylated alleles. Our data suggest that allele-specific differences in the globular histone domains may constitute a layer of the "histone code" at imprinted genes.

  3. Cooperation of Adhesin Alleles in Salmonella-Host Tropism

    PubMed Central

    De Masi, Leon; Yue, Min; Hu, Changmin; Rakov, Alexey V.; Rankin, Shelley C.

    2017-01-01

    ABSTRACT Allelic combinations and host specificities for three fimbrial adhesins, FimH, BcfD, and StfH, were compared for 262 strains of Salmonella enterica serovar Newport, a frequent human and livestock pathogen. Like FimH, BcfD had two major alleles (designated A and B), whereas StfH had two allelic groups, each with two alleles (subgroup A1 and A2 and subgroup B1 and B2). The most prevalent combinations of FimH/BcfD/StfH alleles in S. Newport were A/A/A1 and B/B/B1. The former set was most frequently found in bovine and porcine strains, whereas the latter combination was most frequently found in environmental and human isolates. Bacteria genetically engineered to express Fim, Bcf, or Stf fimbriae on their surface were tested with the different alleles for binding to human, porcine, and bovine intestinal epithelial cells. The major allelic combinations with bovine and porcine strains (A/A/A1) or with human isolates (B/B/B1) provided at least two alleles capable of binding significantly better than the other alleles to an intestinal epithelial cell line from the respective host(s). However, each combination of alleles kept at least one allele mediating binding to an intestinal epithelial cell from another host. These findings indicated that allelic variation in multiple adhesins of S. Newport contributes to bacterial adaptation to certain preferential hosts without losing the capacity to maintain a broad host range. IMPORTANCE Salmonella enterica remains a leading foodborne bacterial pathogen in the United States; infected livestock serve often as the source of contaminated food products. A study estimated that over a billion Salmonella gastroenteritis cases and up to 33 million typhoid cases occur annually worldwide, with 3.5 million deaths. Although many Salmonella strains with a broad host range present preferential associations with certain host species, it is not clear what determines the various levels of host adaptation. Here, causal properties of host

  4. Allelic exchange of pheromones and their receptors reprograms sexual identity in Cryptococcus neoformans.

    PubMed

    Stanton, Brynne C; Giles, Steven S; Staudt, Mark W; Kruzel, Emilia K; Hull, Christina M

    2010-02-26

    Cell type specification is a fundamental process that all cells must carry out to ensure appropriate behaviors in response to environmental stimuli. In fungi, cell identity is critical for defining "sexes" known as mating types and is controlled by components of mating type (MAT) loci. MAT-encoded genes function to define sexes via two distinct paradigms: 1) by controlling transcription of components common to both sexes, or 2) by expressing specially encoded factors (pheromones and their receptors) that differ between mating types. The human fungal pathogen Cryptococcus neoformans has two mating types (a and alpha) that are specified by an extremely unusual MAT locus. The complex architecture of this locus makes it impossible to predict which paradigm governs mating type. To identify the mechanism by which the C. neoformans sexes are determined, we created strains in which the pheromone and pheromone receptor from one mating type (a) replaced the pheromone and pheromone receptor of the other (alpha). We discovered that these "alpha(a)" cells effectively adopt a new mating type (that of a cells); they sense and respond to alpha factor, they elicit a mating response from alpha cells, and they fuse with alpha cells. In addition, alpha(a) cells lose the alpha cell type-specific response to pheromone and do not form germ tubes, instead remaining spherical like a cells. Finally, we discovered that exogenous expression of the diploid/dikaryon-specific transcription factor Sxi2a could then promote complete sexual development in crosses between alpha and alpha(a) strains. These data reveal that cell identity in C. neoformans is controlled fully by three kinds of MAT-encoded proteins: pheromones, pheromone receptors, and homeodomain proteins. Our findings establish the mechanisms for maintenance of distinct cell types and subsequent developmental behaviors in this unusual human fungal pathogen.

  5. Characterization of the complications associated with plasma exchange for thrombotic thrombocytopaenic purpura and related thrombotic microangiopathic anaemias: a single institution experience

    PubMed Central

    McGuckin, S; Westwood, J-P; Webster, H; Collier, D; Leverett, D; Scully, M

    2014-01-01

    Background Plasma exchange (PEX) is a life-saving therapeutic procedure in patients with thrombotic thrombocytopaenic purpura (TTP) and other thrombotic microangiopathic anaemias (TMAs). However, it may be associated with significant complications, exacerbating the morbidity and mortality in this patient group. Study Design and Methods We reviewed all PEX procedures over a 72-month period, following the exclusive introduction of solvent–detergent double viral-inactivated plasma in high-volume users, such as TTP, in the United Kingdom (UK). We documented allergic reactions to plasma, citrate reactions, complications relating to central venous access insertion and venous thrombotic events (VTE) in 155 patient episodes and >2000 PEX procedures. Results The overall complication rate was low. Allergic plasma reactions occurred in 6·45% of the cohort with only one episode of acute anaphylaxis. Similarly, VTEs were 6·45%, not significantly greater than in medical patients receiving thromboprophylaxis, despite added potential risk factors in TTP. Citrate reactions were the most frequent complication documented, but toxicity was significantly reduced by administration of further calcium infusions during the PEX procedure. There were no serious central line infections and no catheter thrombosis. Conclusion Our data confirms that PEX continues to be a life-saving procedure in the acute TTP setting and, the procedure was not associated with an increased mortality and limited morbidity. PMID:24117855

  6. 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.

  7. Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny

    PubMed Central

    Cuenca, José; Aleza, Pablo; Navarro, Luis; Ollitrault, Patrick

    2013-01-01

    Background Polyploidy is a major component of eukaryote evolution. Estimation of allele copy numbers for molecular markers has long been considered a challenge for polyploid species, while this process is essential for most genetic research. With the increasing availability and whole-genome coverage of single nucleotide polymorphism (SNP) markers, it is essential to implement a versatile SNP genotyping method to assign allelic configuration efficiently in polyploids. Scope This work evaluates the usefulness of the KASPar method, based on competitive allele-specific PCR, for the assignment of SNP allelic configuration. Citrus was chosen as a model because of its economic importance, the ongoing worldwide polyploidy manipulation projects for cultivar and rootstock breeding, and the increasing availability of SNP markers. Conclusions Fifteen SNP markers were successfully designed that produced clear allele signals that were in agreement with previous genotyping results at the diploid level. The analysis of DNA mixes between two haploid lines (Clementine and pummelo) at 13 different ratios revealed a very high correlation (average = 0·9796; s.d. = 0·0094) between the allele ratio and two parameters [θ angle = tan−1 (y/x) and y′ = y/(x + y)] derived from the two normalized allele signals (x and y) provided by KASPar. Separated cluster analysis and analysis of variance (ANOVA) from mixed DNA simulating triploid and tetraploid hybrids provided 99·71 % correct allelic configuration. Moreover, triploid populations arising from 2n gametes and interploid crosses were easily genotyped and provided useful genetic information. This work demonstrates that the KASPar SNP genotyping technique is an efficient way to assign heterozygous allelic configurations within polyploid populations. This method is accurate, simple and cost-effective. Moreover, it may be useful for quantitative studies, such as relative allele-specific expression analysis and bulk segregant analysis

  8. Generation of a Conditional Null Allele of Jumonji

    PubMed Central

    Mysliwiec, Matthew R.; Chen, Junqin; Powers, Patricia A.; Bartley, Christopher R.; Schneider, Michael D.; Lee, Youngsook

    2007-01-01

    Summary: The jumonji (jmj) gene plays important roles in multiple organ development in mouse, including cardiovascular development. Since JMJ is expressed widely during mouse development, it is essential that conditional knockout approaches be employed to ablate JMJ in a tissue-specific manner to identify the cell lineage specific roles of JMJ. In this report, we describe the establishment of a jmj conditional null allele in mice by generating a loxP-flanked (floxed) jmj allele, which allows the in vivo ablation of jmj via Cre recombinase-mediated deletion. Gene targeting was used to introduce loxP sites flanking exon 3 of the jmj allele to mouse embryonic stem cells. Our results indicate that the jmj floxed allele converts to a null allele in a heart-specific manner when embryos homozygous for the floxed jmj allele and carrying the α-myosin heavy chain promoter-Cre transgene were analyzed by Southern and Northern blot analyses. Therefore, this mouse line harboring the conditional jmj null allele will provide a valuable tool for deciphering the tissue and cell lineage specific roles of JMJ. PMID:16900512

  9. Allele Frequencies at Microsatellite Loci: The Stepwise Mutation Model Revisited

    PubMed Central

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

    1993-01-01

    We 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. We 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. We show 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. PMID:8454213

  10. Estimating relatedness and relationships using microsatellite loci with null alleles.

    PubMed

    Wagner, A P; Creel, S; Kalinowski, S T

    2006-11-01

    Relatedness is often estimated from microsatellite genotypes that include null alleles. When null alleles are present, observed genotypes represent one of several possible true genotypes. If null alleles are detected, but analyses do not adjust for their presence (ie, observed genotypes are treated as true genotypes), then estimates of relatedness and relationship can be incorrect. The number of loci available in many wildlife studies is limited, and loci with null alleles are commonly a large proportion of data that cannot be discarded without substantial loss of power. To resolve this problem, we present a new approach for estimating relatedness and relationships from data sets that include null alleles. Once it is recognized that the probability of the observed genotypes is dependent on the probabilities of a limited number of possible true genotypes, the required adjustments are straightforward. The concept can be applied to any existing estimators of relatedness and relationships. We review established maximum likelihood estimators and apply the correction in that setting. In an application of the corrected method to data from striped hyenas, we demonstrate that correcting for the presence of null alleles affect results substantially. Finally, we use simulated data to confirm that this method works better than two common approaches, namely ignoring the presence of null alleles or discarding affected loci.

  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. Exchange frequency in replica exchange molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sindhikara, Daniel; Meng, Yilin; Roitberg, Adrian E.

    2008-01-01

    The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.

  14. The Interaction between Surface-Atmosphere Exchange and Convective Precipitation in the Amazon: Results of the GoAmazon Boundary Layer Experiment

    NASA Astrophysics Data System (ADS)

    Stoy, P. C.; Fuentes, J. D.; Gerken, T.; Trowbridge, A.; Katul, G. G.; Nascimento dos Santos, R. M.; Manzi, A. O.; Mercer, J.; Machado, L.; Tota, J.; von Randow, C.; Fisch, G.; Ramos, F.; Chamecki, M.

    2015-12-01

    We describe results from a field campaign in central Amazonia whose purpose is to quantify the relationship between the surface-atmosphere exchange of biogenic volatile organic compounds (BVOCs) and convective precipitation as mediated by turbulent transport and the production of secondary organic aerosols and cloud condensation nuclei. The chemical speciation of monoterpenes and sesquiterpines emitted by the rainforest were determined using gas chromatography-mass spectroscopy and proton transfer-reaction mass spectroscopy enabled quantification of the concentrations of monoterpenes, sesquiterpenes, and other BVOCs. The temporal and spatial evolution of BVOCs and ozone concentrations within and immediately above the forested canopy were quantified and used to estimate the consumption, production, and transport of BVOCs, ozone, and hydroxyl radical during wet and dry seasons. Fluxes were estimated using above and within canopy flow field measurements from ten sonic anemometers and fitted using a second-order closure approach in conjunction with concentration profiles. Results demonstrate bi-directional fluxes of isoprene and monoterpenes in response to local sources and sinks attributed to deposition and chemical transformation in the air space below the upper canopy and transport to the overlying atmosphere. High hydroxyl radical yields (> 106 radicals cm-3 s-1) were estimated from reactions of ozone with ten monoterpene and six sequiterpene species observed to be emitted by the rainforest. Reactions of ozone and hydroxyl radicals dominated the conversion of BVOCs to secondary organic aerosols and cloud condensation nuclei, whose concentrations were measured using a fast mobility particle sizer and a cloud condensation nuclei counter. Results demonstrate that the rainforest emits sufficient chemical species to generate aerosols that can activate into cloud condensation nuclei and influence regional cloud formation.

  15. Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing.

    PubMed

    Zhang, Rui; Li, Xin; Ramaswami, Gokul; Smith, Kevin S; Turecki, Gustavo; Montgomery, Stephen B; Li, Jin Billy

    2014-01-01

    We developed a targeted RNA sequencing method that couples microfluidics-based multiplex PCR and deep sequencing (mmPCR-seq) to uniformly and simultaneously amplify up to 960 loci in 48 samples independently of their gene expression levels and to accurately and cost-effectively measure allelic ratios even for low-quantity or low-quality RNA samples. We applied mmPCR-seq to RNA editing and allele-specific expression studies. mmPCR-seq complements RNA-seq for studying allelic variations in the transcriptome.

  16. 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.

  17. 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.

  18. Chemical-exchange-saturation-transfer magnetic resonance imaging to map gamma-aminobutyric acid, glutamate, myoinositol, glycine, and asparagine: Phantom experiments

    NASA Astrophysics Data System (ADS)

    Oh, Jang-Hoon; Kim, Hyug-Gi; Woo, Dong-Cheol; Jeong, Ha-Kyu; Lee, Soo Yeol; Jahng, Geon-Ho

    2017-03-01

    The physical and technical development of chemical-exchange-saturation-transfer (CEST) magnetic resonance imaging (MRI) using clinical 3 T MRI was explored with the goal of mapping asparagine (Asn), gamma-aminobutyric acid (GABA), glutamate (Glu), glycine (Gly), and myoinositol (MI), which exist in the brain. Phantoms with nine different conditions at concentrations of 10, 30, and 50 mM and pH values of 5.6, 6.2, and 7.4 were prepared for the five target molecules to evaluate the dependence of the CEST effect in the concentration, the pH, and the amplitude of the applied radiofrequency field B1. CEST images in the offset frequency range of ±6 parts per million (ppm) were acquired using a pulsed radio-frequency saturation scheme with a clinical 3 T MRI system. A voxel-based main magnetic field B0 inhomogeneity correction, where B0 is the center frequency offset at zero ppm, was performed by using the spline interpolation method to fit the full Z-spectrum to estimate the center frequency. A voxel-based CEST asymmetry map was calculated to evaluate amide (-NH), amine (-NH2), and hydroxyl (-OH) groups for the five target molecules. The CEST effect for Glu, GABA, and Gly clearly increased with increasing concentrations. The CEST effect for MI was minimal, with no noticeable differences at different concentrations. The CEST effect for Glu and Gly increased with increasing acidity. The highest CEST asymmetry for GABA was observed at pH 6.2. The CEST effect for Glu, GABA, and Gly increased with increasing B1 amplitude. For all target molecules, the CEST effect for the human 3 T MRI system increased with increasing concentration and B1 amplitude, but varied with pH, depending on the characteristics of the molecules. The CEST effect for MI may be not suitable with clinical MRI systems. These results show that CEST imaging in the brain with the amine protons by using 3 T MRI is possible for several neuronal diseases.

  19. The Effect of a Novel Highly Selective Inhibitor of the Sodium/Calcium Exchanger (NCX) on Cardiac Arrhythmias in In Vitro and In Vivo Experiments

    PubMed Central

    Kohajda, Zsófia; Farkas-Morvay, Nikolett; Jost, Norbert; Nagy, Norbert; Geramipour, Amir; Horváth, András; Varga, Richárd S.; Hornyik, Tibor; Corici, Claudia; Acsai, Károly; Horváth, Balázs; Prorok, János; Ördög, Balázs; Déri, Szilvia; Tóth, Dániel; Levijoki, Jouko; Pollesello, Piero; Koskelainen, Tuula; Otsomaa, Leena; Tóth, András; Baczkó, István; Leprán, István; Nánási, Péter P.; Papp, Julius Gy; Varró, András; Virág, László

    2016-01-01

    Background In this study the effects of a new, highly selective sodium-calcium exchanger (NCX) inhibitor, ORM-10962 were investigated on cardiac NCX current, Ca2+ transients, cell shortening and in experimental arrhythmias. The level of selectivity of the novel inhibitor on several major transmembrane ion currents (L-type Ca2+ current, major repolarizing K+ currents, late Na+ current, Na+/K+ pump current) was also determined. Methods Ion currents in single dog ventricular cells (cardiac myocytes; CM), and action potentials in dog cardiac multicellular preparations were recorded utilizing the whole-cell patch clamp and standard microelectrode techniques, respectively. Ca2+ transients and cell shortening were measured in fluorescent dye loaded isolated dog myocytes. Antiarrhythmic effects of ORM-10962 were studied in anesthetized ouabain (10 μg/kg/min i.v.) pretreated guinea pigs and in ischemia-reperfusion models (I/R) of anesthetized coronary artery occluded rats and Langendorff perfused guinea pigs hearts. Results ORM-10962 significantly reduced the inward/outward NCX currents with estimated EC50 values of 55/67 nM, respectively. The compound, even at a high concentration of 1 μM, did not modify significantly the magnitude of ICaL in CMs, neither had any apparent influence on the inward rectifier, transient outward, the rapid and slow components of the delayed rectifier potassium currents, the late and peak sodium and Na+/K+ pump currents. NCX inhibition exerted moderate positive inotropic effect under normal condition, negative inotropy when reverse, and further positive inotropic effect when forward mode was facilitated. In dog Purkinje fibres 1 μM ORM-10962 decreased the amplitude of digoxin induced delayed afterdepolarizations (DADs). Pre-treatment with 0.3 mg/kg ORM-10962 (i.v.) 10 min before starting ouabain infusion significantly delayed the development and recurrence of ventricular extrasystoles (by about 50%) or ventricular tachycardia (by about 30

  20. Analysis and interpretation of short tandem repeat microvariants and three-banded allele patterns using multiple allele detection systems.

    PubMed

    Crouse, C A; Rogers, S; Amiott, E; Gibson, S; Masibay, A

    1999-01-01

    The Palm Beach County Sheriffs Office (PBSO) Crime Laboratory and the Alabama Department of Forensic Sciences (ADFS) have validated and implemented analysis of short tandem repeat (STR) sequences on casework using silver staining kit and SYBR Green I detection systems and are presently validating fluorescently tagged STR alleles using the Hitachi FMBIO 100 instrument. Concurrently, the Broward County Sheriff's Office (BSO) Crime Laboratory is validating the ABI Prism310 Genetic Analyzer capillary electrophoresis STR detection system (ABI CE310) from Perkin Elmer Applied BioSystems. During the course of analyzing over 10,000 individuals for the STR loci CSF1PO, TPOX and THO1 (CTT) using silver staining for allele detection, 42 samples demonstrated alleles that were "off ladder," contained three-banded patterns at a single locus, or exhibited an apparent THO1 "9.3,10" allele pattern. PBSO, ADFS and BSO Crime Laboratories have collaborated on the verification of the allele patterns observed in these 42 samples using the following allele detection systems: (1) manual silver staining, (2) SYBR Green I staining, and/or (3) fluorescently tagged amplified products separated by polyacrylamide gel electrophoresis or capillary electrophoresis followed by laser detection. Regardless of the CTT allele detection system utilized, concordant results were obtained for 41 of the 42 samples. The only exception was a sample in which a wide band within the THO1 locus was identified as a THO1 "9.3, 10" genotype by silver staining kit and SYBR Green I staining but was verified to be a THO1 "9.3" homozygote by all other allele detection systems. Manual allele detection could readily identify microvariants, as a visual assessment of stained gels clearly shows that alleles do not migrate coincident with well-characterized allele size standards. As would be predicted, however, the manual detection systems did not provide adequate resolution to approximate the basepair size for off

  1. 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...

  2. 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.

  3. Woven heat exchanger

    DOEpatents

    Piscitella, Roger R.

    1987-01-01

    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.

  4. [Effect of space flight factors simulated in ground-based experiments on the behavior, discriminant learning, and exchange of monoamines in different brain structures of rats].

    PubMed

    Shtemberg, A S; Lebedeva-Georgievskaia, K V; Matveeva, M I; Kudrin, V S; Narkevich, V B; Klodt, P M; Bazian, A S

    2014-01-01

    Experimental treatment (long-term fractionated γ-irradiation, antiorthostatic hypodynamia, and the combination of these factors) simulating the effect of space flight in ground-based experiments rapidly restored the motor and orienting-investigative activity of animals (rats) in "open-field" tests. The study of the dynamics of discriminant learning of rats of experimental groups did not show significant differences from the control animals. It was found that the minor effect of these factors on the cognitive performance of animals correlated with slight changes in the concentration ofmonoamines in the brain structures responsible for the cognitive, emotional, and motivational functions.

  5. Robust identification of local adaptation from allele frequencies.

    PubMed

    Günther, Torsten; Coop, Graham

    2013-09-01

    Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of "standardized allele frequencies" that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools-a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org.

  6. Sequencing of 15 new BoLA-DRB3 alleles.

    PubMed

    Wang, K; Sun, D; Zhang, Y

    2008-08-01

    The class II DR of bovine major histocompatibility complex of cattle (BoLA) plays a central role in the regulation of the immune response through their ability to present those peptides to T-cell receptors. In this work, we sequenced the exon2 of DRB3 to identify new alleles in Chinese yellow cattle, a total of 15 new BoLA-DRB3 alleles were found.

  7. 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.

  8. 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.

  9. SSR allelic variation in almond (Prunus dulcis Mill.).

    PubMed

    Xie, Hua; Sui, Yi; Chang, Feng-Qi; Xu, Yong; Ma, Rong-Cai

    2006-01-01

    Sixteen SSR markers including eight EST-SSR and eight genomic SSRs were used for genetic diversity analysis of 23 Chinese and 15 international almond cultivars. EST- and genomic SSR markers previously reported in species of Prunus, mainly peach, proved to be useful for almond genetic analysis. DNA sequences of 117 alleles of six of the 16 SSR loci were analysed to reveal sequence variation among the 38 almond accessions. For the four SSR loci with AG/CT repeats, no insertions or deletions were observed in the flanking regions of the 98 alleles sequenced. Allelic size variation of these loci resulted exclusively from differences in the structures of repeat motifs, which involved interruptions or occurrences of new motif repeats in addition to varying number of AG/CT repeats. Some alleles had a high number of uninterrupted repeat motifs, indicating that SSR mutational patterns differ among alleles at a given SSR locus within the almond species. Allelic homoplasy was observed in the SSR loci because of base substitutions, interruptions or compound repeat motifs. Substitutions in the repeat regions were found at two SSR loci, suggesting that point mutations operate on SSRs and hinder the further SSR expansion by introducing repeat interruptions to stabilize SSR loci. Furthermore, it was shown that some potential point mutations in the flanking regions are linked with new SSR repeat motif variation in almond and peach.

  10. Mutable R-Navajo Alleles of Cyclic Origin in Maize

    PubMed Central

    Brink, R. Alexander; Williams, Elizabeth

    1973-01-01

    The generation in cyclic fashion of 26 mutable R-Navajo (mRnj) alleles in maize involved transposition of a non-specific repressor of gene action, Modulator (Mp), first away from, and then back to, the R locus represented by the R-Navajo (Rnj) allele on chromosome 10. The mRnj alleles reconstituted in this way varied widely, and continuously, in mutability to Rnj—that is, in transposition of Mp away from the R locus, thus derepressing the Rnj gene. They were alike, or nearly so, however, in activating Ds chromosome breakage and in increasing the stability of variegated pericarp, another unstable compound allele comprising Mp conjoined with Prr on chromosomal 1. These latter two phenomena are based primarily on loci elsewhere in the genome. It is postulated that the 26 reconstituted mRnj alleles carry a common Mp which, however, is intercalated at a different site within each allele. Nucleotide sequence in the regions adjacent to Mp is assumed to determine the frequency with which a form of micro-nondisjunction occurs whereby Mp is released from a donor site. Transposition to a new site is interpreted in terms of a chromosome model that gives effect to nicking, or single strand breaks, occurring throughout the genome as a prerequisite to unwinding, strand separation, and replication, of the DNA double helix. PMID:17248592

  11. 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.

  12. Overdominant alleles in a population of variable size.

    PubMed Central

    Slatkin, M; Muirhead, C A

    1999-01-01

    An approximate method is developed to predict the number of strongly overdominant alleles in a population of which the size varies with time. The approximation relies on the strong-selection weak-mutation (SSWM) method introduced by J. H. Gillespie and leads to a Markov chain model that describes the number of common alleles in the population. The parameters of the transition matrix of the Markov chain depend in a simple way on the population size. For a population of constant size, the Markov chain leads to results that are nearly the same as those of N. Takahata. The Markov chain allows the prediction of the numbers of common alleles during and after a population bottleneck and the numbers of alleles surviving from before a bottleneck. This method is also adapted to modeling the case in which there are two classes of alleles, with one class causing a reduction in fitness relative to the other class. Very slight selection against one class can strongly affect the relative frequencies of the two classes and the relative ages of alleles in each class. PMID:10353917

  13. 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.

  14. Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis

    PubMed Central

    Kerdaffrec, Envel; Filiault, Danièle L; Korte, Arthur; Sasaki, Eriko; Nizhynska, Viktoria; Seren, Ümit; Nordborg, Magnus

    2016-01-01

    Seed dormancy is a complex life history trait that determines the timing of germination and is crucial for local adaptation. Genetic studies of dormancy are challenging, because the trait is highly plastic and strongly influenced by the maternal environment. Using a combination of statistical and experimental approaches, we show that multiple alleles at the previously identified dormancy locus DELAY OF GERMINATION1 jointly explain as much as 57% of the variation observed in Swedish Arabidopsis thaliana, but give rise to spurious associations that seriously mislead genome-wide association studies unless modeled correctly. Field experiments confirm that the major alleles affect germination as well as survival under natural conditions, and demonstrate that locally adaptive traits can sometimes be dissected genetically. DOI: http://dx.doi.org/10.7554/eLife.22502.001 PMID:27966430

  15. 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.

  16. Apparent exchange rate mapping with diffusion MRI.

    PubMed

    Lasič, Samo; Nilsson, Markus; Lätt, Jimmy; Ståhlberg, Freddy; Topgaard, Daniel

    2011-08-01

    Water exchange through the cell membranes is an important feature of cells and tissues. The rate of exchange is determined by factors such as membrane lipid composition and organization, as well as the type and activity of aquaporins. A method for noninvasively estimating the rate of water exchange would be useful for characterizing pathological conditions, e.g., tumors, multiple sclerosis, and ischemic stroke, expected to be associated with a change of the membrane barrier properties. This study describes the filter exchange imaging method for determining the rate of water exchange between sites having different apparent diffusion coefficients. The method is based on the filter-exchange pulsed gradient spin-echo NMR spectroscopy experiment, which is here modified to be compatible with the constraints of clinical MR scanners. The data is analyzed using a model-free approach yielding maps of the apparent exchange rate, here being introduced in analogy with the concept of the apparent diffusion coefficient. Proof-of-principle experiments are performed on microimaging and whole-body clinical scanners using yeast suspension phantoms. The limitations and appropriate experimental conditions are examined. The results demonstrate that filter exchange imaging is a fast and reliable method for characterizing exchange, and that it has the potential to become a powerful diagnostic tool.

  17. 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.

  18. Distribution of BoLA-DRB3 allelic frequencies and identification of two new alleles in Iranian buffalo breed.

    PubMed

    Mosafer, J; Heydarpour, M; Manshad, E; Russell, G; Sulimova, G E

    2012-01-01

    The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 ∗48, ∗20, ∗21, and obe) in Iranian buffalo. The DRB3.2 ∗48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 ∗20 and DRB3.2 ∗21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found.

  19. Distribution of BoLA-DRB3 Allelic Frequencies and Identification of Two New Alleles in Iranian Buffalo Breed

    PubMed Central

    Mosafer, J.; Heydarpour, M.; Manshad, E.; Russell, G.; Sulimova, G. E.

    2012-01-01

    The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 ∗48, ∗20, ∗21, and obe) in Iranian buffalo. The DRB3.2 ∗48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 ∗20 and DRB3.2 ∗21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found. PMID:22454612

  20. 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.

  1. 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.

  2. [Comparison of the effects of exchange forms on social solidarity].

    PubMed

    Inaba, Misato; Takahashi, Nobuyuki

    2012-04-01

    Although social solidarity is an essential component that helps maintaining social order, what produces solidarity and how does it work have not been fully investigated. We conducted an experiment to examine whether experiencing different forms of social exchange produces different levels of solidarity. We compared four forms of social exchange: reciprocal exchange (exchange resources without negotiation), negotiated exchange (with negotiation), pure-generalized exchange (giver can choose who to give) and chain-generalized exchange (giver cannot choose who to give). Two dimensions classify these exchanges: the number of players (two vs. more than two), and involvement of negotiation. Reciprocal and negotiated exchanges occur within dyads, while pure- and chain-generalized exchanges involve three or more players. Only the negotiated exchange involves negotiation process; the other exchanges are purely unilateral giving. Participants played a one-shot social dilemma game (SDG) before and after social exchange session. The more the players cooperated in SDG, the stronger the social solidarity. Results show that the cooperation rate in SDG increased more in the reciprocal, pure- and chain-generalized exchange conditions than that in the negotiated exchange condition, suggesting that social solidarity is facilitated by experiencing social exchange which does not involve negotiation.

  3. 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.

  4. 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.

  5. 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.

  6. Association between ACE D allele and elite short distance swimming.

    PubMed

    Costa, Aldo Matos; Silva, António José; Garrido, Nuno Domingos; Louro, Hugo; de Oliveira, Ricardo Jacó; Breitenfeld, Luiza

    2009-08-01

    The influence of ACE gene on athletic performance has been widely explored, and most of the published data refers to an I/D polymorphism leading to the presence (I allele) or absence (D allele) of a 287-bp sequence in intron 16, determining ACE activity in serum and tissues. A higher I allele frequency has been reported among elite endurance athletes, while the D allele was more frequent among those engaged in more power-orientated sports. However, on competitive swimming, the reproducibility of such associations is controversial. We thus compared the ACE genotype of elite swimmers with that of non-elite swimming cohort and of healthy control subjects. We thus sought an association of the ACE genotype of elite swimmers with their competitive distance. 39 Portuguese Olympic swimming candidates were classified as: short (<200 m) and middle (400-1,500 m) distance swimmers, respectively. A group of 32 non-elite swimmers were studied and classified as well, and a control group (n = 100) was selected from the Portuguese population. Chelex 100 was used for DNA extraction and genotype was determined by PCR-RFLP methods. We found that ACE genotype distribution and allelic frequency differs significantly by event distance only among elite swimmers (P < or = 0.05). Moreover, the allelic frequency of the elite short distance swimmers differed significantly from that of the controls (P = 0.021). No associations were found between middle distance swimmers and controls. Our results seem to support an association between the D allele and elite short distance swimming.

  7. Efficient CRISPR-rAAV engineering of endogenous genes to study protein function by allele-specific RNAi.

    PubMed

    Kaulich, Manuel; Lee, Yeon J; Lönn, Peter; Springer, Aaron D; Meade, Bryan R; Dowdy, Steven F

    2015-04-20

    Gene knockout strategies, RNAi and rescue experiments are all employed to study mammalian gene function. However, the disadvantages of these approaches include: loss of function adaptation, reduced viability and gene overexpression that rarely matches endogenous levels. Here, we developed an endogenous gene knockdown/rescue strategy that combines RNAi selectivity with a highly efficient CRISPR directed recombinant Adeno-Associated Virus (rAAV) mediated gene targeting approach to introduce allele-specific mutations plus an allele-selective siRNA Sensitive (siSN) site that allows for studying gene mutations while maintaining endogenous expression and regulation of the gene of interest. CRISPR/Cas9 plus rAAV targeted gene-replacement and introduction of allele-specific RNAi sensitivity mutations in the CDK2 and CDK1 genes resulted in a >85% site-specific recombination of Neo-resistant clones versus ∼8% for rAAV alone. RNAi knockdown of wild type (WT) Cdk2 with siWT in heterozygotic knockin cells resulted in the mutant Cdk2 phenotype cell cycle arrest, whereas allele specific knockdown of mutant CDK2 with siSN resulted in a wild type phenotype. Together, these observations demonstrate the ability of CRISPR plus rAAV to efficiently recombine a genomic locus and tag it with a selective siRNA sequence that allows for allele-selective phenotypic assays of the gene of interest while it remains expressed and regulated under endogenous control mechanisms.

  8. Diversity of S-alleles and mate availability in 3 populations of self-incompatible wild pear (Pyrus pyraster).

    PubMed

    Hoebee, S E; Angelone, S; Csencsics, D; Määttänen, K; Holderegger, R

    2012-01-01

    Small populations of self-incompatible plants may be expected to be threatened by the limitation of compatible mating partners (i.e., S-Allee effect). However, few empirical studies have explicitly tested the hypothesis of mate limitation in small populations of self-incompatible plants. To do so, we studied wild pear (Pyrus pyraster), which possesses a gametophytic self-incompatibility system. We determined the S-genotypes in complete samplings of all adult trees from 3 populations using a PCR-RFLP approach. We identified a total of 26 different S-alleles, homologous to S-alleles of other woody Rosaceae. The functionality of S-alleles and their Mendelian inheritance were verified in artificial pollination experiments and investigations of pollen tube growth. The smallest population (N = 8) harbored 9 different S-alleles and showed a mate availability of 92.9%, whereas the 2 larger populations harbored 18 and 25 S-alleles and exhibited mate availabilities of 98.4% and 99.2%, respectively. Therefore, we conclude that even small populations of gametophytic self-incompatible plants may exhibit high diversity at the S-locus and are not immediately threatened owing to reduced mate availability.

  9. Cloning and characterization of a dominant-negative vps1 allele of the yeast Saccharomyces cerevisiae.

    PubMed

    Finken-Eigen, M; Müller, S; Köhrer, K

    1997-10-01

    The gene product of the yeast VPS1 gene is a member of a family of high-molecular-weight GTP-binding proteins that are involved in diverse cellular processes. The Vps1 protein (Vps1p) was shown to perform an essential function in the yeast secretory pathway. Here, we report the isolation and characterization of a mutant allele of the VPS1 gene, causing a dominant-negative vacuolar protein sorting (vps) defect, as demonstrated by the mislocalization of the vacuolar hydrolase carboxypeptidase Y (CPY). DNA sequence analysis of the mutant vps1 allele (vps1d-293) revealed a single point mutation, resulting in an amino acid exchange at position 293 from Ala to Asp. The mutation is located downstream of the tripartite GTP-binding motif found in the amino-terminal half of the protein. The observation that expression of wild-type Vps1p partially suppressed the dominant-negative CPY sorting phenotype indicates competition of a non-functional mutant Vps1 protein and a functional wild-type VPS1p for a Vps1p-binding site of an as yet unknown vacuolar protein sorting factor.

  10. Construction of a library of cloned short tandem repeat (STR) alleles as universal templates for allelic ladder preparation.

    PubMed

    Wang, Le; Zhao, Xing-Chun; Ye, Jian; Liu, Jin-Jie; Chen, Ting; Bai, Xue; Zhang, Jian; Ou, Yuan; Hu, Lan; Jiang, Bo-Wei; Wang, Feng

    2014-09-01

    Short tandem repeat (STR) genotyping methods are widely used for human identity testing applications, including forensic DNA analysis. Samples of DNA containing the length-variant STR alleles are typically separated and genotyped by comparison to an allelic ladder. Here, we describe a newly devised library of cloned STR alleles. The library covers alleles X and Y for the sex-determining locus Amelogenin and 259 other alleles for 22 autosomal STR loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, D16S539, D18S51, D21S11, D2S1338, D6S1043, D12S391, Penta E, D19S433, D11S4463, D17S974, D3S4529 and D12ATA63). New primers were designed for all these loci to construct recombinant plasmids so that the library retains core repeat elements of STR as well as 5'- and 3'-flanking sequences of ∼500 base pairs. Since amplicons of commercial STR genotyping kits and systems developed in laboratories are usually distributed from 50 to <500 base pairs, this library could provide universal templates for allelic ladder preparation. We prepared three different sets of allelic ladders for this locus TH01 and an updated version of an allelic ladder for the DNATyper(®)19 multiplex system using these plasmids to confirm the suitability of the library as a good source for allelic ladder preparation. Importantly, the authenticity of each construct was confirmed by bidirectional nucleotide sequencing and we report the repeat structures of the 259 STR alleles. The sequencing results showed all repeat structures we obtained for TPOX, CSF1PO, D7S820, TH01, D16S539, D18S51 and Penta E were the same as reported. However, we identified 102 unreported repeat structures from the other 15 STR loci, supplementing our current knowledge of repeat structures and leading to further understanding of these widely used loci.

  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.

  12. Estimating Relatedness in the Presence of Null Alleles

    PubMed Central

    Huang, Kang; Ritland, Kermit; Dunn, Derek W.; Qi, Xiaoguang; Guo, Songtao; Li, Baoguo

    2016-01-01

    Studies of genetics and ecology often require estimates of relatedness coefficients based on genetic marker data. However, with the presence of null alleles, an observed genotype can represent one of several possible true genotypes. This results in biased estimates of relatedness. As the numbers of marker loci are often limited, loci with null alleles cannot be abandoned without substantial loss of statistical power. Here, we show how loci with null alleles can be incorporated into six estimators of relatedness (two novel). We evaluate the performance of various estimators before and after correction for null alleles. If the frequency of a null allele is <0.1, some estimators can be used directly without adjustment; if it is >0.5, the potency of estimation is too low and such a locus should be excluded. We make available a software package entitled PolyRelatedness v1.6, which enables researchers to optimize these estimators to best fit a particular data set. PMID:26500259

  13. Assessing allelic dropout and genotype reliability using maximum likelihood.

    PubMed Central

    Miller, Craig R; Joyce, Paul; Waits, Lisette P

    2002-01-01

    A growing number of population genetic studies utilize nuclear DNA microsatellite data from museum specimens and noninvasive sources. Genotyping errors are elevated in these low quantity DNA sources, potentially compromising the power and accuracy of the data. The most conservative method for addressing this problem is effective, but requires extensive replication of individual genotypes. In search of a more efficient method, we developed a maximum-likelihood approach that minimizes errors by estimating genotype reliability and strategically directing replication at loci most likely to harbor errors. The model assumes that false and contaminant alleles can be removed from the dataset and that the allelic dropout rate is even across loci. Simulations demonstrate that the proposed method marks a vast improvement in efficiency while maintaining accuracy. When allelic dropout rates are low (0-30%), the reduction in the number of PCR replicates is typically 40-50%. The model is robust to moderate violations of the even dropout rate assumption. For datasets that contain false and contaminant alleles, a replication strategy is proposed. Our current model addresses only allelic dropout, the most prevalent source of genotyping error. However, the developed likelihood framework can incorporate additional error-generating processes as they become more clearly understood. PMID:11805071

  14. 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

  15. Rare allelic forms of PRDM9 associated with childhood leukemogenesis.

    PubMed

    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

    2013-03-01

    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.

  16. A Platform for Interrogating Cancer-Associated p53 Alleles

    PubMed Central

    D’Brot, Alejandro; Kurtz, Paula; Regan, Erin; Jakubowski, Brandon; Abrams, John M

    2016-01-01

    p53 is the most frequently mutated gene in human cancer. Compelling evidence argues that full transformation involves loss of growth suppression encoded by wild-type p53 together with poorly understood oncogenic activity encoded by missense mutations. Furthermore, distinguishing disease alleles from natural polymorphisms is an important clinical challenge. To interrogate the genetic activity of human p53 variants, we leveraged the Drosophila model as an in vivo platform. We engineered strains that replace the fly p53 gene with human alleles, producing a collection of stocks that are, in effect, ‘humanized’ for p53 variants. Like the fly counterpart, human p53 transcriptionally activated a biosensor and induced apoptosis after DNA damage. However, all humanized strains representing common alleles found in cancer patients failed to complement in these assays. Surprisingly, stimulus-dependent activation of hp53 occurred without stabilization, demonstrating that these two processes can be uncoupled. Like its fly counterpart, hp53 formed prominent nuclear foci in germline cells but cancer-associated p53 variants did not. Moreover, these same mutant alleles disrupted hp53 foci and inhibited biosensor activity, suggesting that these properties are functionally linked. Together these findings establish a functional platform for interrogating human p53 alleles and suggest that simple phenotypes could be used to stratify disease variants. PMID:26996664

  17. Identification and characterization of variant alleles at CODIS STR loci.

    PubMed

    Allor, Catherine; Einum, David D; Scarpetta, Marco

    2005-09-01

    Short tandem repeat (STR) profiles from 32,671 individuals generated by the ABI Profiler Plus and Cofiler systems were screened for variant alleles not represented within manufacturer-provided allelic ladders. A total of 85 distinct variants were identified at 12 of the 13 CODIS loci, most of which involve a truncated tetranucleotide repeat unit. Twelve novel alleles, identified at D3S1358, FGA, D18S51, D5S818, D7S820 and TPOX, were confirmed by nucleotide sequence analysis and include both insertions and deletions involving the repeat units themselves as well as DNA flanking the repeat regions. Population genetic data were collected for all variants and frequencies range from 0.0003 (many single observations) to 0.0042 (D7S820 '10.3' in North American Hispanics). In total, the variant alleles identified in this study are carried by 1.6% of the estimated 1 million individuals tested annually in the U.S. for the purposes of parentage resolution. A paternity case involving a recombination event of paternal origin is presented and demonstrates how variant alleles can significantly strengthen the genetic evidence in troublesome cases. In such instances, increased costs and turnaround time associated with additional testing may be eliminated.

  18. Description and Power Analysis of Two Tests for Detecting Recent Population Bottlenecks from Allele Frequency Data

    PubMed Central

    Cornuet, J. M.; Luikart, G.

    1996-01-01

    When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a heterozygosity excess are described. They require measurements of the number of alleles and heterozygosity at each of several loci from a population sample. The first test determines if the proportion of loci with heterozygosity excess is significantly larger than expected at equilibrium. The second test establishes if the average of standardized differences between observed and expected heterozygosities is significantly different from zero. Type I and II errors have been evaluated by computer simulations, varying sample size, number of loci, bottleneck size, time elapsed since the beginning of the bottleneck and level of variability of loci. These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. The usefulness of these tests for conservation biology is discussed. PMID:8978083

  19. 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

  20. 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.

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

    PubMed Central

    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

    2015-01-01

    Abstract 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+), ComtB2i 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

  2. Identification of two novel human CD1E alleles.

    PubMed

    Mirones, I; Oteo, M; Parra-Cuadrado, J F; Martínez-Naves, E

    2000-08-01

    CD1 is a family of proteins structurally related to major histocompatibility complex (MHC) molecules and specialized in presenting lipids or glycolipids to T cells. In humans, there are five CD1 genes (CD1A to CD1E). It has been shown that, in contrast with classical MHC genes, CD1 loci display a very limited polymorphism. In the present work we describe two novel CD1E alleles found in two healthy Caucasian individuals. One allele differs from the wild-type by a point mutation resulting in a replacement of arginine at position 154 by a tryptophan. In the second allele we found a substitution of the leucine 184 by a proline.

  3. Generation and characterization of an analog-sensitive PERK allele.

    PubMed

    Maas, Nancy L; Singh, Nickpreet; Diehl, J Alan

    2014-08-01

    Restriction of nutrients and oxygen in the tumor microenvironment disrupts ER homeostasis and adaptation to such stress is mediated by the key UPR effector PERK. Given its pro-tumorigenic activity, significant efforts have been made to elucidate the molecular mechanisms that underlie PERK function. Chemical-genetic approaches have recently proven instrumental in pathway mapping and interrogating kinase function. To enable a detailed study of PERK signaling we have generated an analog-sensitive PERK allele that accepts N(6)-alkylated ATP analogs. We find that this allele can be regulated by bulky ATP-competitive inhibitors, confirming the identity of the PERK gatekeeper residue as methionine 886. Furthermore, this analog-sensitive allele can be used to specifically label substrates with thiophosphate both in vitro and in cells. These data highlight the potential for using chemical-genetic techniques to identify novel PERK substrates, thereby providing an expanded view of PERK function and further definition of its signaling networks.

  4. 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

  5. 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.

  6. 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.

  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. The murine Cd48 gene: allelic polymorphism in the IgV-like region.

    PubMed

    Cabrero, J G; Freeman, G J; Reiser, H

    1998-12-01

    The murine CD48 molecule is a member of the immunoglobulin superfamily which regulates the activation of T lymphocytes. prior cloning experiments using mRNA from two different mouse strains had yielded discrepant sequences within the IgV-like domain of murine CD48. To resolve this issue, we have directly sequenced genomic DNA of 10 laboratory strains and two inbred strains of wild origin. The results of our analysis reveal an allelic polymorphism within the IgV-like domain of murine CD48.

  9. Characterization of chromosomal qnrB and ampC alleles in Citrobacter freundii isolates from different origins.

    PubMed

    Liao, Xiaoping; Fang, Liangxing; Li, Liang; Sun, Jian; Li, Xingping; Chen, Muya; Deng, Hui; Yang, Qiu'e; Li, Xue; Liu, Yahong

    2015-10-01

    The association of ESBLs (extended-spectrum beta-lactamases)/pAmpCs (plasmid-mediated AmpC β-lactamases) with PMQR (plasmid mediated quinolone resistance) in gram-negative bacteria has been of great concern. The present study was performed to characterize the diversity, gene location, genetic context, and evolution of ampC and qnrB alleles in isolates of Citrobacter freundii. Fifteen isolates of C. freundii were identified from a total of 788 isolates of Enterobacteriaceae derived from humans, animals, animal food products, and the environment between 2010 and 2012. Co-existence of qnrB/ΔqnrB with ampC was detected in all C. freundii isolates. Both ampC and qnrB genes were found to be located on the chromosome, but were distantly separated on the chromosome. Seven and six novel alleles were discovered for the 10 ampC and qnrB variants detected in this study, respectively. Phylogenetic analysis showed that the new alleles differed a little from the variants of ampC/qnrB previously described in this genus. The genetic context surrounding ampC genes was AmpR-AmpC-Blc-SugE. However, five different genetic contexts surrounding qnrB/ΔqnrB genes were observed, but they occurred in all cases between the pspF and sapA genes. Additionally, cloning experiments showed that the regions containing different qnrB alleles, even with different genetic contexts, contributed to the reduction of quinolone susceptibility. Our results showed that the chromosomal ampC and qnrB alleles are closely related to C. freundii. However, unlike ampC, qnrB alleles seemed to be related to the genetic contexts surrounding them. The evolution of these two genes in C. freundii isolates might be through different pathways.

  10. Natural allelic variations of TCS1 play a crucial role in caffeine biosynthesis of tea plant and its related species.

    PubMed

    Jin, Ji-Qiang; Yao, Ming-Zhe; Ma, Chun-Lei; Ma, Jian-Qiang; Chen, Liang

    2016-03-01

    Tea caffeine synthase 1 (TCS1) is an enzyme that catalyzes the methylation of N-3 and N-1 and considered to be the most critical enzyme in the caffeine biosynthetic pathway of tea plant. This study shows that TCS1 has six types of allelic variations, namely, TCS1a, TCS1b, TCS1c, TCS1d, TCS1e, and TCS1f, with a 252 bp insertion/deletion mutation in the 5'-untranslated region. Among tea plant and its related species, TCS1a is the predominant allele, and TCS1b-f are the rare alleles that mainly appear in few wild germplasms. The full-length cDNA sequences of three new alleles, namely, TCS1d, TCS1e, and TCS1f, were isolated from specific germplasms, and all of recombinant proteins have higher caffeine synthase (CS, EC 2.1.1.160) activity than theobromine synthase (TS, EC 2.1.1.159). Amino acid residue 269 is responsible for the difference in TCS activity and substrate recognition, which was demonstrated by using site-directed mutagenesis experiments. Furthermore, natural variations in TCS1 change the transcription levels. There are two molecular mechanisms controlling the caffeine biosynthesis in low-caffeine-accumulating tea germplasms, i.e., TCS1 allele with low transcription level or its encoded protein with only TS activity. Allelic variations of TCS1 play a crucial role in caffeine biosynthesis. Taken together, our work provides valuable foundation for a comprehensive understanding of the mechanism of caffeine biosynthesis in section Thea plants and useful guidance for effective breeding.

  11. 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.

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

    PubMed

    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

    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.

  13. 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

    2015-04-30

    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.

  14. Allelism and Molecular Mapping of Soybean Necrotic Root Mutants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mutability of the w4 flower color locus in soybean [Glycine max (L.) Merr.] is conditioned by an allele designated w4-m. Germinal revertants recovered among self-pollinated progeny of mutable plants have been associated with the generation of necrotic root mutations, chlorophyll-deficiency mutation...

  15. A genotype probability index for multiple alleles and haplotypes.

    PubMed

    Percy, A; Kinghorn, B P

    2005-12-01

    We use linear algebra to calculate an index of information content in genotype probabilities which has previously been calculated using trigonometry. The new method can be generalized allowing the index to be calculated for loci with more than two alleles. Applications of this index include its use in genotyping strategies, strategies to manage genetic disorders and in estimation of genotype effects.

  16. 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...

  17. 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

  18. 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...

  19. 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

  20. 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.

  1. 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.

  2. 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...

  3. The hydrogen exchange core and protein folding.

    PubMed Central

    Li, R.; Woodward, C.

    1999-01-01

    A database of hydrogen-deuterium exchange results has been compiled for proteins for which there are published rates of out-exchange in the native state, protection against exchange during folding, and out-exchange in partially folded forms. The question of whether the slow exchange core is the folding core (Woodward C, 1993, Trends Biochem Sci 18:359-360) is reexamined in a detailed comparison of the specific amide protons (NHs) and the elements of secondary structure on which they are located. For each pulsed exchange or competition experiment, probe NHs are shown explicitly; the large number and broad distribution of probe NHs support the validity of comparing out-exchange with pulsed-exchange/competition experiments. There is a strong tendency for the same elements of secondary structure to carry NHs most protected in the native state, NHs first protected during folding, and NHs most protected in partially folded species. There is not a one-to-one correspondence of individual NHs. Proteins for which there are published data for native state out-exchange and theta values are also reviewed. The elements of secondary structure containing the slowest exchanging NHs in native proteins tend to contain side chains with high theta values or be connected to a turn/loop with high theta values. A definition for a protein core is proposed, and the implications for protein folding are discussed. Apparently, during folding and in the native state, nonlocal interactions between core sequences are favored more than other possible nonlocal interactions. Other studies of partially folded bovine pancreatic trypsin inhibitor (Barbar E, Barany G, Woodward C, 1995, Biochemistry 34:11423-11434; Barber E, Hare M, Daragan V, Barany G, Woodward C, 1998, Biochemistry 37:7822-7833), suggest that developing cores have site-specific energy barriers between microstates, one disordered, and the other(s) more ordered. PMID:10452602

  4. 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.

  5. KIR2DL2/2DL3-E(35) alleles are functionally stronger than -Q(35) alleles.

    PubMed

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

    2016-03-31

    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 (E(35)) are functionally stronger than those with glutamine at the same position (Q(35)). Cytotoxicity assay showed that NK cells from HLA-C1 positive donors with KIR2DL2/L3-E(35) could kill more target cells lacking their ligands than NK cells with the weaker -Q(35) 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.

  6. 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.

  7. 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...

  8. Tri-allelic pattern at the TPOX locus: a familial study.

    PubMed

    Picanço, Juliane Bentes; Raimann, Paulo Eduardo; Paskulin, Giorgio Adriano; Alvarez, Luís; Amorim, António; Batista Dos Santos, Sidney Emanuel; Alho, Clarice Sampaio

    2014-02-10

    Alleles at the TPOX STR locus have 6-14 different numbers of a four-nucleotide (AATG) repeat motif arranged in tandem. Although tri-allelic genotypes are generally rare, the TPOX tri-allelic pattern has a higher frequency, varying widely among populations. Despite this, there are few accurate reports to disclose the nature of the TPOX third allele. In this work we present data obtained from 45 individuals belonging to the same pedigree, in which there are cases of tri-allelic TPOX genotypes. The subjects were apparently healthy with a normal biological development. We noticed six tri-allelic cases in this family, and all of them were women. Karyotype analysis showed no occurrence of partial 2p trisomy. All the tri-allelic cases had the genotype 8-10-11, probably due to three copies of the TPOX STR sequence in all cells (Type 2 tri-allelic pattern). Based on previous data we assumed the allele 10 as the TPOX third allele. The pedigree analyses show evidences that the TPOX extra-allele was the allele10, it is placed far from the main TPOX locus, and that there is a potential linkage of the TPOX extra-allele-10 with Xq. This was the first study that included a large pedigree analysis in order to understand the nature TPOX tri-allelic pattern.

  9. Nonfrequent but well-documented, rare and very rare HLA alleles observed in the Croatian population.

    PubMed

    Grubic, Z; Burek Kamenaric, M; Maskalan, M; Stingl Jankovic, K; Zunec, R

    2014-12-01

    The aim of the study was to evaluate the presence of nonfrequent, rare and very rare alleles among Croats and to estimate whether they are associated with specific alleles at other human leukocyte antigen (HLA) loci. This retrospective study included the typing results from the last 10 years; total number of individuals included was approximately 45,000. Among 17 alleles so far observed only once in our population, 6 (A*24:41, B*07:02:28, B*35:03:03, B*39:40N, DRB1*13:23 and DRB1*14:111) belong to very rare alleles, 2 (B*44:16 and DRB1*01:31) belong to rare alleles according to the 'Rare Alleles Detector' tool ( www.allelefrequencies.net), while for the B*35:101:01 allele published data exist only in the IMGT/HLA database. The remaining eight HLA alleles observed only once among Croats are considered as frequent according to the 'Rare Alleles Detector'. Those 17 HLA alleles are not declared as common well defined (CWD) alleles in the CWD allele catalogue 2.0.0. Haplotype analysis of nonfrequent alleles detected in our sample supports the idea that different populations, although similar in some aspects regarding HLA allele and haplotype distribution, still have some unique characteristics. This is the case for A*01:02, B*39:10 and DRB1*13:32 which form haplotypes unreported to date among our subjects.

  10. 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.

  11. 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.

  12. 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.

  13. 78 FR 62907 - Self-Regulatory Organizations; BATS Y-Exchange, Inc.; Notice of Filing and Immediate...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-22

    ... for adding liquidity to the Exchange. Specifically, the Exchange is proposing to amend the methodology... that eliminating days where the Exchange experiences an Exchange Outage from the definition of ADV and... among Exchange constituents as the methodology for calculating ADV and TCV will apply equally to...

  14. MHC class II complexes sample intermediate states along the peptide exchange pathway

    PubMed Central

    Wieczorek, Marek; Sticht, Jana; Stolzenberg, Sebastian; Günther, Sebastian; Wehmeyer, Christoph; El Habre, Zeina; Álvaro-Benito, Miguel; Noé, Frank; Freund, Christian

    2016-01-01

    The presentation of peptide-MHCII complexes (pMHCIIs) for surveillance by T cells is a well-known immunological concept in vertebrates, yet the conformational dynamics of antigen exchange remain elusive. By combining NMR-detected H/D exchange with Markov modelling analysis of an aggregate of 275 microseconds molecular dynamics simulations, we reveal that a stable pMHCII spontaneously samples intermediate conformations relevant for peptide exchange. More specifically, we observe two major peptide exchange pathways: the kinetic stability of a pMHCII's ground state defines its propensity for intrinsic peptide exchange, while the population of a rare, intermediate conformation correlates with the propensity of the HLA-DM-catalysed pathway. Helix-destabilizing mutants designed based on our model shift the exchange behaviour towards the HLA-DM-catalysed pathway and further allow us to conceptualize how allelic variation can shape an individual's MHC restricted immune response. PMID:27827392

  15. 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.

  16. Characterization of 18 new BoLA-DRB3 alleles.

    PubMed

    Maillard, J C; Renard, C; Chardon, P; Chantal, I; Bensaid, A

    1999-06-01

    The second exon of the bovine MHC class II DRB3 gene was amplified by polymerase chain reaction (PCR) from DNA samples of 568 zebu Brahman cattle (Bos indicus) from Martinique (French West Indies). Cloning of these PCR products allowed the isolation of both alleles from each animal, which were characterized by the PCR-restriction fragment length polymorphism (RFLP) technique using the restriction enzymes RsaI, BstYI and HaeIII. Four new PCR-RFLP patterns were obtained by digestion with RsaI. These patterns were named 'v', 'w', 'x' and 'y' continuing the accepted nomenclature. Sequencing of each allele allowed the identification of 18 new BoLA-DRB3 exon 2 nucleotide sequences and their deduced amino acid sequences.

  17. 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.

  18. 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

  19. 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.

  20. Citrobacter spp. as a source of qnrB Alleles.

    PubMed

    Jacoby, George A; Griffin, Caitlin M; Hooper, David C

    2011-11-01

    qnrB is the most common of the five qnr families and has the greatest number of allelic variants. Almost two-thirds of the qnrB alleles have been reported in Citrobacter spp., and several were shown to be located on the chromosome. In this study, PCR was used to investigate the prevalence of plasmid-mediated quinolone resistance genes in 71 clinical isolates belonging to the Citrobacter freundii complex. Thirty-seven percent contained qnrB alleles, including 7 (qnrB32 to qnrB38) that were novel and 1 pseudogene, while none contained qnrA, qnrC, qnrD, qnrS, or aac(6')-Ib-cr. When the strains were arrayed by related 16S rRNA sequence and further separated into subspecies by biochemical criteria, clustering of qnrB-positive strains was evident. In only two strains with qnrB2 and qnrB4 was quinolone resistance transferable by conjugation, and only these strains contained the ISCR1 sequence that is often associated with qnrB on plasmids. Five of 26 qnrB-positive strains contained integrase genes, but these included the strains with qnrB2 and qnrB4 as well as two strains with other transmissible plasmids. In a fully sequenced genome of Citrobacter youngae, a member of the C. freundii complex, another novel qnrB allele, qnrB39, occurs in a sequence of genes that is 90% identical to sequence surrounding integron-associated qnrB4 incorporated into plasmids. The chromosome of Citrobacter is the likely source of plasmid-mediated qnrB.

  1. 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

  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.

  3. RNA-FISH to analyze allele-specific expression.

    PubMed

    Braidotti, G

    2001-01-01

    One of the difficulties associated with the analysis of imprinted gene expression is the need to distinguish RNA synthesis occurring at the maternal vs the paternally inherited copy of the gene. Most of the techniques used to examine allele-specific expression exploit naturally occurring polymorphisms and measure steady-state levels of RNA isolated from a pool of cells. Hence, a restriction fragment length polymorphism (RFLP) an be exploited in a heterozygote, by a reverse transcriptase polymerase chain reaction (RT-PCR)- based procedure, to analyze maternal vs paternal gene expression. The human IGF2R gene was analyzed in this way. Smrzka et al. (1) were thus able to show that the IGF2R gene possesses a hemimethylated, intronic CpG island analogous to the mouse imprinting box. However, IGF2R mRNA was detected that possessed the RFLP from both the maternal and paternal alleles in all but one of the 70 lymphoblastoid samples. (The one monoallelic sample reactivated its paternal allele with continued cell culturing.) It was concluded that monoallelic expression of the human gene is a polymorphic trait occurring in a small minority of all tested samples (reviewed in refs. 2,3). Although this is a sound conclusion, the question remains: Is the human IGF2R gene imprinted?

  4. 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.

  5. A survey of FRAXE allele sizes in three populations

    SciTech Connect

    Zhong, N.; Ju, W.; Curley, D.

    1996-08-09

    FRAXE is a fragile site located at Xq27-8, which contains polymorphic triplet GCC repeats associated with a CpG island. Similar to FRAXA, expansion of the GCC repeats results in an abnormal methylation of the CpG island and is associated with a mild mental retardation syndrome (FRAXE-MR). We surveyed the GCC repeat alleles of FRAXE from 3 populations. A total of 665 X chromosomes including 416 from a New York Euro-American sample (259 normal and 157 with FRAXA mutations), 157 from a Chinese sample (144 normal and 13 FRAXA), and 92 from a Finnish sample (56 normal and 36 FRAXA) were analyzed by polymerase chain reaction. Twenty-seven alleles, ranging from 4 to 39 GCC repeats, were observed. The modal repeat number was 16 in the New York and Finnish samples and accounted for 24% of all the chromosomes tested (162/665). The modal repeat number in the Chinese sample was 18. A founder effect for FRAXA was suggested among the Finnish FRAXA samples in that 75% had the FRAXE 16 repeat allele versus only 30% of controls. Sequencing of the FRAXE region showed no imperfections within the GCC repeat region, such as those commonly seen in FRAXA. The smaller size and limited range of repeats and the lack of imperfections suggests the molecular mechanisms underlying FRAXE triplet mutations may be different from those underlying FRAXA. 27 refs., 4 figs., 1 tab.

  6. Mutant power: using mutant allele collections for yeast functional genomics.

    PubMed

    Norman, Kaitlyn L; Kumar, Anuj

    2016-03-01

    The budding yeast has long served as a model eukaryote for the functional genomic analysis of highly conserved signaling pathways, cellular processes and mechanisms underlying human disease. The collection of reagents available for genomics in yeast is extensive, encompassing a growing diversity of mutant collections beyond gene deletion sets in the standard wild-type S288C genetic background. We review here three main types of mutant allele collections: transposon mutagen collections, essential gene collections and overexpression libraries. Each collection provides unique and identifiable alleles that can be utilized in genome-wide, high-throughput studies. These genomic reagents are particularly informative in identifying synthetic phenotypes and functions associated with essential genes, including those modeled most effectively in complex genetic backgrounds. Several examples of genomic studies in filamentous/pseudohyphal backgrounds are provided here to illustrate this point. Additionally, the limitations of each approach are examined. Collectively, these mutant allele collections in Saccharomyces cerevisiae and the related pathogenic yeast Candida albicans promise insights toward an advanced understanding of eukaryotic molecular and cellular biology.

  7. 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…

  8. Higher Education Exchange, 2004

    ERIC Educational Resources Information Center

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

    2004-01-01

    The Higher Education Exchange is part of a movement to strengthen higher education's democratic mission and foster a more democratic culture throughout American society. Working in this tradition, the Higher Education Exchange publishes case studies, analyses, news, and ideas about efforts within higher education to develop more democratic…

  9. 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.

  10. 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…

  11. 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.…

  12. 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…

  13. 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…

  14. Differences in allele frequencies of autosomal dominant hypercholesterolemia SNPs in the Malaysian population.

    PubMed

    Alex, Livy; Chahil, Jagdish Kaur; Lye, Say Hean; Bagali, Pramod; Ler, Lian Wee

    2012-06-01

    Hypercholesterolemia is caused by different interactions of lifestyle and genetic determinants. At the genetic level, it can be attributed to the interactions of multiple polymorphisms, or as in the example of familial hypercholesterolemia (FH), it can be the result of a single mutation. A large number of genetic markers, mostly single nucleotide polymorphisms (SNP) or mutations in three genes, implicated in autosomal dominant hypercholesterolemia (ADH), viz APOB (apolipoprotein B), LDLR (low density lipoprotein receptor) and PCSK9 (proprotein convertase subtilisin/kexin type-9), have been identified and characterized. However, such studies have been insufficiently undertaken specifically in Malaysia and Southeast Asia in general. The main objective of this study was to identify ADH variants, specifically ADH-causing mutations and hypercholesterolemia-associated polymorphisms in multiethnic Malaysian population. We aimed to evaluate published SNPs in ADH causing genes, in this population and to report any unusual trends. We examined a large number of selected SNPs from previous studies of APOB, LDLR, PCSK9 and other genes, in clinically diagnosed ADH patients (n=141) and healthy control subjects (n=111). Selection of SNPs was initiated by searching within genes reported to be associated with ADH from known databases. The important finding was 137 mono-allelic markers (44.1%) and 173 polymorphic markers (55.8%) in both subject groups. By comparing to publicly available data, out of the 137 mono-allelic markers, 23 markers showed significant differences in allele frequency among Malaysians, European Whites, Han Chinese, Yoruba and Gujarati Indians. Our data can serve as reference for others in related fields of study during the planning of their experiments.

  15. 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.

  16. 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.

  17. Novel method for analysis of allele specific expression in triploid Oryzias latipes reveals consistent pattern of allele exclusion.

    PubMed

    Garcia, Tzintzuni I; Matos, Isa; Shen, Yingjia; Pabuwal, Vagmita; Coelho, Maria Manuela; Wakamatsu, Yuko; Schartl, Manfred; Walter, Ronald B

    2014-01-01

    Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity. Tools to assess ASE in a diploid biological system are becoming more reliable. Non-diploid systems are, however, not uncommon. In humans full or partial polyploid states are regularly found in both healthy (meiotic cells, polynucleated cell types) and diseased tissues (trisomies, non-disjunction events, cancerous tissues). In this work we have studied ASE in the medaka fish model system. We have developed a method for determining ASE in polyploid organisms from RNAseq data and we have implemented this method in a software tool set. As a biological model system we have used nuclear transplantation to experimentally produce artificial triploid medaka composed of three different haplomes. We measured ASE in RNA isolated from the livers of two adult, triploid medaka fish that showed a high degree of similarity. The majority of genes examined (82%) shared expression more or less evenly among the three alleles in both triploids. The rest of the genes (18%) displayed a wide range of ASE levels. Interestingly the majority of genes (78%) displayed generally consistent ASE levels in both triploid individuals. A large contingent of these genes had the same allele entirely suppressed in both triploids. When viewed in a chromosomal context, it is revealed that these genes are from large sections of 4 chromosomes and may be indicative of some broad scale suppression of gene expression.

  18. The number of alleles at a microsatellite defines the allele frequency spectrum and facilitates fast accurate estimation of theta.

    PubMed

    Haasl, Ryan J; Payseur, Bret A

    2010-12-01

    Theoretical work focused on microsatellite variation has produced a number of important results, including the expected distribution of repeat sizes and the expected squared difference in repeat size between two randomly selected samples. However, closed-form expressions for the sampling distribution and frequency spectrum of microsatellite variation have not been identified. Here, we use coalescent simulations of the stepwise mutation model to develop gamma and exponential approximations of the microsatellite allele frequency spectrum, a distribution central to the description of microsatellite variation across the genome. For both approximations, the parameter of biological relevance is the number of alleles at a locus, which we express as a function of θ, the population-scaled mutation rate, based on simulated data. Discovered relationships between θ, the number of alleles, and the frequency spectrum support the development of three new estimators of microsatellite θ. The three estimators exhibit roughly similar mean squared errors (MSEs) and all are biased. However, across a broad range of sample sizes and θ values, the MSEs of these estimators are frequently lower than all other estimators tested. The new estimators are also reasonably robust to mutation that includes step sizes greater than one. Finally, our approximation to the microsatellite allele frequency spectrum provides a null distribution of microsatellite variation. In this context, a preliminary analysis of the effects of demographic change on the frequency spectrum is performed. We suggest that simulations of the microsatellite frequency spectrum under evolutionary scenarios of interest may guide investigators to the use of relevant and sometimes novel summary statistics.

  19. 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...

  20. Investigation of a transient energetic charge exchange flux enhancement ('spike-on-tail') observed in neutral-beam-heated H-mode discharges in the National Spherical Torus Experiment

    NASA Astrophysics Data System (ADS)

    Medley, S. S.; Kolesnichenko, Ya. I.; Yakovenko, Yu. V.; Bell, R. E.; Bortolon, A.; Crocker, N. A.; Darrow, D. S.; Diallo, A.; Domier, C. W.; Fonck, R. J.; Fredrickson, E. D.; Gerhardt, S. P.; Gorelenkov, N. N.; Kramer, G. J.; Kubota, S.; LeBlanc, B. P.; Lee, K. C.; Mazzucato, E.; McKee, G. R.; Podestà, M.; Ren, Y.; Roquemore, A. L.; Smith, D. R.; Stutman, D.; Tritz, K.; White, R. B.

    2012-01-01

    In the National Spherical Torus Experiment (NSTX), a large increase in the charge exchange neutral flux localized around the neutral beam (NB) injection full energy is measured using a neutral particle analyser. Termed the high-energy feature (HEF), it appears on the NB-injected energetic-ion spectrum only in discharges where tearing or kink-type modes (f < 50 kHz) are absent, toroidal Alfvén eigenmode activity (f ~ 50-150 kHz) is weak and global Alfvén eigenmode (GAE) activity (f ~ 400-1000 kHz) is robust. Compressional Alfvén eigenmode activity (f > 1000 kHz) is usually sporadic or absent during the HEF event. The HEF exhibits growth times of Δt ~ 20-80 ms, durations spanning 100-600 ms and peak-to-base flux ratios up to H = Fmax/Fmin ~ 10. In infrequent cases, a slowing-down distribution below the HEF energy can develop that continues to evolve over periods of order 100 ms, a time scale long compared with the typical fast-ion equilibration times. HEFs are observed only in H-mode (not L-mode) discharges with injected power Pb >= 4 MW and in the pitch range χ ≡ v||/v ~ 0.7-0.9 i.e. only for passing particles. Increases of order 10-30% in the measured neutron yield and total stored energy that are observed to coincide with the feature appear to be driven by concomitant broadening of measured Te(r), Ti(r) and ne(r) profiles and not the HEF itself. While the HEF has minimal impact on plasma performance, it nevertheless poses a challenging wave-particle interaction phenomenon to understand. Candidate mechanisms for HEF formation are developed based on quasilinear (QL) theory of wave-particle interaction. The only mechanism found to lead to the large NPA flux ratios, H = Fmax/Fmin, observed in NSTX is the QL evolution of the energetic-ion distribution, Fb(E, χ, r), in phase space. A concomitant loss of some particles is observed due to interaction through cyclotron resonance of the particles with destabilized modes having sufficiently high frequencies, f ~ 700

  1. The maize d2003, a novel allele of VP8, is required for maize internode elongation.

    PubMed

    Lv, Hongkun; Zheng, Jun; Wang, Tianyu; Fu, Junjie; Huai, Junling; Min, Haowei; Zhang, Xiang; Tian, Baohua; Shi, Yunsu; Wang, Guoying

    2014-02-01

    The d2003 is a natural dwarf mutant from maize inbred line K36 and has less than one-third of K36 plant height with severely shortened internodes. In this study, we reported the cloning of d2003 gene using positional cloning. The results showed that there was a single-base insertion in the coding region of Viviparous8 (VP8) in d2003 mutant, which resulted in a premature stop codon. Further genetic allelism tests confirmed that d2003 mutation is a novel allele of VP8. VP8 is mainly expressed in the stem apex, young leaves, and developing vascular tissues, and its expression levels in nodes are significantly higher than that in internodes at 12-leaf stage. Subcellular localization demonstrated that the VP8 protein is localized to the endoplasmic reticulum and the N-terminal 26 amino acids (aa) of VP8 protein are essential to its localization in ER. Further transgenic experiments showed that lack of the 26 aa leads to loss of VP8 function in Arabidopsis amp1 phenotype rescue. These results strongly suggested that the N-terminal 26 aa is critical for VP8 protein localization, and the correct protein localization of VP8 in ER is necessary for its function.

  2. Utilising polymorphisms to achieve allele-specific genome editing in zebrafish

    PubMed Central

    Capon, Samuel J.; Baillie, Gregory J.; Bower, Neil I.; da Silva, Jason A.; Paterson, Scott; Hogan, Benjamin M.; Simons, Cas

    2017-01-01

    ABSTRACT The advent of genome editing has significantly altered genetic research, including research using the zebrafish model. To better understand the selectivity of the commonly used CRISPR/Cas9 system, we investigated single base pair mismatches in target sites and examined how they affect genome editing in the zebrafish model. Using two different zebrafish strains that have been deep sequenced, CRISPR/Cas9 target sites containing polymorphisms between the two strains were identified. These strains were crossed (creating heterozygotes at polymorphic sites) and CRISPR/Cas9 complexes that perfectly complement one strain injected. Sequencing of targeted sites showed biased, allele-specific editing for the perfectly complementary sequence in the majority of cases (14/19). To test utility, we examined whether phenotypes generated by F0 injection could be internally controlled with such polymorphisms. Targeting of genes bmp7a and chordin showed reduction in the frequency of phenotypes in injected ‘heterozygotes’ compared with injecting the strain with perfect complementarity. Next, injecting CRISPR/Cas9 complexes targeting two separate sites created deletions, but deletions were biased to selected chromosomes when one CRISPR/Cas9 target contained a polymorphism. Finally, integration of loxP sequences occurred preferentially in alleles with perfect complementarity. These experiments demonstrate that single nucleotide polymorphisms (SNPs) present throughout the genome can be utilised to increase the efficiency of in cis genome editing using CRISPR/Cas9 in the zebrafish model. PMID:27895053

  3. Utilising polymorphisms to achieve allele-specific genome editing in zebrafish.

    PubMed

    Capon, Samuel J; Baillie, Gregory J; Bower, Neil I; da Silva, Jason A; Paterson, Scott; Hogan, Benjamin M; Simons, Cas; Smith, Kelly A

    2017-01-15

    The advent of genome editing has significantly altered genetic research, including research using the zebrafish model. To better understand the selectivity of the commonly used CRISPR/Cas9 system, we investigated single base pair mismatches in target sites and examined how they affect genome editing in the zebrafish model. Using two different zebrafish strains that have been deep sequenced, CRISPR/Cas9 target sites containing polymorphisms between the two strains were identified. These strains were crossed (creating heterozygotes at polymorphic sites) and CRISPR/Cas9 complexes that perfectly complement one strain injected. Sequencing of targeted sites showed biased, allele-specific editing for the perfectly complementary sequence in the majority of cases (14/19). To test utility, we examined whether phenotypes generated by F0 injection could be internally controlled with such polymorphisms. Targeting of genes bmp7a and chordin showed reduction in the frequency of phenotypes in injected 'heterozygotes' compared with injecting the strain with perfect complementarity. Next, injecting CRISPR/Cas9 complexes targeting two separate sites created deletions, but deletions were biased to selected chromosomes when one CRISPR/Cas9 target contained a polymorphism. Finally, integration of loxP sequences occurred preferentially in alleles with perfect complementarity. These experiments demonstrate that single nucleotide polymorphisms (SNPs) present throughout the genome can be utilised to increase the efficiency of in cis genome editing using CRISPR/Cas9 in the zebrafish model.

  4. 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.

  5. 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.

  6. Cryptographic Securities Exchanges

    NASA Astrophysics Data System (ADS)

    Thorpe, Christopher; Parkes, David C.

    While transparency in financial markets should enhance liquidity, its exploitation by unethical and parasitic traders discourages others from fully embracing disclosure of their own information. Traders exploit both the private information in upstairs markets used to trade large orders outside traditional exchanges and the public information present in exchanges' quoted limit order books. Using homomorphic cryptographic protocols, market designers can create "partially transparent" markets in which every matched trade is provably correct and only beneficial information is revealed. In a cryptographic securities exchange, market operators can hide information to prevent its exploitation, and still prove facts about the hidden information such as bid/ask spread or market depth.

  7. Advancing allele group-specific amplification of the complete HLA-C gene--isolation of novel alleles from three allele groups (C*04, C*07 and C*08).

    PubMed

    Cisneros, E; Martínez-Pomar, N; Vilches, M; Martín, P; de Pablo, R; Nuñez Del Prado, N; Nieto, A; Matamoros, N; Moraru, M; Vilches, C

    2013-10-01

    A variety of strategies have been designed for sequence-based HLA typing (SBT) and for the isolation of new human leucocyte antigen (HLA) alleles, but unambiguous characterization of complete genomic sequences remains a challenge. We recently reported a simple method for the group-specific amplification (GSA) and sequencing of a full-length C*04 genomic sequence in isolation from the accompanying allele. Here we build on this strategy and present homologous methods that enable the isolation of HLA-C alleles belonging to another two allele groups. Using this approach, which can be applied to sequence-based typing in some clinical settings, we have successfully characterized three novel HLA-C alleles (C*04:128, C*07:01:01:02, and C*08:62).

  8. Apparent exchange rate for breast cancer characterization.

    PubMed

    Lasič, Samo; Oredsson, Stina; Partridge, Savannah C; Saal, Lao H; Topgaard, Daniel; Nilsson, Markus; Bryskhe, Karin

    2016-05-01

    Although diffusion MRI has shown promise for the characterization of breast cancer, it has low specificity to malignant subtypes. Higher specificity might be achieved if the effects of cell morphology and molecular exchange across cell membranes could be disentangled. The quantification of exchange might thus allow the differentiation of different types of breast cancer cells. Based on differences in diffusion rates between the intra- and extracellular compartments, filter exchange spectroscopy/imaging (FEXSY/FEXI) provides non-invasive quantification of the apparent exchange rate (AXR) of water between the two compartments. To test the feasibility of FEXSY for the differentiation of different breast cancer cells, we performed experiments on several breast epithelial cell lines in vitro. Furthermore, we performed the first in vivo FEXI measurement of water exchange in human breast. In cell suspensions, pulsed gradient spin-echo experiments with large b values and variable pulse duration allow the characterization of the intracellular compartment, whereas FEXSY provides a quantification of AXR. These experiments are very sensitive to the physiological state of cells and can be used to establish reliable protocols for the culture and harvesting of cells. Our results suggest that different breast cancer subtypes can be distinguished on the basis of their AXR values in cell suspensions. Time-resolved measurements allow the monitoring of the physiological state of cells in suspensions over the time-scale of hours, and reveal an abrupt disintegration of the intracellular compartment. In vivo, exchange can be detected in a tumor, whereas, in normal tissue, the exchange rate is outside the range experimentally accessible for FEXI. At present, low signal-to-noise ratio and limited scan time allows the quantification of AXR only in a region of interest of relatively large tumors.

  9. The dominant mechanisms of hyporheic exchange

    NASA Astrophysics Data System (ADS)

    McCluskey, Alexander H.; Stewardson, Michael J.; Grant, Stanley B.

    2013-04-01

    The mechanisms driving hyporheic exchange are of significant interest facilitating transfer of nutrients, oxygen and energy essential for benthic ecology. The hyporheic zone is the region directly beneath the sediment-water interface (SWI) marking the transition from stream to porous flow. Hyporheic exchange is controlled by a range of variables of the stream, streambed and the geometry of the SWI. The boundary layer of a stream is characterized by a slip velocity across the SWI, facilitating transition from free fluid to Darcian flow. Mass and momentum transfer across the SWI are driven by either (1) advective pumping from variation in dynamic head at the SWI causing potential flow into and out of the streambed, or; (2) turbulent structures in the boundary layer which penetrate into the streambed. Unlike the advective pumping, turbulent structures penetrate well beyond the characteristic mixing length scale and lead to permanent displacement of fluid. The advective pumping model assumes a potential field directly beneath the SWI, despite the slip layer propagating into the bed. Furthermore, turbulent exchange can lead to a permanent displacement of fluid, while advective pumping is multidirectional and periodic. Models derived from flume experiments have been based on one of these mechanisms and have been presented as two alternative approaches for modelling hyporheic exchange. However, the incongruence of these mechanisms leads us to investigate and model each individually. Our investigation treats coherent turbulent penetration and advective pumping as unique mechanisms which both contribute to rates of hyporheic exchange. Using bedforms as a proxy for advective pumping allowed us to gain insight into the dynamics of exchange mechanisms. Analysis of 93 past flume experiments has shown that bedforms alter the dependence of hyporheic exchange on these exchange mechanisms. Power models developed through a multilinear regression analysis showed that exchange in

  10. 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.

  11. Allelic melanism in American and British peppered moths.

    PubMed

    Grant, B S

    2004-01-01

    Parallel evolutionary changes in the incidence of melanism are well documented in widely geographically separated subspecies of the peppered moth (Biston betularia). The British melanic phenotype (f. carbonaria) and the American melanic phenotype (f. swettaria) are indistinguishable in appearance, and previous genetic analysis has established that both are inherited as autosomal dominants. This report demonstrates through hybridizations of the subspecies and Mendelian testcrosses of melanic progeny that carbonaria and swettaria are phenotypes produced by alleles (isoalleles) at a single locus. The possibility of close linkage at two loci remains, but the simpler one-locus model cannot be rejected in the absence of contrary evidence.

  12. Compact, super heat exchanger

    NASA Technical Reports Server (NTRS)

    Fortini, A.; Kazaroff, J. M.

    1980-01-01

    Heat exchanger uses porous media to enhance heat transfer through walls of cooling channels, thereby lowering wall temperature. Porous media within cooling channel increases internal surface area from which heat can be transferred to coolant. Comparison data shows wall has lower temperature and coolant has higher temperature when porous medium is used within heat exchanger. Media can be sintered powedered metal, metal fibers, woven wire layers, or any porous metal having desired permeability and porosity.

  13. Hibernation and gas exchange.

    PubMed

    Milsom, William K; Jackson, Donald C

    2011-01-01

    Hibernation in endotherms and ectotherms is characterized by an energy-conserving metabolic depression due to low body temperatures and poorly understood temperature-independent mechanisms. Rates of gas exchange are correspondly reduced. In hibernating mammals, ventilation falls even more than metabolic rate leading to a relative respiratory acidosis that may contribute to metabolic depression. Breathing in some mammals becomes episodic and in some small mammals significant apneic gas exchange may occur by passive diffusion via airways or skin. In ectothermic vertebrates, extrapulmonary gas exchange predominates and in reptiles and amphibians hibernating underwater accounts for all gas exchange. In aerated water diffusive exchange permits amphibians and many species of turtles to remain fully aerobic, but hypoxic conditions can challenge many of these animals. Oxygen uptake into blood in both endotherms and ectotherms is enhanced by increased affinity of hemoglobin for O₂ at low temperature. Regulation of gas exchange in hibernating mammals is predominately linked to CO₂/pH, and in episodic breathers, control is principally directed at the duration of the apneic period. Control in submerged hibernating ectotherms is poorly understood, although skin-diffusing capacity may increase under hypoxic conditions. In aerated water blood pH of frogs and turtles either adheres to alphastat regulation (pH ∼8.0) or may even exhibit respiratory alkalosis. Arousal in hibernating mammals leads to restoration of euthermic temperature, metabolic rate, and gas exchange and occurs periodically even as ambient temperatures remain low, whereas body temperature, metabolic rate, and gas exchange of hibernating ectotherms are tightly linked to ambient temperature.

  14. Microtube strip heat exchanger

    SciTech Connect

    Doty, F.D.

    1992-07-09

    The purpose of this contract has been to explore the limits of miniaturization of heat exchangers with the goals of (1) improving the theoretical understanding of laminar heat exchangers, (2) evaluating various manufacturing difficulties, and (3) identifying major applications for the technology. A low-cost, ultra-compact heat exchanger could have an enormous impact on industry in the areas of cryocoolers and energy conversion. Compact cryocoolers based on the reverse Brayton cycle (RBC) would become practical with the availability of compact heat exchangers. Many experts believe that hardware advances in personal computer technology will rapidly slow down in four to six years unless lowcost, portable cryocoolers suitable for the desktop supercomputer can be developed. Compact refrigeration systems would permit dramatic advances in high-performance computer work stations with conventional'' microprocessors operating at 150 K, and especially with low-cost cryocoolers below 77 K. NASA has also expressed strong interest in our MTS exchanger for space-based RBC cryocoolers for sensor cooling. 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.

  15. 48 CFR 1446.170 - Government-Industry Data Exchange Program (GIDEP).

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... THE INTERIOR CONTRACT MANAGEMENT QUALITY ASSURANCE General 1446.170 Government-Industry Data Exchange... cooperative program managed and funded by the U.S. Government to exchange engineering, failure experience... construction materials), manufacturing processes, environmental issues associated with those...

  16. 48 CFR 1446.170 - Government-Industry Data Exchange Program (GIDEP).

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... THE INTERIOR CONTRACT MANAGEMENT QUALITY ASSURANCE General 1446.170 Government-Industry Data Exchange... cooperative program managed and funded by the U.S. Government to exchange engineering, failure experience... construction materials), manufacturing processes, environmental issues associated with those...

  17. 48 CFR 1446.170 - Government-Industry Data Exchange Program (GIDEP).

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... THE INTERIOR CONTRACT MANAGEMENT QUALITY ASSURANCE General 1446.170 Government-Industry Data Exchange... cooperative program managed and funded by the U.S. Government to exchange engineering, failure experience... construction materials), manufacturing processes, environmental issues associated with those...

  18. Identification of guanine exchange factor key residues involved in exchange activity and Ras interaction.

    PubMed

    Camus, C; Hermann-Le Denmat, S; Jacquet, M

    1995-09-07

    We have carried out a functional analysis of the human HGRF55 exchange factor in the yeast Saccharomyces cerevisiae. Twelve residues conserved among most of all known guanine exchange factors (GEFs) have been independently changed to alanine. Taking advantage of the ability of Hgrf55p to replace the yeast Cdc25p exchange factor, and using the two-hybrid system with RAS2ala22 allele, we have identified key residues for the interaction with Ras and/or its activation. Substitution of arginine 392 to alanine leads to a complete loss of interaction with Ras, though the protein remains stable. Substitution of Asp266 or Arg359 to alanine results in inactive proteins at 39 degrees C, still able however to interact with Ras. The other charged-to-alanine substitutions led to no detectable phenotype when present alone but most of them dramatically increased the temperature sensitive phenotype observed with [Asp266Ala] substitution. Surprisingly, the cysteine to alanine substitution in the highly conserved PCVPF/Y motif proved to be without effect, suggesting that the sulfhydryl group is not essential for stability or interaction with Ras.

  19. 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.

  20. 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.

  1. An allele of sequoia dominantly enhances a trio mutant phenotype to influence Drosophila larval behavior.

    PubMed

    Dean, Kathryn E; Fields, April; Geer, Marcus J; King, Eric C; Lynch, Brian T; Manohar, Rohan R; McCall, Julianne R; Palozola, Katherine C; Zhang, Yan; 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.

  2. Accurate size comparison of short tandem repeat alleles amplified by PCR.

    PubMed

    Smith, R N

    1995-01-01

    A strategy is presented for classifying complex short tandem repeat (STR) alleles by size. Such alleles can differ in length by only 1 bp. The HUMACTBP2 locus was used as a model. Dye-labeled, PCR-amplified alleles were analyzed on an automated DNA sequencer with laser-induced fluorescence detection and fragment-sizing software. Between-gel allele sizes calculated against an in-lane allelic ladder or viral DNA size standard were too imprecise to distinguish a 1-bp difference. However, the size difference between a sample allele and its matching ladder allele provided a reliable criterion for size classification. The mean size difference +/- 3 SDs was 0.5 bp, and so an individual result within this interval signified a match. Statistically, 99.7% of the results should lie within +/- 3 SDs with virtually no chance of encountering the 9-SD difference from the mean necessary to misclassify an allele by 1 bp. The method was valid for sample alleles sized against the allelic ladder and for both sample and ladder alleles sized against the viral DNA standard. A correction for the effect of different dye labels on mobility was included in the calculations.

  3. MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout

    PubMed Central

    2013-01-01

    Background The Major Histocompatibility Complex (MHC) is the most important genetic marker to study patterns of adaptive genetic variation determining pathogen resistance and associated life history decisions. It is used in many different research fields ranging from human medical, molecular evolutionary to functional biodiversity studies. Correct assessment of the individual allelic diversity pattern and the underlying structural sequence variation is the basic requirement to address the functional importance of MHC variability. Next-generation sequencing (NGS) technologies are likely to replace traditional genotyping methods to a great extent in the near future but first empirical studies strongly indicate the need for a rigorous quality control pipeline. Strict approaches for data validation and allele calling to distinguish true alleles from artefacts are required. Results We developed the analytical methodology and validated a data processing procedure which can be applied to any organism. It allows the separation of true alleles from artefacts and the evaluation of genotyping reliability, which in addition to artefacts considers for the first time the possibility of allelic dropout due to unbalanced amplification efficiencies across alleles. Finally, we developed a method to assess the confidence level per genotype a-posteriori, which helps to decide which alleles and individuals should be included in any further downstream analyses. The latter method could also be used for optimizing experiment designs in the future. Conclusions Combining our workflow with the study of amplification efficiency offers the chance for researchers to evaluate enormous amounts of NGS-generated data in great detail, improving confidence over the downstream analyses and subsequent applications. PMID:23937623

  4. 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

  5. Analysis of elite variety tag SNPs reveals an important allele in upland rice.

    PubMed

    Lyu, Jun; Zhang, Shilai; Dong, Yang; He, Weiming; Zhang, Jing; Deng, Xianneng; Zhang, Yesheng; Li, Xin; Li, Baoye; Huang, Wangqi; Wan, Wenting; Yu, Yang; Li, Qiong; Li, Jun; Liu, Xin; Wang, Bo; Tao, Dayun; Zhang, Gengyun; Wang, Jun; Xu, Xun; Hu, Fengyi; Wang, Wen

    2013-01-01

    Elite crop varieties usually fix alleles that occur at low frequencies within non-elite gene pools. Dissecting these alleles for desirable agronomic traits can be accomplished by comparing the genomes of elite varieties with those from non-elite populations. Here we deep-sequence six elite rice varieties and use two large control panels to identify elite variety tag single-nucleotide polymorphism alleles (ETASs). Guided by this preliminary analysis, we comprehensively characterize one protein-altering ETAS in the 9-cis-epoxycarotenoid dioxygenase gene of the IRAT104 upland rice variety. This allele displays a drastic frequency difference between upland and irrigated rice, and a selective sweep is observed around this allele. Functional analysis indicates that in upland rice, this allele is associated with significantly higher abscisic acid levels and denser lateral roots, suggesting its association with upland rice suitability. This report provides a potential strategy to mine rare, agronomically important alleles.

  6. Exchanging Lives: Middle School Writers Online.

    ERIC Educational Resources Information Center

    Christian, Scott

    This book, which began as a teacher research project, goes inside the Anne Frank Conference, an online literary exchange among middle school students, to examine how the conference experience has fundamentally changed who the students are as writers. The book provides background by discussing the implementation of the Bread Loaf Rural Teachers…

  7. 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…

  8. The Science Exchange Program - A Proposal.

    ERIC Educational Resources Information Center

    Klausen, James

    An exchange program is described in which two groups of high school science students, one from Long Island, New York, and one from upstate New York, visited each other's school districts for three days to broaden their experiences with different physical and geological surroundings. The inland group of students was exposed to marine geology and…

  9. 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.

  10. 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.

  11. 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

  12. Spin-locking versus chemical exchange saturation transfer MRI for investigating chemical exchange process between water and labile metabolite protons.

    PubMed

    Jin, Tao; Autio, Joonas; Obata, Takayuki; Kim, Seong-Gi

    2011-05-01

    Chemical exchange saturation transfer (CEST) and spin-locking (SL) experiments were both able to probe the exchange process between protons of nonequivalent chemical environments. To compare the characteristics of the CEST and SL approaches in the study of chemical exchange effects, we performed CEST and SL experiments at varied pH and concentrated metabolite phantoms with exchangeable amide, amine, and hydroxyl protons at 9.4 T. Our results show that: (i) on-resonance SL is most sensitive to chemical exchanges in the intermediate-exchange regime and is able to detect hydroxyl and amine protons on a millimolar concentration scale. Off-resonance SL and CEST approaches are sensitive to slow-exchanging protons when an optimal SL or saturation pulse power matches the exchanging rate, respectively. (ii) Offset frequency-dependent SL and CEST spectra are very similar and can be explained well with an SL model recently developed by Trott and Palmer (J Magn Reson 2002;154:157-160). (iii) The exchange rate and population of metabolite protons can be determined from offset-dependent SL or CEST spectra or from on-resonance SL relaxation dispersion measurements. (iv) The asymmetry of the magnetization transfer ratio (MTR(asym)) is highly dependent on the choice of saturation pulse power. In the intermediate-exchange regime, MTR(asym) becomes complicated and should be interpreted with care.

  13. 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.

  14. 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?

  15. 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.

  16. Characterization of ROP18 alleles in human toxoplasmosis.

    PubMed

    Sánchez, Víctor; de-la-Torre, Alejandra; Gómez-Marín, Jorge Enrique

    2014-04-01

    The role of the virulent gene ROP18 polymorphisms is not known in human toxoplasmosis. A total of 320 clinical samples were analyzed. In samples positive for ROP18 gene, we determined by an allele specific PCR, if patients got the upstream insertion positive ROP18 sequence Toxoplasma strain (mouse avirulent strain) or the upstream insertion negative ROP18 sequence Toxoplasma strain (mouse virulent strain). We designed an ELISA assay for antibodies against ROP18 derived peptides from the three major clonal lineages of Toxoplasma. 20 clinical samples were of quality for ROP18 allele analysis. In patients with ocular toxoplasmosis, a higher inflammatory reaction on eye was associated to a PCR negative result for the upstream region of ROP18. 23.3%, 33% and 16.6% of serums from individuals with ocular toxoplasmosis were positive for type I, type II and type III ROP18 derived peptides, respectively but this assay was affected by cross reaction. The absence of Toxoplasma ROP18 promoter insertion sequence in ocular toxoplasmosis was correlated with severe ocular inflammatory response. Determination of antibodies against ROP18 protein was not useful for serotyping in human toxoplasmosis.

  17. Allelic loss and linkage studies in prostate cancer

    SciTech Connect

    Johnson, D.R.; Bale, A.E.; Lytton, B.

    1994-09-01

    Prostate cancer is the most common malignancy in U.S. males. Many examples of familial aggregation have been reported, and segregration analysis suggests that an autosomal dominant gene with a penetrance of 88% by age 85 accounts for 9% of all cases. Because many dominant cancer predisposition syndromes are related to germline mutations in tumor suppressor genes, we analyzed a series of sporadic and hereditary tumors for allelic loss. High grade sporadic, paraffin-embedded, primary prostate tumors were obtained from the archival collection in the Department of Pathology at Yale and hereditary tumors from three families were obtained by an advertisement in the New York Times and from referrals by urologists. PCR analysis showed loss in 4/7 informative sporadic prostate tumors with NEFL (8p21), in 8/22 informative tumors with D10S169 (10q26-qter), in 2/8 informative tumors with D10S108 (10q) and in 4/23 informative tumors with D10S89 (10p) in agreement with previous studies. PYGM on chromosome 11 and D9S127 on chromosome 9 showed no loss. Linkage analysis with NEFL in 3 prostate cancer families gave strongly negative results for close linkage (Z=-2.1 at {theta}=0.01) but LOD scores were very dependent on parameters, e.g. gene frequency, phenocopy rate, and penetrance. Linkage analysis with chromosome 10 markers and systematic analysis of the genome for other area of allelic loss are underway.

  18. A genetic model of melanoma tumorigenesis based on allelic losses

    SciTech Connect

    Hayward, N.K.; Palmer, J.M.; Walters, M.K.

    1994-09-01

    Previous karyotypic studies have indicated a possible series of non-random chromosomal events involved in the progression of melanoma. We sought to define a model of melanocyte tumorigenesis by studying allelic deletions of polymorphic simple tandem repeat markers mapping to chromosome 1, 6q, 7, 9p, 10, 11, 17, and 21 in thirty matched pairs of melanoma and constitutional DNAs. The most frequent and earliest deletions were found on 9p (57%) and 10q (32%) and with the exception of one case, no sample has loss of markers on another chromosome without concomitant loss of markers on 9p and/or 10q. Losses on 6q were also a frequent (32%) event that sometimes occurred in primary melanomas, whereas losses of loci on distal 1p (26%) or 11q (26%) occurred only in metastic melanomas. A background rate (0-17%) of allele loss was seen on chromosomes 7, 17, and 21. Homozygous deletions in a panel of 31 melanoma cell lines were only detected for markers on 9p (4 cases). These data strongly support the previous model of melanoma tumorigenesis based primarily on karyotypic findings in melanocytic lesions. However, we have been able to further augment the model by delimiting the regions of loss on 10q to a region distal to D10S254, and on 1p, to between D1S243 and D1S160.

  19. An allele of the crm gene blocks cyanobacterial circadian rhythms.

    PubMed

    Boyd, Joseph S; Bordowitz, Juliana R; Bree, Anna C; Golden, Susan S

    2013-08-20

    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.

  20. 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.

  1. 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"…

  2. Characterization of Mhc-DRB allelic diversity in white-tailed deer (Odocoileus virginianus) provides insight into Mhc-DRB allelic evolution within Cervidae.

    PubMed

    Van Den Bussche, R A; Hoofer, S R; Lochmiller, R L

    1999-05-01

    Although white-tailed deer (Odocoileus virginianus) are one of North America's best studied mammals, no information is available concerning allelic diversity at any locus of the major histocompatibility complex in this taxon. Using the polymerase chain reaction, single-stranded conformation polymorphism analysis, and DNA sequencing techniques, 15 DRB exon 2 alleles were identified among 150 white-tailed deer from a single population in southeastern Oklahoma. These alleles represent a single locus and exhibit a high degree of nucleotide and amino acid polymorphism, with most amino acid variation occurring at positions forming the peptide binding sites. Furthermore, twenty-seven amino acid residues unique to white-tailed deer DRB alleles were detected, with 19 of these occurring at residues forming contact points of the peptide binding region. Significantly higher rates of nonsynonymous than synonymous substitutions were detected among these DRB alleles. In contrast to other studies of Artiodactyla DRB sequences, interallelic recombination does not appear to be playing a significant role in the generation of allelic diversity at this locus in white-tailed deer. To examine evolution of white-tailed deer (Odvi-DRB) alleles within Cervidae, we performed a phylogenetic analysis of all published red deer (Ceel-DRB), roe deer (Caca-DRB), and moose (Alal-DRB) DRB alleles. The phylogenetic tree clearly shows a trans-species persistence of DRB lineages among these taxa. Moreover, this phylogenetic tree provides insight into evolution of DRB allelic lineages within Cervidae and may aid in assignment of red deer DRB alleles to specific loci.

  3. Both the nature of KIR3DL1 alleles and the KIR3DL1/S1 allele combination affect the KIR3DL1 NK-cell repertoire in the French population.

    PubMed

    Gagne, Katia; Willem, Catherine; Legrand, Nolwenn; Djaoud, Zakia; David, Gaëlle; Rettman, Pauline; Bressollette-Bodin, Céline; Senitzer, David; Esbelin, Julie; Cesbron-Gautier, Anne; Schneider, Thierry; Retière, Christelle

    2013-04-01

    NK-cell functions are regulated by many activating and inhibitory receptors including KIR3DL1. Extensive allelic polymorphism and variability in expression can directly alter NK-cell phenotype and functions. Here we investigated the KIR3DL1(+) NK-cell repertoire, taking into account the allelic KIR3DL1/S1 polymorphism, KIR3DL1 phenotype, and function. All 109 studied individuals possessed at least one KIR3DL1 allele, with weak KIR3DL1*054, or null alleles being frequently present. In KIR3DL1(high/null) individuals, we observed a bimodal distribution of KIR3DL1(+) NK cells identified by a different KIR3DL1 expression level and cell frequency regardless of a similar amount of both KIR3DL1 transcripts, HLA background, or KIR2D expression. However, this bimodal distribution can be explained by a functional selection following a hierarchy of KIR3DL1 receptors. The higher expression of KIR3DL1 observed on cord blood NK cells suggests the expression of the functional KIR3DL1*004 receptors. Thus, the low amplification of KIR3DL1(high) , KIR3DL1*004 NK-cell subsets during development may be due to extensive signaling via these two receptors. Albeit in a nonexclusive manner, individual immunological experience may contribute to shaping the KIR3DL1 NK-cell repertoire. Together, this study provides new insight into the mechanisms regulating the KIR3DL1 NK-cell repertoire.

  4. Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield

    PubMed Central

    Guo, Mei

    2014-01-01

    Crop improvement for yield and drought tolerance is challenging due to the complex genetic nature of these traits and environmental dependencies. This study reports that transgenic over-expression of Zea mays ARGOS1 (ZAR1) enhanced maize organ growth, grain yield, and drought-stress tolerance. The ZAR1 transgene exhibited environmental interactions, with yield increase under Temperate Dry and yield reduction under Temperate Humid or High Latitude environments. Native ZAR1 allele variation associated with drought-stress tolerance. Two founder alleles identified in the mid-maturity germplasm of North America now predominate in Pioneer’s modern breeding programme, and have distinct proteins, promoters and expression patterns. These two major alleles show heterotic group partitioning, with one predominant in Pioneer’s female and the other in the male heterotic groups, respectively. These two alleles also associate with favourable crop performance when heterozygous. Allele-specific transgene testing showed that, of the two alleles discussed here, each allele differed in their impact on yield and environmental interactions. Moreover, when transgenically stacked together the allelic pair showed yield and environmental performance advantages over either single allele, resembling heterosis effects. This work demonstrates differences in transgenic efficacy of native alleles and the differences reflect their association with hybrid breeding performance. PMID:24218327

  5. Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield.

    PubMed

    Guo, Mei; Rupe, Mary A; Wei, Jun; Winkler, Chris; Goncalves-Butruille, Marymar; Weers, Ben P; Cerwick, Sharon F; Dieter, Jo Ann; Duncan, Keith E; Howard, Richard J; Hou, Zhenglin; Löffler, Carlos M; Cooper, Mark; Simmons, Carl R

    2014-01-01

    Crop improvement for yield and drought tolerance is challenging due to the complex genetic nature of these traits and environmental dependencies. This study reports that transgenic over-expression of Zea mays AR GOS1 (ZAR1) enhanced maize organ growth, grain yield, and drought-stress tolerance. The ZAR1 transgene exhibited environmental interactions, with yield increase under Temperate Dry and yield reduction under Temperate Humid or High Latitude environments. Native ZAR1 allele variation associated with drought-stress tolerance. Two founder alleles identified in the mid-maturity germplasm of North America now predominate in Pioneer's modern breeding programme, and have distinct proteins, promoters and expression patterns. These two major alleles show heterotic group partitioning, with one predominant in Pioneer's female and the other in the male heterotic groups, respectively. These two alleles also associate with favourable crop performance when heterozygous. Allele-specific transgene testing showed that, of the two alleles discussed here, each allele differed in their impact on yield and environmental interactions. Moreover, when transgenically stacked together the allelic pair showed yield and environmental performance advantages over either single allele, resembling heterosis effects. This work demonstrates differences in transgenic efficacy of native alleles and the differences reflect their association with hybrid breeding performance.

  6. SNP-Based Quantification of Allele-Specific DNA Methylation Patterns by Pyrosequencing®.

    PubMed

    Busato, Florence; Tost, Jörg

    2015-01-01

    The analysis of allele-specific DNA methylation patterns has recently attracted much interest as loci of allele-specific DNA methylation overlap with known risk loci for complex diseases and the analysis might contribute to the fine-mapping and interpretation of non-coding genetic variants associated with complex diseases and improve the understanding between genotype and phenotype. In the presented protocol, we present a method for the analysis of DNA methylation patterns on both alleles separately using heterozygous Single Nucleotide Polymorphisms (SNPs) as anchor for allele-specific PCR amplification followed by analysis of the allele-specific DNA methylation patterns by Pyrosequencing(®). Pyrosequencing is an easy-to-handle, quantitative real-time sequencing method that is frequently used for genotyping as well as for the analysis of DNA methylation patterns. The protocol consists of three major steps: (1) identification of individuals heterozygous for a SNP in a region of interest using Pyrosequencing; (2) analysis of the DNA methylation patterns surrounding the SNP on bisulfite-treated DNA to identify regions of potential allele-specific DNA methylation; and (3) the analysis of the DNA methylation patterns associated with each of the two alleles, which are individually amplified using allele-specific PCR. The enrichment of the targeted allele is re-enforced by modification of the allele-specific primers at the allele-discriminating base with Locked Nucleic Acids (LNA). For the proof-of-principle of the developed approach, we provide assay details for three imprinted genes (IGF2, IGF2R, and PEG3) within this chapter. The mean of the DNA methylation patterns derived from the individual alleles corresponds well to the overall DNA methylation patterns and the developed approach proved more reliable compared to other protocols for allele-specific DNA methylation analysis.

  7. The effect of different alleles at the r locus on the synthesis of seed storage proteins in Pisum sativum.

    PubMed

    Turner, S R; Barratt, D H; Casey, R

    1990-05-01

    Rocket immunoelectrophoresis was used to measure the accumulation of storage proteins in developing cotyledons of two Pisum sativum (pea) genotypes, that were close to isogenic except for the nature of the allele at the r locus. There was a marked decrease in legumin accumulation in the rr (wrinkled-seeded) genotype compared to the RR (round-seeded) genotype. The accumulation of vicilin did not differ greatly between the two genotypes. Pulse-labelling studies indicated that the differences in rates of accumulation of legumin between the rr and RR genotypes were a consequence of differences in rates of protein synthesis. Measurements of relative amounts of specific mRNAs, using cDNA clones as probes, showed lower amounts of legumin mRNA in developing cotyledons of the rr, compared to the RR, genotype. Both vicilin mRNAs and convicilin mRNA, the latter of which shows a similar temporal pattern of expression to those of the major legumin species, are relatively unaffected by the nature of the allele at the r locus. Nuclear run-on transcription experiments indicated no differences in the rate of synthesis of legumin transcripts in the rr and RR near-isolines. The consequences of homozygosity for the r allele on storage protein mRNA levels in vitro may be mimicked by manipulating the sucrose concentration of the culture medium.

  8. 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

  9. Observer-based monitoring of heat exchangers.

    PubMed

    Astorga-Zaragoza, Carlos-Manuel; Alvarado-Martínez, Víctor-Manuel; Zavala-Río, Arturo; Méndez-Ocaña, Rafael-Maxim; Guerrero-Ramírez, Gerardo-Vicente

    2008-01-01

    The goal of this work is to provide a method for monitoring performance degradation in counter-flow double-pipe heat exchangers. The overall heat transfer coefficient is estimated by an adaptive observer and monitored in order to infer when the heat exchanger needs preventive or corrective maintenance. A simplified mathematical model is used to synthesize the adaptive observer and a more complex model is used for simulation. The reliability of the proposed method was demonstrated via numerical simulations and laboratory experiments with a bench-scale pilot plant.

  10. Microgravity condensing heat exchanger

    NASA Technical Reports Server (NTRS)

    Thomas, Christopher M. (Inventor); Ma, Yonghui (Inventor); North, Andrew (Inventor); Weislogel, Mark M. (Inventor)

    2011-01-01

    A heat exchanger having a plurality of heat exchanging aluminum fins with hydrophilic condensing surfaces which are stacked and clamped between two cold plates. The cold plates are aligned radially along a plane extending through the axis of a cylindrical duct and hold the stacked and clamped portions of the heat exchanging fins along the axis of the cylindrical duct. The fins extend outwardly from the clamped portions along approximately radial planes. The spacing between fins is symmetric about the cold plates, and are somewhat more closely spaced as the angle they make with the cold plates approaches 90.degree.. Passageways extend through the fins between vertex spaces which provide capillary storage and communicate with passageways formed in the stacked and clamped portions of the fins, which communicate with water drains connected to a pump externally to the duct. Water with no entrained air is drawn from the capillary spaces.

  11. Ion exchange phenomena

    SciTech Connect

    Bourg, I.C.; Sposito, G.

    2011-05-01

    Ion exchange phenomena involve the population of readily exchangeable ions, the subset of adsorbed solutes that balance the intrinsic surface charge and can be readily replaced by major background electrolyte ions (Sposito, 2008). These phenomena have occupied a central place in soil chemistry research since Way (1850) first showed that potassium uptake by soils resulted in the release of an equal quantity of moles of charge of calcium and magnesium. Ion exchange phenomena are now routinely modeled in studies of soil formation (White et al., 2005), soil reclamation (Kopittke et al., 2006), soil fertilitization (Agbenin and Yakubu, 2006), colloidal dispersion/flocculation (Charlet and Tournassat, 2005), the mechanics of argillaceous media (Gajo and Loret, 2007), aquitard pore water chemistry (Tournassat et al., 2008), and groundwater (Timms and Hendry, 2007; McNab et al., 2009) and contaminant hydrology (Chatterjee et al., 2008; van Oploo et al., 2008; Serrano et al., 2009).

  12. Hydrogen and oxygen isotope exchange reactions between clay minerals and water

    USGS Publications Warehouse

    O'Neil, J.R.; Kharaka, Y.K.

    1976-01-01

    The extent of hydrogen and oxygen isotope exchange between clay minerals and water has been measured in the temperature range 100-350?? for bomb runs of up to almost 2 years. Hydrogen isotope exchange between water and the clays was demonstrable at 100??. Exchange rates were 3-5 times greater for montmorillonite than for kaolinite or illite and this is attributed to the presence of interlayer water in the montmorillonite structure. Negligible oxygen isotope exchange occurred at these low temperatures. The great disparity in D and O18 exchange rates observed in every experiment demonstrates that hydrogen isotope exchange occurred by a mechanism of proton exchange independent of the slower process of O18 exchange. At 350?? kaolinite reacted to form pyrophyllite and diaspore. This was accompanied by essentially complete D exchange but minor O18 exchange and implies that intact structural units in the pyrophyllite were inherited from the kaolinite precursor. ?? 1976.

  13. Ion Exchange Separation of the Oxidation State of Vanadium.

    ERIC Educational Resources Information Center

    Cornelius, Richard

    1980-01-01

    Describes an experiment that emphasizes the discrete nature of the different oxidation states of vanadium by the separation of ammonium metavanadate into all four species by ion exchange chromatography. (CS)

  14. Heat exchanger panel

    NASA Technical Reports Server (NTRS)

    Warburton, Robert E. (Inventor); Cuva, William J. (Inventor)

    2005-01-01

    The present invention relates to a heat exchanger panel which has broad utility in high temperature environments. The heat exchanger panel has a first panel, a second panel, and at least one fluid containment device positioned intermediate the first and second panels. At least one of the first panel and the second panel have at least one feature on an interior surface to accommodate the at least one fluid containment device. In a preferred embodiment, each of the first and second panels is formed from a high conductivity, high temperature composite material. Also, in a preferred embodiment, the first and second panels are joined together by one or more composite fasteners.

  15. Alert Exchange Process Protocol

    NASA Technical Reports Server (NTRS)

    Groen, Frank

    2015-01-01

    The National Aeronautics and Space Administration of the United States of America (NASA), and the European Space Agency (ESA), and the Japanese Aerospace Exploration Agency (JAXA), acknowledging that NASA, ESA and JAXA have a mutual interest in exchanging Alerts and Alert Status Lists to enhance the information base for each system participant while fortifying the general level of cooperation between the policy agreement subscribers, and each Party will exchange Alert listings on regular basis and detailed Alert information on a need to know basis to the extent permitted by law.

  16. Microscale Regenerative Heat Exchanger

    NASA Technical Reports Server (NTRS)

    Moran, Matthew E.; Stelter, Stephan; Stelter, Manfred

    2006-01-01

    The device described herein is designed primarily for use as a regenerative heat exchanger in a miniature Stirling engine or Stirling-cycle heat pump. A regenerative heat exchanger (sometimes called, simply, a "regenerator" in the Stirling-engine art) is basically a thermal capacitor: Its role in the Stirling cycle is to alternately accept heat from, then deliver heat to, an oscillating flow of a working fluid between compression and expansion volumes, without introducing an excessive pressure drop. These volumes are at different temperatures, and conduction of heat between these volumes is undesirable because it reduces the energy-conversion efficiency of the Stirling cycle.

  17. Non-Equilibrium Allele Frequency Spectra Via Spectral Methods

    PubMed Central

    Hey, Jody; Chen, Kevin

    2011-01-01

    A major challenge in the analysis of population genomics data consists of isolating signatures of natural selection from background noise caused by random drift and gene flow. Analyses of massive amounts of data from many related populations require high-performance algorithms to determine the likelihood of different demographic scenarios that could have shaped the observed neutral single nucleotide polymorphism (SNP) allele frequency spectrum. In many areas of applied mathematics, Fourier Transforms and Spectral Methods are firmly established tools to analyze spectra of signals and model their dynamics as solutions of certain Partial Differential Equations (PDEs). When spectral methods are applicable, they have excellent error properties and are the fastest possible in high dimension; see [15]. In this paper we present an explicit numerical solution, using spectral methods, to the forward Kolmogorov equations for a Wright-Fisher process with migration of K populations, influx of mutations, and multiple population splitting events. PMID:21376069

  18. New York State TrueAllele® Casework Validation Study*

    PubMed Central

    Perlin, Mark W; Belrose, Jamie L; Duceman, Barry W

    2013-01-01

    DNA evidence can pose interpretation challenges, particularly with low-level or mixed samples. It would be desirable to make full use of the quantitative data, consider every genotype possibility, and objectively produce accurate and reproducible DNA match results. Probabilistic genotype computing is designed to achieve these goals. This validation study assessed TrueAllele® probabilistic computer interpretation on 368 evidence items in 41 test cases and compared the results with human review of the same data. Whenever there was a human result, the computer's genotype was concordant. Further, the computer produced a match statistic on 81 mixture items (for 87 inferred matching genotypes) in the test cases, while human review reported a statistic on 25 of these items (30.9%). Using match statistics to quantify information, probabilistic genotyping was shown to be sensitive, specific, and reproducible. These results demonstrate that objective probabilistic genotyping of biological evidence can reliably preserve DNA identification information. PMID:23865896

  19. Four p67 alleles identified in South African Theileria parva field samples.

    PubMed

    Sibeko, Kgomotso P; Geysen, Dirk; Oosthuizen, Marinda C; Matthee, Conrad A; Troskie, Milana; Potgieter, Frederick T; Coetzer, Jacobus A W; Collins, Nicola E

    2010-02-10

    Previous studies characterizing the Theileria parva p67 gene in East Africa revealed two alleles. Cattle-derived isolates associated with East Coast fever (ECF) have a 129bp deletion in the central region of the p67 gene (allele 1), compared to buffalo-derived isolates with no deletion (allele 2). In South Africa, Corridor disease outbreaks occur if there is contact between infected buffalo and susceptible cattle in the presence of vector ticks. Although ECF was introduced into South Africa in the early 20th century, it has been eradicated and it is thought that there has been no cattle to cattle transmission of T. parva since. The variable region of the p67 gene was amplified and the gene sequences analyzed to characterize South African T. parva parasites that occur in buffalo, in cattle from farms where Corridor disease outbreaks were diagnosed and in experimentally infected cattle. Four p67 alleles were identified, including alleles 1 and 2 previously detected in East African cattle and buffalo, respectively, as well as two novel alleles, one with a different 174bp deletion (allele 3), the other with a similar sequence to allele 3 but with no deletion (allele 4). Sequence variants of allele 1 were obtained from field samples originating from both cattle and buffalo. Allele 1 was also obtained from a bovine that tested T. parva positive from a farm near Ladysmith in the KwaZulu-Natal Province. East Coast fever was not diagnosed on this farm, but the p67 sequence was identical to that of T. parva Muguga, an isolate that causes ECF in Kenya. Variants of allele 2 were obtained from all T. parva samples from both buffalo and cattle, except Lad 10 and Zam 5. Phylogenetic analysis revealed that alleles 3 and 4 are monophyletic and diverged early from the other alleles. These novel alleles were not identified from South African field samples collected from cattle; however allele 3, with a p67 sequence identical to those obtained in South African field samples from

  20. Suppressing exchange effects in diffusion-ordered NMR spectroscopy.

    PubMed

    Aguilar, Juan A; Adams, Ralph W; Nilsson, Mathias; Morris, Gareth A

    2014-01-01

    In diffusion-ordered spectroscopy (DOSY) the aim is to separate signals from different molecular species according to their different diffusion coefficients. Each species has its individual diffusion coefficient (that may accidentally coincide with that of another species, e.g. if they are of very similar size). In exchanging systems, however, there is a serious complication in that the apparent diffusion coefficient of an exchanging signal will be a compromise that depends, among other factors, on the diffusion coefficients of the exchange partners and the rate of exchange between them. The DOSY spectrum will be much harder to interpret and can often give the appearance of extra (spurious) components in the mixture. Here a new and surprisingly simple experiment is described that suppresses the effects of exchange on apparent diffusion coefficients, restoring the simplicity of interpretation enjoyed by non-exchanging systems.

  1. 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.

  2. The Microcephalin Ancestral Allele in a Neanderthal Individual

    PubMed Central

    Lari, Martina; Rizzi, Ermanno; Milani, Lucio; Corti, Giorgio; Balsamo, Carlotta; Vai, Stefania; Catalano, Giulio; Pilli, Elena; Longo, Laura; Condemi, Silvana; Giunti, Paolo; Hänni, Catherine; De Bellis, Gianluca; Orlando, Ludovic; Barbujani, Guido; Caramelli, David

    2010-01-01

    Background The high frequency (around 0.70 worlwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. Methodology/Principal Findings Here we report the first PCR amplification and high- throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination. Conclusions/Significance The MCPH1 genotype of the Monti Lessini (MLS) Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA. PMID:20498832

  3. Generation of humoral immune responses to multi-allele PfAMA1 vaccines; effect of adjuvant and number of component alleles on the breadth of response.

    PubMed

    Kusi, Kwadwo A; Faber, Bart W; Riasat, Vanessa; Thomas, Alan W; Kocken, Clemens H M; Remarque, Edmond J

    2010-11-03

    There is increasing interest in multi-allele vaccines to overcome strain-specificity against polymorphic vaccine targets such as Apical Membrane Antigen 1 (AMA1). These have been shown to induce broad inhibitory antibodies in vitro and formed the basis for the design of three Diversity-Covering (DiCo) proteins with similar immunological effects. The antibodies produced are to epitopes that are shared between vaccine alleles and theoretically, increasing the number of component AMA1 alleles is expected to broaden the antibody response. A plateau effect could however impose a limit on the number of alleles needed to achieve the broadest specificity. Moreover, production cost and the vaccine formulation process would limit the number of component alleles. In this paper, we compare rabbit antibody responses elicited with multi-allele vaccines incorporating seven (three DiCos and four natural AMA1 alleles) and three (DiCo mix) antigens for gains in broadened specificity. We also investigate the effect of three adjuvant platforms on antigen specificity and antibody functionality. Our data confirms a broadened response after immunisation with DiCo mix in all three adjuvants. Higher antibody titres were elicited with either CoVaccine HT™ or Montanide ISA 51, resulting in similar in vitro inhibition (65-82%) of five out of six culture-adapted P. falciparum strains. The antigen binding specificities of elicited antibodies were also similar and independent of the adjuvant used or the number of vaccine component alleles. Thus neither the four extra antigens nor adjuvant had any observable benefits with respect to specificity broadening, although adjuvant choice influenced the absolute antibody levels and thus the extent of parasite inhibition. Our data confirms the feasibility and potential of multi-allele PfAMA1 formulations, and highlights the need for adjuvants with improved antibody potentiation properties for AMA1-based vaccines.

  4. 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.

  5. Molecular definition of an allelic series of mutations disrupting the mouse Lmx1a (dreher) gene.

    PubMed

    Chizhikov, Victor; Steshina, Ekaterina; Roberts, Richard; Ilkin, Yesim; Washburn, Linda; Millen, Kathleen J

    2006-10-01

    Mice homozygous for the dreher (dr) mutation are characterized by pigmentation and skeletal abnormalities and striking behavioral phenotypes, including ataxia, vestibular deficits, and hyperactivity. The ataxia is associated with a cerebellar malformation that is remarkably similar to human Dandy-Walker malformation. Previously, positional cloning identified mutations in LIM homeobox transcription factor 1 alpha gene (Lmx1a) in three dr alleles. Two of these alleles, however, are extinct and unavailable for further analysis. In this article we report a new spontaneous dr allele and describe the Lmx1a mutations in this and six additional dr alleles. Strikingly, deletion null, missense, and frameshift mutations in these alleles all cause similar cerebellar malformations, suggesting that all dr mutations analyzed to date are null alleles.

  6. 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

  7. A Novel Dominant Transformer Allele of the Sex-Determining Gene Her-1 of Caenorhabditis Elegans

    PubMed Central

    Trent, C.; Wood, W. B.; Horvitz, H. R.

    1988-01-01

    We have characterized a novel dominant allele of the sex-determining gene her-1 of Caenorhabditis elegans. This allele, called n695, results in the incomplete transformation of XX animals into phenotypic males. Previously characterized recessive her-1 alleles transform XO animals into phenotypic hermaphrodites. We have identified five new recessive her-1 mutations as intragenic suppressors of n695. Three of these suppressors are weak, temperature-sensitive alleles. We show that the recessive her-1 mutations are loss-of-function alleles, and that the her-1(n695) mutation results in a gain-of-function at the her-1 locus. The existence of dominant and recessive alleles that cause opposite phenotypic transformations demonstrates that the her-1 gene acts to control sexual identity in C. elegans. PMID:3220248

  8. Identification and characterization of novel HLA alleles: Utility of next-generation sequencing methods.

    PubMed

    Brown, Nicholas K; Kheradmand, Taba; Wang, Jinguo; Marino, Susana R

    2016-04-01

    The HLA genes are the most polymorphic of the human genome, and novel HLA alleles are continuously identified, often by clinical Sanger sequencing-based typing (SBT) assays. Introduction of next-generation sequencing (NGS) technologies for clinical HLA typing may significantly improve this process. Here we compare four cases of novel HLA alleles identified and characterized by both SBT and NGS. The tested NGS system sequenced broader regions of the HLA loci, and identified novel polymorphisms undetected by SBT. Subsequent characterization of the novel alleles in isolation of coencoded alleles by SBT required custom-designed primers, while the NGS system was able to sequence both alleles in phase. However, the tested assay was unable to amplify buccal cell DNA for subsequent NGS sequencing, presumably due to the lower quality of these samples. While NGS assays will undoubtedly increase novel allele identification, more stringent DNA sample requirements may be necessary for this new technology.

  9. 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

  10. 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

  11. Allelic Spectra of Risk SNPs Are Different for Environment/Lifestyle Dependent versus Independent Diseases.

    PubMed

    Gorlov, Ivan P; Gorlova, Olga Y; Amos, Christopher I

    2015-07-01

    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.

  12. Sequence of a novel HLA-B*51 allele in a volunteer haematopoietic stem cell donor.

    PubMed

    Cosentini, E; Longhi, E; Frison, S; Luongo, V; Mantovani, M; Ciardiello, G; Bruno, P; Poli, F

    2010-10-01

    We describe a novel HLA-B*51 allele detected by DNA direct sequencing. The sequence of this allele has been officially named B*51:78 as a confirmatory sequence. This new allele nucleotide sequence differs from HLA-B*51:01:01 for two point mutations in exon 2 where codons 79-80 change from CGG-ATC to CGC-ACC (p.Ile80Thr).

  13. Increased prevalence of mutant null alleles that cause hereditary fructose intolerance in the American population.

    PubMed

    Coffee, Erin M; Yerkes, Laura; Ewen, Elizabeth P; Zee, Tiffany; Tolan, Dean R

    2010-02-01

    Mutations in the aldolase B gene (ALDOB) impairing enzyme activity toward fructose-1-phosphate cleavage cause hereditary fructose intolerance (HFI). Diagnosis of the disease is possible by identifying known mutant ALDOB alleles in suspected patients; however, the frequencies of mutant alleles can differ by population. Here, 153 American HFI patients with 268 independent alleles were analyzed to identify the prevalence of seven known HFI-causing alleles (A149P, A174D, N334K, Delta4E4, R59Op, A337V, and L256P) in this population. Allele-specific oligonucleotide hybridization analysis was performed on polymerase chain reaction (PCR)-amplified genomic DNA from these patients. In the American population, the missense mutations A149P and A174D are the two most common alleles, with frequencies of 44% and 9%, respectively. In addition, the nonsense mutations Delta4E4 and R59Op are the next most common alleles, with each having a frequency of 4%. Together, the frequencies of all seven alleles make up 65% of HFI-causing alleles in this population. Worldwide, these same alleles make up 82% of HFI-causing mutations. This difference indicates that screening for common HFI alleles is more difficult in the American population. Nevertheless, a genetic screen for diagnosing HFI in America can be improved by including all seven alleles studied here. Lastly, identification of HFI patients presenting with classic symptoms and who have homozygous null genotypes indicates that aldolase B is not required for proper development or metabolic maintenance.

  14. Giant SCA8 alleles in nine children whose mother has two moderately large ones.

    PubMed

    Corral, Jordi; Genís, David; Banchs, Isabel; San Nicolás, Hector; Armstrong, Judith; Volpini, Víctor

    2005-04-01

    We report here a family in which each of nine children has inherited giant SCA8 CTG expansions from a homozygous mother who has two moderately large SCA8 CTG alleles. In contrast, three homozygous male individuals and a case of coexistence of two expansions of the FRDA gene and one of SCA8, all of them with moderately large alleles, have transmitted their respective SCA8 expanded alleles with minor changes, as usually occurs in heterozygous male transmissions.

  15. 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.

  16. 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

  17. Increased prevalence of mutant null alleles that cause hereditary fructose intolerance in the American population

    PubMed Central

    Coffee, Erin M.; Yerkes, Laura; Ewen, Elizabeth P.; Zee, Tiffany

    2010-01-01

    Mutations in the aldolase B gene (ALDOB) impairing enzyme activity toward fructose-1-phosphate cleavage cause hereditary fructose intolerance (HFI). Diagnosis of the disease is possible by identifying known mutant ALDOB alleles in suspected patients; however, the frequencies of mutant alleles can differ by population. Here, 153 American HFI patients with 268 independent alleles were analyzed to identify the prevalence of seven known HFI-causing alleles (A149P, A174D, N334K, Δ4E4, R59Op, A337V, and L256P) in this population. Allele-specific oligonucleotide hybridization analysis was performed on polymerase chain reaction (PCR)-amplified genomic DNA from these patients. In the American population, the missense mutations A149P and A174D are the two most common alleles, with frequencies of 44% and 9%, respectively. In addition, the nonsense mutations Δ4E4 and R59Op are the next most common alleles, with each having a frequency of 4%. Together, the frequencies of all seven alleles make up 65% of HFI-causing alleles in this population. Worldwide, these same alleles make up 82% of HFI-causing mutations. This difference indicates that screening for common HFI alleles is more difficult in the American population. Nevertheless, a genetic screen for diagnosing HFI in America can be improved by including all seven alleles studied here. Lastly, identification of HFI patients presenting with classic symptoms and who have homozygous null genotypes indicates that aldolase B is not required for proper development or metabolic maintenance. PMID:20033295

  18. Currency Exchange Rates.

    ERIC Educational Resources Information Center

    Siler, Carl R.

    This curriculum unit of the Muncie (Indiana) Southside High School is to simulate the dynamics of foreign currency exchange rates from the perspectives of: (1) a major U.S. corporation, ABB Power T & D Company, Inc., of Muncie, Indiana, a manufacturer of large power transformers for the domestic and foreign markets; and (2) individual…

  19. Chimney heat exchanger

    SciTech Connect

    Whiteley, I.C.

    1981-09-01

    A heat exchanger for installation on the top of a chimney of a building includes a housing having a lower end receiving the top of the chimney and an upper end with openings permitting the escape of effluent from the chimney and a heat exchanger assembly disposed in the housing including a central chamber and a spirally arranged duct network defining an effluent spiral path between the top of the chimney and the central chamber and a fresh air spiral path between an inlet disposed at the lower end of the housing and the central chamber, the effluent and fresh air spiral paths being in heat exchange relationship such that air passing through the fresh air spiral path is heated by hot effluent gases passing upward through the chimney and the effluent spiral path for use in heating the building. A pollution trap can be disposed in the central chamber of the heat exchanger assembly for removing pollutants from the effluent, the pollution trap including a rotating cage carrying pumice stones for absorbing pollutants from the effluent with the surface of the pumice gradually ground off to reveal fresh stone as the cage rotates.

  20. Technology Performance Exchange

    SciTech Connect

    2015-09-01

    To address the need for accessible, high-quality data, the Department of Energy has developed the Technology Performance Exchange (TPEx). TPEx enables technology suppliers, third-party testing laboratories, and other entities to share product performance data. These data are automatically transformed into a format that technology evaluators can easily use in their energy modeling assessments to inform procurement decisions.

  1. Nature's Heat Exchangers.

    ERIC Educational Resources Information Center

    Barnes, George

    1991-01-01

    Discusses the heat-transfer systems of different animals. Systems include heat conduction into the ground, heat transferred by convection, heat exchange in lizards, fish and polar animals, the carotid rete system, electromagnetic radiation from animals and people, and plant and animal fiber optics. (MDH)

  2. Research Exchange, 2002.

    ERIC Educational Resources Information Center

    Research Exchange, 2002

    2002-01-01

    These three issues of the "Research Exchange" focus on how better to conduct disability research and disseminate research results. The first issue examines the topic of human subject/human research participant protection, with a focus on research funded through the National Institute on Disability and Rehabilitation Research (NIDRR). It…

  3. Visiting Scholar Exchange Reports.

    ERIC Educational Resources Information Center

    Rubin, Kyna, Ed.

    1986-01-01

    Provides reports of four United States scholars who visited China as part of the Visiting Scholar Exchange Program. The titles of the reports are (1) "China Journey: A Political Scientist's Look at Yan'an," (2) "The Social Consequences of Land Reclamation in Chinese Coastal Ecosystems," (3) "Anthropology Lectures in South…

  4. Higher Education Exchange

    ERIC Educational Resources Information Center

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

    2009-01-01

    This volume begins with an essay by Noelle McAfee, a contributor who is familiar to readers of Higher Education Exchange (HEX). She reiterates Mathews' argument regarding the disconnect between higher education's sense of engagement and the public's sense of engagement, and suggests a way around the epistemological conundrum of "knowledge…

  5. Microtube strip heat exchanger

    NASA Astrophysics Data System (ADS)

    Doty, F. D.

    1991-04-01

    During the last quarter, Doty Scientific, Inc. (DSI) continued to make progress on the microtube strip (MTS) heat exchangers. The team has begun a heat exchanger stress analysis; however, they have been concentrating the bulk of their analytical energies on a computational fluid dynmaics (CFD) model to determine the location and magnitude of shell-side flow maldistribution which decreases heat exchanger effectiveness. DSI received 120 fineblanked tubestrips from Southern Fineblanking (SFB) for manufacturing process development. Both SFB and NIST provided inspection reports of the tubestrips. DSI completed the tooling required to encapsulate a tube array and press tubestrips on the array. Pressing the tubestrips on tube arrays showed design deficiencies both in the tubestrip design and the tooling design. DSI has a number of revisions in process to correct these deficiencies. The research effort has identified a more economical fusible alloy for encapsulating the tube array, and determined the parameters required to successfully encapsulate the tube array with the new alloy. A more compact MTS heat exchanger bank was designed.

  6. Higher Education Exchange 2006

    ERIC Educational Resources Information Center

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

    2006-01-01

    Contributors to this issue of the Higher Education Exchange debate the issues around knowledge production, discuss the acquisition of deliberative skills for democracy, and examine how higher education prepares, or does not prepare, students for citizenship roles. Articles include: (1) "Foreword" (Deborah Witte); (2) "Knowledge,…

  7. Genome sequencing reveals widespread virulence gene exchange among human Neisseria species.

    PubMed

    Marri, Pradeep Reddy; Paniscus, Mary; Weyand, Nathan J; Rendón, María A; Calton, Christine M; Hernández, Diana R; Higashi, Dustin L; Sodergren, Erica; Weinstock, George M; Rounsley, Steven D; So, Magdalene

    2010-07-28

    Commensal bacteria comprise a large part of the microbial world, playing important roles in human development, health and disease. However, little is known about the genomic content of commensals or how related they are to their pathogenic counterparts. The genus Neisseria, containing both commensal and pathogenic species, provides an excellent opportunity to study these issues. We undertook a comprehensive sequencing and analysis of human commensal and pathogenic Neisseria genomes. Commensals have an extensive repertoire of virulence alleles, a large fraction of which has been exchanged among Neisseria species. Commensals also have the genetic capacity to donate DNA to, and take up DNA from, other Neisseria. Our findings strongly suggest that commensal Neisseria serve as reservoirs of virulence alleles, and that they engage extensively in genetic exchange.

  8. Genome Sequencing Reveals Widespread Virulence Gene Exchange among Human Neisseria Species

    PubMed Central

    Marri, Pradeep Reddy; Paniscus, Mary; Hernández, Diana R.; Higashi, Dustin L.; Sodergren, Erica; Weinstock, George M.; Rounsley, Steven D.; So, Magdalene

    2010-01-01

    Commensal bacteria comprise a large part of the microbial world, playing important roles in human development, health and disease. However, little is known about the genomic content of commensals or how related they are to their pathogenic counterparts. The genus Neisseria, containing both commensal and pathogenic species, provides an excellent opportunity to study these issues. We undertook a comprehensive sequencing and analysis of human commensal and pathogenic Neisseria genomes. Commensals have an extensive repertoire of virulence alleles, a large fraction of which has been exchanged among Neisseria species. Commensals also have the genetic capacity to donate DNA to, and take up DNA from, other Neisseria. Our findings strongly suggest that commensal Neisseria serve as reservoirs of virulence alleles, and that they engage extensively in genetic exchange. PMID:20676376

  9. Chemical exchange program analysis.

    SciTech Connect

    Waffelaert, Pascale

    2007-09-01

    As part of its EMS, Sandia performs an annual environmental aspects/impacts analysis. The purpose of this analysis is to identify the environmental aspects associated with Sandia's activities, products, and services and the potential environmental impacts associated with those aspects. Division and environmental programs established objectives and targets based on the environmental aspects associated with their operations. In 2007 the most significant aspect identified was Hazardous Materials (Use and Storage). The objective for Hazardous Materials (Use and Storage) was to improve chemical handling, storage, and on-site movement of hazardous materials. One of the targets supporting this objective was to develop an effective chemical exchange program, making a business case for it in FY07, and fully implementing a comprehensive chemical exchange program in FY08. A Chemical Exchange Program (CEP) team was formed to implement this target. The team consists of representatives from the Chemical Information System (CIS), Pollution Prevention (P2), the HWMF, Procurement and the Environmental Management System (EMS). The CEP Team performed benchmarking and conducted a life-cycle analysis of the current management of chemicals at SNL/NM and compared it to Chemical Exchange alternatives. Those alternatives are as follows: (1) Revive the 'Virtual' Chemical Exchange Program; (2) Re-implement a 'Physical' Chemical Exchange Program using a Chemical Information System; and (3) Transition to a Chemical Management Services System. The analysis and benchmarking study shows that the present management of chemicals at SNL/NM is significantly disjointed and a life-cycle or 'Cradle-to-Grave' approach to chemical management is needed. This approach must consider the purchasing and maintenance costs as well as the cost of ultimate disposal of the chemicals and materials. A chemical exchange is needed as a mechanism to re-apply chemicals on site. This will not only reduce the quantity of

  10. Homozygosity for the HLA-DRB1 allele selects for extraarticular manifestations in rheumatoid arthritis.

    PubMed Central

    Weyand, C M; Xie, C; Goronzy, J J

    1992-01-01

    Seropositive rheumatoid arthritis is genetically linked to a group of HLA-DRB1 alleles sharing a sequence motif within the third hypervariable region. Controversy exists over the role of the distinct allelic variants in affecting not only the risk to develop disease, but also in modifying the expression of the disease. We have stratified 81 patients according to their patterns of disease manifestations and identified the HLA-DRB1 alleles by polymerase chain reaction amplification and subsequent oligonucleotide hybridization. To identify precisely the allelic combinations at the HLA-DRB1 locus, homozygosity was confirmed by locus-specific cDNA amplification and subsequent sequencing. Our study demonstrated a high correlation of allelic combinations of disease-associated HLA-DRB1 alleles with the clinical manifestations. Characteristic genotypes were identified for patients who had progressed toward nodular disease and patients who had developed major organ involvement. Rheumatoid nodules were highly associated with a heterozygosity for two disease associated HLA-DRB1 alleles. Homozygosity for the HLA-DRB1*0401 allele was a characteristic finding for RA patients with major organ involvement. Our data suggest a role of the disease-associated sequence motif in determining severity of the disease. The finding of a codominant function of HLA-DRB1 alleles suggests that the biological function of HLA-DR molecules in thymic selection might be important in the pathogenesis of RA. Images PMID:1602009

  11. RAET1/ULBP alleles and haplotypes among Kolla South American Indians.

    PubMed

    Cox, Steven T; Arrieta-Bolaños, Esteban; Pesoa, Susanna; Vullo, Carlos; Madrigal, J Alejandro; Saudemont, Aurore

    2013-06-01

    NK cell cytolysis of infected or transformed cells can be mediated by engagement of the activating immunoreceptor NKG2D with one of eight known ligands (MICA, MICB and RAET1E-N) and is essential for innate immunity. As well as diversity of NKG2D ligands having the same function, allelic polymorphism and ethnic diversity has been reported. We previously determined HLA class I allele and haplotype frequencies in Kolla South American Indians who inhabit the northwest provinces of Argentina, and were found to have a similar restricted allelic profile to other South American Indians and novel alleles not seen in other tribes. In our current study, we characterized retinoic acid early transcription-1 (RAET1) alleles by sequencing 58 unrelated Kolla people. Only three of six RAET1 ligands were polymorphic. RAET1E was most polymorphic with five alleles in the Kolla including an allele we previously described, RAET1E*009 (allele frequency (AF) 5.2%). Four alleles of RAET1L were also found and RAET1E*002 was most frequent (AF=78%). Potential functional diversity only affected RAET1E and RAET1L, which were in linkage disequilibrium indicating a selective advantage. The results suggest that limited RAET1 polymorphism in the Kolla was not detrimental to human survival but still necessary and may affect disease susceptibility or severity.

  12. FMR1 alleles in Tasmania: a screening study of the special educational needs population.

    PubMed

    Mitchell, R J; Holden, J J A; Zhang, C; Curlis, Y; Slater, H R; Burgess, T; Kirkby, K C; Carmichael, A; Heading, K D; Loesch, D Z

    2005-01-01

    The distribution of fragile X mental retardation-1 (FMR1) allele categories, classified by the number of CGG repeats, in the population of Tasmania was investigated in 1253 males with special educational needs (SEN). The frequencies of these FMR1 categories were compared with those seen in controls as represented by 578 consecutive male births. The initial screening was based on polymerase chain reaction analysis of dried blood spots. Inconclusive results were verified by Southern analysis of a venous blood sample. The frequencies of common FMR1 alleles in both samples, and of grey zone alleles in the controls, were similar to those in other Caucasian populations. Consistent with earlier reports, we found some (although insignificant) increase of grey zone alleles in SEN subjects compared with controls. The frequencies of predisposing flanking haplotypes among grey zone males FMR1 alleles were similar to those seen in other Caucasian SEN samples. Contrary to expectation, given the normal frequency of grey zone alleles, no premutation (PM) or full mutation (FM) allele was detected in either sample, with only 15 fragile X families diagnosed through routine clinical admissions registered in Tasmania up to 2002. An explanation of this discrepancy could be that the C19th founders of Tasmania carried few PM or FM alleles. The eight to ten generations since white settlement of Tasmania has been insufficient time for susceptible grey zone alleles to evolve into the larger expansions.

  13. 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

  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. Validation study of the TrueAllele automated data review system.

    PubMed

    Kadash, Kristy; Kozlowski, Brian E; Biega, Lisa A; Duceman, Barry W

    2004-07-01

    The New York State Convicted Offender DNA Databank is the first U.S. lab to complete an internal validation of the TrueAllele expert data review system. TrueAllele is designed to assess short tandem repeat (STR) DNA data based on several key features such as peak height, shape, area, and position relative to a standard ladder and use this information to make accurate allele calls. The software then prioritizes the allele calls based on several user-defined rules. As a result, the user need only review low-quality data. The validation of this system consisted of an extensive optimization phase and a large concordance phase. During optimization, the rule settings were tailored to minimize the amount of high-quality data viewed by the user. In the concordance phase, a large dataset was typed in parallel with the ABI software Gene Scan and Genotyper (manual review) and TrueAllele (automated review) for comparison of allele calls and sample state assignment. Only one significant difference was discovered out of 2048 samples in the concordance study. In this case, TrueAllele revealed a spike in the profile that was interpreted as a DNA peak by the analyst in Genotyper. TrueAllele was designed to focus the review on poor data and to eliminate the need for complete reanalysis technical review. This validation project proved TrueAllele to be dependable for use at the NYS Convicted Offender DNA Databank.

  16. Counterflow Regolith Heat Exchanger

    NASA Technical Reports Server (NTRS)

    Zubrin, Robert; Jonscher, Peter

    2013-01-01

    A problem exists in reducing the total heating power required to extract oxygen from lunar regolith. All such processes require heating a great deal of soil, and the heat energy is wasted if it cannot be recycled from processed material back into new material. The counterflow regolith heat exchanger (CoRHE) is a device that transfers heat from hot regolith to cold regolith. The CoRHE is essentially a tube-in-tube heat exchanger with internal and external augers attached to the inner rotating tube to move the regolith. Hot regolith in the outer tube is moved in one direction by a right-hand - ed auger, and the cool regolith in the inner tube is moved in the opposite direction by a left-handed auger attached to the inside of the rotating tube. In this counterflow arrangement, a large fraction of the heat from the expended regolith is transferred to the new regolith. The spent regolith leaves the heat exchanger close to the temperature of the cold new regolith, and the new regolith is pre-heated close to the initial temperature of the spent regolith. Using the CoRHE can reduce the heating requirement of a lunar ISRU system by 80%, reducing the total power consumption by a factor of two. The unique feature of this system is that it allows for counterflow heat exchange to occur between solids, instead of liquids or gases, as is commonly done. In addition, in variants of this concept, the hydrogen reduction can be made to occur within the counterflow heat exchanger itself, enabling a simplified lunar ISRU (in situ resource utilization) system with excellent energy economy and continuous nonbatch mode operation.

  17. A corrosive resistant heat exchanger

    DOEpatents

    Richlen, S.L.

    1987-08-10

    A corrosive and erosive 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 pumped 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. 3 figs., 3 tabs.

  18. The ITALSAT experiment

    NASA Technical Reports Server (NTRS)

    Paraboni, A.

    1989-01-01

    Some information is given on the ITALSAT millimetric waves propagation experiment, which is to be conducted with the ITALSAT satellite, whose launch is foreseen for the middle of 1990. The purpose of the experiment is one of experimenting with advanced technologies and techniques employing the 20/30 GHz bands in wideband telecommunications. Among the most qualified features of this system are the multispot antenna and the exchange function performed directly onboard. Details of the experiment are given.

  19. Distribution of BoLA-DRB3 allelic frequencies and identification of a new allele in the iranian cattle breed sistani (Bos indicus).

    PubMed

    Mohammadi, A; Nassiry, M R; Mosafer, J; Mohammadabadi, M R; Sulimova, G E

    2009-02-01

    The distribution of the frequencies of BoLA-DRB3 gene alleles in the Iranian cattle breed Sistani was studied by the PCR-RFLP ("hemi-nested") assay using restriction endonucleases RsaI, HaeIII and BstYI. In the examined cattle breed (65 animals) 32 alleles have been identified one of which being described for the first time (6.15% frequency). The nucleotide sequence of the polymorphic region of exon 2 of this allele has been determined and submitted in the GeneBank database under accession number DQ486519. The submitted sequence has maximum homology (92%) with the previously described sequence DRB3-mRNA from Bos indicus (AccN X79346) and differs from it by 24 nucleotide substitutions which result in 16 amino acid substitutions. The peptide (on the basis of the reconstructed amino acid sequence) has 89% identity to the sequence encoded by the BIDRBF 188 locus (Bos indicus). The results obtained permit the sequence described by us to be considered as a new allele of the BoLA-DRB3 gene (DRB3.2**X). The total frequency of the main six alleles (DRB3.2*X, *10, *11, *20, *34 and *X) occurring with a frequency of over 5% is about 60% in Iranian Sistani cattle. Fifteen alleles have <1% frequency. The highest frequency was observed for DRB3.2*8 allele (21.54%) like in other previously described breeds of Bos indicus (up to 23.07%). The Iranian breed Sistani has a high level of similarity by the spectrum of BoLA-DRB3 alleles and their frequencies to other Bos indicus breeds and significantly differs by these criteria from the Bos taurus breeds. The Iranian Sistani herd under study includes alleles associated with to resistance to leukemia (DRB3.2*ll and *23) and to different forms of mastitis (DRB3.2*2, *7, *11, *23 and *24) although their frequencies are low (from 0.77 to 5.37%). On the whole, a high level of diversity of BoLA-DRB3 gene alleles and the availability of alleles associated with resistance to different diseases makes this breed of interest for breeding practice.

  20. Laboratory-Scale Column Testing Using IONSIV IE-911 for Removing Cesium from Acidic Tank Waste Simulant. 2: Determination of Cesium Exchange Capacity and Effective Mass Transfer Coefficient from a 500-cm3 Column Experiement

    SciTech Connect

    T.J. Tranter; R.D. Tillotson; T.A. Todd

    2005-04-01

    A semi-scale column test was performed using a commercial form of crystalline silicotitanate (CST) for removing radio-cesium from a surrogate acidic tank solution, which represents liquid waste stored at the Idaho National Engineering and Environmental Laboratory (INEEL). The engineered form of CST ion exchanger, known as IONSIVtmIE-911 (UOP, Mt. Laurel,NJ, USA), was tested in a 500-cm3 column to obtain a cesium breakthrough curve. The cesium exchange capacity of this column matched that obtained from previous testing with a 15-mc3 column. A numerical algorithm using implicit finite difference approximations was developed to solve the governing mass transport equations for the CST columns. An effective mass transfer coefficient was derived from solving these equations for previously reported 15 cm3 tests. The effective mass transfer coefficient was then used to predict the cesium breakthrough curve for the 500-cm3 column and compared to the experimental data reported in this paper. The calculated breakthrough curve showed excellent agreement with the data from the 500-cm3 column even though the interstitial velocity was a factor of two greater. Thus, this approach should provide a reasonable method for scale up to larger columns for treating actual tank waste.

  1. Allele specific-PCR and melting curve analysis showed relatively high frequency of β-casein gene A1 allele in Iranian Holstein, Simmental and native cows.

    PubMed

    Gholami, M; Hafezian, S H; Rahimi, G; Farhadi, A; Rahimi, Z; Kahrizi, D; Kiani, S; Karim, H; Vaziri, S; Muhammadi, S; Veisi, F; Ghadiri, K; Shetabi, H; Zargooshi, J

    2016-10-31

    There are two allelic forms of A1 and A2 of β-casein gene in dairy cattle. Proteolytic digestion of bovine β-casein A1 type produces bioactive peptide of β-casomorphin-7 known as milk devil. β-casomorphin-7 causes many diseases, including type 1 diabetes, cardiovascular disease syndrome, sudden death and madness. The aim of the present study was to determine the different allelic forms of β-casein gene in Iranian Holstein, Simmental and native cattle in order to identify A1 and A2 variants. The blood samples were collected randomly and DNA was extracted using modified salting out method. An 854 bp fragment including part of exon 7 and part of intron 6 of β-casein gene was amplified by allele specific polymerase chain reaction (AS-PCR). Also, the accuracy of AS-PCR genotyping has been confirmed by melting temperature curve analysis using Real-time PCR machinery. The comparison of observed allele and genotype frequency among the studied breeds was performed using the Fisher exact and Chi-squared test, respectively by SAS program. Obtained results showed the A1 allele frequencies of 50, 51.57, 54.5, 49.4 and 46.6% in Holstein, Simmental, Sistani, Taleshi and Mazandarani cattle populations, respectively. The chi-square test was shown that no any populations were in Hardy-Weinberg equilibrium for studied marker locus. Comparison and analysis of the test results for allelic frequency showed no any significant differences between breeds (P>0.05). The frequency of observed genotypes only differs significantly between Holstein and Taleshi breeds but no any statistically significant differences were found for other breeds (P>0.05). A relatively high frequency of β-casein A1 allele was observed in Iranian native cattle. Therefore, determine the genotypes and preference alleles A2 in these native and commercial cattle is recommended.

  2. 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.

  3. T2-Filtered T2 - T2 Exchange NMR

    NASA Astrophysics Data System (ADS)

    d'Eurydice, Marcel Nogueira; Montrazi, Elton Tadeu; Fortulan, Carlos Alberto; Bonagamba, Tito José

    2016-05-01

    This work introduces an alternative way to perform the T2 - T2 Exchange NMR experiment. Rather than varying the number of π pulses in the first CPMG cycle of the T2 - T2 Exchange NMR pulse sequence, as used to obtain the 2D correlation maps, it is fixed and small enough to act as a short T2-filter. By varying the storage time, a set of 1D measurements of T2 distributions can be obtained to reveal the effects of the migration dynamics combined with relaxation effects. This significantly reduces the required time to perform the experiment, allowing a more in-depth study of exchange dynamics and relaxation processes with improved signal-to-noise ratio. These aspects stand as basis of this novel experiment, T2-Filtered T2 - T2 Exchange NMR or simply T2 F-TREx.

  4. 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.

  5. Allelic variation at the VRN-1 promoter region in polyploid wheat.

    PubMed

    Yan, L; Helguera, M; Kato, K; Fukuyama, S; Sherman, J; Dubcovsky, J

    2004-11-01

    Vernalization, the requirement of a long exposure to low temperatures to induce flowering, is an essential adaptation of plants to cold winters. We have shown recently that the vernalization gene VRN-1 from diploid wheat Triticum monococcum is the meristem identity gene APETALA1, and that deletions in its promoter were associated with spring growth habit. In this study, we characterized the allelic variation at the VRN-1 promoter region in polyploid wheat. The Vrn-A1a allele has a duplication including the promoter region. Each copy has similar foldback elements inserted at the same location and is flanked by identical host direct duplications (HDD). This allele was found in more than half of the hexaploid varieties but not among the tetraploid lines analyzed here. The Vrn-A1b allele has two mutations in the HDD region and a 20-bp deletion in the 5' UTR compared with the winter allele. The Vrn-A1b allele was found in both tetraploid and hexaploid accessions but at a relatively low frequency. Among the tetraploid wheat accessions, we found two additional alleles with 32 bp and 54 bp deletions that included the HDD region. We found no size polymorphisms in the promoter region among the winter wheat varieties. The dominant Vrn-A1 allele from two spring varieties from Afghanistan and Egypt ( Vrn-A1c allele) and all the dominant Vrn-B1 and Vrn-D1 alleles included in this study showed no differences from their respective recessive alleles in promoter sequences. Based on these results, we concluded that the VRN-1 genes should have additional regulatory sites outside the promoter region studied here.

  6. 5' and 3' untranslated regions contribute to the differential expression of specific HLA-A alleles.

    PubMed

    René, Céline; Lozano, Claire; Villalba, Martin; Eliaou, Jean-François

    2015-12-01

    In hematopoietic stem cell transplantation (HSCT), when no HLA full-matched donor is available, alternative donors could include one HLA-mismatched donor. Recently, the low expressed HLA-C alleles have been identified as permissive mismatches for the best donor choice. Concerning HLA-A, the degree of variability of expression is poorly understood. Here, we evaluated HLA-A expression in healthy individuals carrying HLA-A*02 allele in different genotypes using flow cytometry and allele-specific quantitative RT-PCR. While an interindividual variability of HLA-A*02 cell surface expression, not due to the allele associated, was observed, no difference of the mRNA expression level was shown, suggesting the involvement of the posttranscriptional regulation. The results of qRT-PCR analyses exhibit a differential expression of HLA-A alleles with HLA-A*02 as the strongest expressed allele independently of the second allele. The associated non-HLA-A*02 alleles were differentially expressed, particularly the HLA-A*31 and HLA-A*33 alleles (strong expression) and the HLA-A*29 (low expression). The presence of specific polymorphisms in the 5' and 3' untranslated regions of the HLA-A*31 and HLA-A*33 alleles could contribute to this high level of expression. As previously described for HLA-C, low-expressed HLA-A alleles, such as HLA-A*29, could be considered as a permissive mismatch, although this needs to be confirmed by clinical studies.

  7. Phosphonic acid based exchange resins

    DOEpatents

    Horwitz, E.P.; Alexandratos, S.D.; Gatrone, R.C.; Chiarizia, R.

    1995-09-12

    An ion exchange resin is described for extracting metal ions from a liquid waste stream. An ion exchange resin is prepared by copolymerizing a vinylidene diphosphonic acid with styrene, acrylonitrile and divinylbenzene. 10 figs.

  8. Phosphonic acid based exchange resins

    DOEpatents

    Horwitz, E. Philip; Alexandratos, Spiro D.; Gatrone, Ralph C.; Chiarizia, Ronato

    1995-01-01

    An ion exchange resin for extracting metal ions from a liquid waste stream. An ion exchange resin is prepared by copolymerizing a vinylidene diphosphonic acid with styrene, acrylonitrile and divinylbenzene.

  9. Identification and DNA sequence analysis of 15 new {alpha}{sub 1}-antitrypsin variants, including two PI*QO alleles and one deficient PI*M allele

    SciTech Connect

    Faber, J.P.; Kirchgesser, M.; Schwaab, R.; Bidlingmaier, F.; Poller, W.; Weidinger, S.; Olek, K. |

    1994-12-01

    The authors have investigated the molecular basis of 15 new {alpha}{sub 1}-antitrypsin ({alpha}1AT) variants. Phenotyping by isoelectric focusing (IEF) was used as a screening method to detect {alpha}1AT variants at the protein level. Genotyping was then performed by sequence analysis of all coding exons, exon-intron junctions, and the hepatocyte-specific promotor region including exon Ic. Three of these rare variants are alleles of clinical relevance, associated with undetectable or very low serum levels of {alpha}1AT: the PI*Q0saarbruecken allele generated by a 1-bp C-nucleotide insertion within a stretch of seven cytosines spanning residues 360-362, resulting in a 3{prime} frameshift and the acquisition of a stop codon at residue 376; a point mutation in the PI*Q0lisbon allele, resulting in a single amino acid substitution Thr{sup 68}(ACC){yields}Ile(ATC); and an in-frame trinucleotide deletion {Delta}Phe{sup 51} (TTC) in the highly deficient PI*Mpalermo allele. The remaining 12 alleles are associated with normal {alpha}1AT serum levels and are characterized by point mutations causing single amino acid substitutions in all but one case. This exception is a silent mutation, which does not affect the amino acid sequence. The limitation of IEF compared with DNA sequence analysis, for identification of new variants, their generation by mutagenesis, and the clinical relevance of the three deficiency alleles are discussed.

  10. Seven novel HLA alleles reflect different mechanisms involved in the evolution of HLA diversity: description of the new alleles and review of the literature.

    PubMed

    Adamek, Martina; Klages, Cornelia; Bauer, Manuela; Kudlek, Evelina; Drechsler, Alina; Leuser, Birte; Scherer, Sabine; Opelz, Gerhard; Tran, Thuong Hien

    2015-01-01

    The human leukocyte antigen (HLA) loci are among the most polymorphic genes in the human genome. The diversity of these genes is thought to be generated by different mechanisms including point mutation, gene conversion and crossing-over. During routine HLA typing, we discovered seven novel HLA alleles which were probably generated by different evolutionary mechanisms. HLA-B*41:21, HLA-DQB1*02:10 and HLA-DQA1*01:12 likely emerged from the common alleles of their groups by point mutations, all of which caused non-synonymous amino acid substitutions. In contrast, a deletion of one nucleotide leading to a frame shift with subsequent generation of a stop codon is responsible for the appearance of a null allele, HLA-A*01:123N. Whereas HLA-B*35:231 and HLA-B*53:31 were probably products of intralocus gene conversion between HLA-B alleles, HLA-C*07:294 presumably evolved by interlocus gene conversion between an HLA-C and an HLA-B allele. Our analysis of these novel alleles illustrates the different mechanisms which may have contributed to the evolution of HLA polymorphism.

  11. Suppression among alleles encoding nucleotide-binding-leucine-rich repeat resistance proteins interferes with resistance in F1 hybrid and allele-pyramided wheat plants.

    PubMed

    Stirnweis, Daniel; Milani, Samira D; Brunner, Susanne; Herren, Gerhard; Buchmann, Gabriele; Peditto, David; Jordan, Tina; Keller, Beat

    2014-09-01

    The development of high-yielding varieties with broad-spectrum durable disease resistance is the ultimate goal of crop breeding. In plants, immune receptors of the nucleotide-binding-leucine-rich repeat (NB-LRR) class mediate race-specific resistance against pathogen attack. When employed in agriculture this type of resistance is often rapidly overcome by newly adapted pathogen races. The stacking of different resistance genes or alleles in F1 hybrids or in pyramided lines is a promising strategy for achieving more durable resistance. Here, we identify a molecular mechanism which can negatively interfere with the allele-pyramiding approach. We show that pairwise combinations of different alleles of the powdery mildew resistance gene Pm3 in F1 hybrids and stacked transgenic wheat lines can result in suppression of Pm3-based resistance. This effect is independent of the genetic background and solely dependent on the Pm3 alleles. Suppression occurs at the post-translational level, as levels of RNA and protein in the suppressed alleles are unaffected. Using a transient expression system in Nicotiana benthamiana, the LRR domain was identified as the domain conferring suppression. The results of this study suggest that the expression of closely related NB-LRR resistance genes or alleles in the same genotype can lead to dominant-negative interactions. These findings provide a molecular explanation for the frequently observed ineffectiveness of resistance genes introduced from the secondary gene pool into polyploid crop species and mark an important step in overcoming this limitation.

  12. Investigating the relationship between FMR1 allele length and cognitive ability in children: a subtle effect of the normal allele range on the normal ability range?

    PubMed

    Loat, C S; Craig, G; Plomin, R; Craig, I W

    2006-09-01

    The FMR1 gene contains a trinucleotide repeat tract which can expand from a normal size of around 30 repeats to over 200 repeats, causing mental retardation (Fragile X Syndrome). Evidence suggests that premutation males (55-200 repeats) are susceptible to a late-onset tremor/ataxia syndrome and females to premature ovarian failure, and that intermediate alleles ( approximately 41-55 repeats) and premutations may be in excess in samples with special educational needs. We explored the relationship between FMR1 allele length and cognitive ability in 621 low ability and control children assessed at 4 and 7 years, as well as 122 students with high IQ. The low and high ability and control samples showed no between-group differences in incidence of longer alleles. In males there was a significant negative correlation between allele length and non-verbal ability at 4 years (p = 0.048), academic achievement in maths (p = 0.003) and English (p = 0.011) at 7 years, and IQ in the high ability group (p = 0.018). There was a significant negative correlation between allele length and a standardised score for IQ and general cognitive ability at age 7 in the entire male sample (p = 0.002). This suggests that, within the normal spectrum of allele length, increased repeat numbers may have a limiting influence on cognitive performance.

  13. Developing Sustainable International Library Exchange Programs: The CUNY-Shanghai Library Faculty Exchange Model

    ERIC Educational Resources Information Center

    Chao, Sheau-yueh J.; Evans, Beth; Phillips, Ryan; Polger, Mark Aaron; Posner, Beth; Sexton, Ellen

    2013-01-01

    This paper describes the City University of New York (CUNY)-Shanghai Librarian Faculty Exchange Program. By observing and working in academic library services at CUNY, Shanghai University (SU), and Shanghai Normal University (SNU), participants were able to teach and learn from their colleagues, bringing their experiences back to further share…

  14. Exchange-dependent relaxation in the rotating frame for slow and intermediate exchange -- modeling off-resonant spin-lock and chemical exchange saturation transfer.

    PubMed

    Zaiss, Moritz; Bachert, Peter

    2013-05-01

    Chemical exchange observed by NMR saturation transfer (CEST) and spin-lock (SL) experiments provide an MRI contrast by indirect detection of exchanging protons. The determination of the relative concentrations and exchange rates is commonly achieved by numerical integration of the Bloch-McConnell equations. We derive an analytical solution of the Bloch-McConnell equations that describes the magnetization of coupled spin populations under radiofrequency irradiation. As CEST and off-resonant SL are equivalent, their steady-state magnetization and dynamics can be predicted by the same single eigenvalue: the longitudinal relaxation rate in the rotating frame R1ρ . For the case of slowly exchanging systems, e.g. amide protons, the saturation of the small proton pool is affected by transverse relaxation (R2b ). It turns out, that R2b is also significant for intermediate exchange, such as amine- or hydroxyl-exchange or paramagnetic CEST agents, if pools are only partially saturated. We propose a solution for R1ρ that includes R2 of the exchanging pool by extending existing approaches, and verify it by numerical simulations. With the appropriate projection factors, we obtain an analytical solution for CEST and SL for nonzero R2 of the exchanging pool, exchange rates in the range 1-10(4) Hz, B1 from 0.1 to 20 μT and arbitrary chemical shift differences between the exchanging pools, whilst considering the dilution by direct water saturation across the entire Z-spectra. This allows the optimization of irradiation parameters and the quantification of pH-dependent exchange rates and metabolite concentrations. In addition, we propose evaluation methods that correct for concomitant direct saturation effects. It is shown that existing theoretical treatments for CEST are special cases of this approach.

  15. Harnessing Private-Sector Innovation to Improve Health Insurance Exchanges.

    PubMed

    Gresenz, Carole Roan; Hoch, Emily; Eibner, Christine; Rudin, Robert S; Mattke, Soeren

    2016-05-09

    Overhauling the individual health insurance market-including through the creation of health insurance exchanges-was a key component of the Patient Protection and Affordable Care Act's multidimensional approach to addressing the long-standing problem of the uninsured in the United States. Despite succeeding in enrolling millions of Americans, the exchanges still face several challenges, including poor consumer experience, high operational and development costs, and incomplete market penetration. In light of these challenges, analysts considered a different model for the exchanges-privately facilitated exchanges-which could address these challenges and deepen the Affordable Care Act's impact. In this model, the government retains control over sovereign exchange functions but allows the private sector to assume responsibility for more-peripheral exchange functions, such as developing and sustaining exchange websites. Although private-sector entities have already undertaken exchange-related functions on a limited basis, privately facilitated exchanges could conceivably relieve the government of its responsibility for front-end website operations and consumer decision-support functions entirely. A shift to privately facilitated exchanges could improve the consumer experience, increase enrollment, and lower costs for state and federal governments. A move to such a model requires, nonetheless, managing its risks, such as reduced consumer protection, increased consumer confusion, and the possible lack of a viable revenue base for privately facilitated exchanges, especially in less populous states. On net, the benefits are large enough and the risks sufficiently manageable to seriously consider such a shift. This paper provides background information and more detail on the analysts' assessment.

  16. Exchange rate rebounds after foreign exchange market interventions

    NASA Astrophysics Data System (ADS)

    Hoshikawa, Takeshi

    2017-03-01

    This study examined the rebounds in the exchange rate after foreign exchange intervention. When intervention is strongly effective, the exchange rate rebounds at next day. The effect of intervention is reduced slightly by the rebound after the intervention. The exchange rate might have been 67.12-77.47 yen to a US dollar without yen-selling/dollar-purchasing intervention of 74,691,100 million yen implemented by the Japanese government since 1991, in comparison to the actual exchange rate was 103.19 yen to the US dollar at the end of March 2014.

  17. Intergranular exchange coupling

    NASA Astrophysics Data System (ADS)

    Muller, M. W.; Indeck, R. S.

    1994-02-01

    We evaluate the exchange interaction between neighboring grains of a polycrystalline magnetic material with uniaxial magnetocrystalline anisotropy, based on the energy of the domain wall formed at the portion of the interface in atomic contact. The analysis suggests that previous work [J.-G. Zhu and H. N. Bertram, in Solid State Physics Vol. 46, edited by H. Ehrenreich and T. Turnbull (Academic, San Diego, 1992)] may underestimate the interaction, and it predicts a different dependence on grain size.

  18. Heat exchange apparatus

    DOEpatents

    Degtiarenko, Pavel V.

    2003-08-12

    A heat exchange apparatus comprising a coolant conduit or heat sink having attached to its surface a first radial array of spaced-apart parallel plate fins or needles and a second radial array of spaced-apart parallel plate fins or needles thermally coupled to a body to be cooled and meshed with, but not contacting the first radial array of spaced-apart parallel plate fins or needles.

  19. Heat exchanger tube mounts

    DOEpatents

    Wolowodiuk, W.; Anelli, J.; Dawson, B.E.

    1974-01-01

    A heat exchanger in which tubes are secured to a tube sheet by internal bore welding is described. The tubes may be moved into place in preparation for welding with comparatively little trouble. A number of segmented tube support plates are provided which allow a considerable portion of each of the tubes to be moved laterally after the end thereof has been positioned in preparation for internal bore welding to the tube sheet. (auth)

  20. New Trends in Magnetic Exchange Bias

    NASA Astrophysics Data System (ADS)

    Mougin, Alexandra; Mangin, Stéphane; Bobo, Jean-Francois; Loidl, Alois

    2005-05-01

    -of-plane exchange bias, depending on the field cooling direction. This is of particular interest since it allows probing of the three-dimensional spin structure of the AF layer. The interface magnetic configuration is extremely important in the perpendicular geometry, as the short-range exchange coupling competes with a long-range dipolar interaction; the induced uniaxial anisotropy must overcome the demagnetization energy to establish perpendicular anisotropy films. Those new studies are of primary importance for the magnetic media industry as perpendicular recording exhibits potential for strongly increased storage densities. 3. Parameters tuning exchange bias in polycrystalline samples and magnetic configurations: Different parameters can be used to tune the exchange bias coupling in polycrystalline samples similar to those used in devices. Particularly fascinating aspects are the questions of the appearance of exchange bias or coercivity in ferromagnet/antiferromagnet heterostructures, and its relation to magnetic configurations formed on either side of the interface. Several papers report on either growth choices or post preparation treatments that enable tuning of the exchange bias in bilayers. The additional complexity and novel features of the exchange coupled interface make the problem particularly rich. 4. Dynamics and magnetization reversal: Linear response experiments, such as ferromagnetic resonance, have been used with great success to identify interface, surface anisotropies and interlayer exchange in multilayer systems. The exchange bias structure is particularly well suited to study because interface driven changes in the spin wave frequencies in the ferromagnet can be readily related to interlayer exchange and anisotropy parameters associated with the antiferromagnet. Because the exchange bias is intimately connected with details of the magnetization process during reversal and the subsequent formation of hysteresis, considerations of time dependence and