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Sample records for allele frequencies observed

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

    SciTech Connect

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

    1993-03-01

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

  2. Statistical Studies on Protein Polymorphism in Natural Populations. III. Distribution of Allele Frequencies and the Number of Alleles per Locus

    PubMed Central

    Chakraborty, Ranajit; Fuerst, Paul A.; Nei, Masatoshi

    1980-01-01

    With the aim of understanding the mechanism of maintenance of protein polymorphism, we have studied the properties of allele frequency distribution and the number of alleles per locus, using gene-frequency data from a wide range of organisms (mammals, birds, reptiles, amphibians, Drosophila and non-Drosophila invertebrates) in which 20 or more loci with at least 100 genes were sampled. The observed distribution of allele frequencies was U-shaped in all of the 138 populations (mostly species or subspecies) examined and generally agreed with the theoretical distribution expected under the mutation-drift hypothesis, though there was a significant excess of rare alleles (gene frequency, 0 ∼ 0.05) in about a quarter of the populations. The agreement between the mutation-drift theory and observed data was quite satisfactory for the numbers of polymorphic (gene frequency, 0.05 ∼ 0.95) and monomorphic (0.95 ∼ 1.0) alleles.—The observed pattern of allele-frequency distribution was incompatible with the prediction from the overdominance hypothesis. The observed correlations of the numbers of rare alleles, polymorphic alleles and monomorphic alleles with heterozygosity were of the order of magnitude that was expected under the mutation-drift hypothesis. Our results did not support the view that intracistronic recombination is an important source of genetic variation. The total number of alleles per locus was positively correlated with molecular weight in most of the species examined, and the magnitude of the correlation was consistent with the theoretical prediction from mutation-drift hypothesis. The correlation between molecular weight and the number of alleles was generally higher than the correlation between molecular weight and heterozygosity, as expected. PMID:17249018

  3. 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.

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

    PubMed Central

    Thompson, E A; Neel, J V

    1997-01-01

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

  5. ALFRED: an allele frequency resource for research and teaching

    PubMed Central

    Rajeevan, Haseena; Soundararajan, Usha; Kidd, Judith R.; Pakstis, Andrew J.; Kidd, Kenneth K.

    2012-01-01

    ALFRED (http://alfred.med.yale.edu) is a free, web accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. Currently, ALFRED has allele frequency tables on over 663 400 polymorphic sites; 170 of them have frequency tables for more than 100 different population samples. In ALFRED, a population may have multiple samples with each ‘sample’ consisting of many individuals on which an allele frequency is based. There are 3566 population samples from 710 different populations with allele frequency tables on at least one polymorphism. Fifty of those population samples have allele frequency data for over 650 000 polymorphisms. Records also have active links to relevant resources (dbSNP, PharmGKB, OMIM, Ethnologue, etc.). The flexible search options and data display and download capabilities available through the web interface allow easy access to the large quantity of high-quality data in ALFRED. PMID:22039151

  6. 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.

  7. 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. PMID:23821598

  8. Robust Identification of Local Adaptation from Allele Frequencies

    PubMed Central

    Günther, Torsten; Coop, Graham

    2013-01-01

    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. PMID:23821598

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2016-03-01

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

  11. Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations.

    PubMed

    Gonzalez-Galarza, Faviel F; Christmas, Stephen; Middleton, Derek; Jones, Andrew R

    2011-01-01

    The allele frequency net database (http://www.allelefrequencies.net) is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. The extensive variability observed in genes and alleles related to the immune system response and its significance in transplantation, disease association studies and diversity in populations led to the development of this electronic resource. At present, the system contains data from 1133 populations in 608,813 individuals on the frequency of genes from different polymorphic regions such as human leukocyte antigens, killer-cell immunoglobulin-like receptors, major histocompatibility complex Class I chain-related genes and a number of cytokine gene polymorphisms. The project was designed to create a central source for the storage of frequency data and provide individuals with a set of bioinformatics tools to analyze the occurrence of these variants in worldwide populations. The resource has been used in a wide variety of contexts, including clinical applications (histocompatibility, immunology, epidemiology and pharmacogenetics) and population genetics. Demographic information, frequency data and searching tools can be freely accessed through the website.

  12. 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

  13. Models of Frequency-Dependent Selection with Mutation from Parental Alleles

    PubMed Central

    Trotter, Meredith V.; Spencer, Hamish G.

    2013-01-01

    Frequency-dependent selection (FDS) remains a common heuristic explanation for the maintenance of genetic variation in natural populations. The pairwise-interaction model (PIM) is a well-studied general model of frequency-dependent selection, which assumes that a genotype’s fitness is a function of within-population intergenotypic interactions. Previous theoretical work indicated that this type of model is able to sustain large numbers of alleles at a single locus when it incorporates recurrent mutation. These studies, however, have ignored the impact of the distribution of fitness effects of new mutations on the dynamics and end results of polymorphism construction. We suggest that a natural way to model mutation would be to assume mutant fitness is related to the fitness of the parental allele, i.e., the existing allele from which the mutant arose. Here we examine the numbers and distributions of fitnesses and alleles produced by construction under the PIM with mutation from parental alleles and the impacts on such measures due to different methods of generating mutant fitnesses. We find that, in comparison with previous results, generating mutants from existing alleles lowers the average number of alleles likely to be observed in a system subject to FDS, but produces polymorphisms that are highly stable and have realistic allele-frequency distributions. PMID:23852384

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

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-01

    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.

  15. 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.

  16. The Joint Allele-Frequency Spectrum in Closely Related Species

    PubMed Central

    Chen, Hua; Green, Richard E.; Pääbo, Svante; Slatkin, Montgomery

    2007-01-01

    We develop the theory for computing the joint frequency spectra of alleles in two closely related species. We allow for arbitrary population growth in both species after they had a common ancestor. We focus on the case in which a single chromosome is sequenced from one of the species. We use classical diffusion theory to show that, if the ancestral species was at equilibrium under mutation and drift and a chromosome from one of the descendant species carries the derived allele, the frequency spectrum in the other species is uniform, independently of the demographic history of both species. We also predict the expected densities of segregating and fixed sites when the chromosome from the other species carries the ancestral allele. We compare the predictions of our model with the site-frequency spectra of SNPs in the four HapMap populations of humans when the nucleotide present in the Neanderthal DNA sequence is ancestral or derived, using the chimp genome as the outgroup. PMID:17603120

  17. Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids.

    PubMed

    Blischak, Paul D; Kubatko, Laura S; Wolfe, Andrea D

    2016-05-01

    Despite the increasing opportunity to collect large-scale data sets for population genomic analyses, the use of high-throughput sequencing to study populations of polyploids has seen little application. This is due in large part to problems associated with determining allele copy number in the genotypes of polyploid individuals (allelic dosage uncertainty-ADU), which complicates the calculation of important quantities such as allele frequencies. Here, we describe a statistical model to estimate biallelic SNP frequencies in a population of autopolyploids using high-throughput sequencing data in the form of read counts. We bridge the gap from data collection (using restriction enzyme based techniques [e.g. GBS, RADseq]) to allele frequency estimation in a unified inferential framework using a hierarchical Bayesian model to sum over genotype uncertainty. Simulated data sets were generated under various conditions for tetraploid, hexaploid and octoploid populations to evaluate the model's performance and to help guide the collection of empirical data. We also provide an implementation of our model in the R package polyfreqs and demonstrate its use with two example analyses that investigate (i) levels of expected and observed heterozygosity and (ii) model adequacy. Our simulations show that the number of individuals sampled from a population has a greater impact on estimation error than sequencing coverage. The example analyses also show that our model and software can be used to make inferences beyond the estimation of allele frequencies for autopolyploids by providing assessments of model adequacy and estimates of heterozygosity.

  18. Haplotypic Background of a Private Allele at High Frequency in the Americas

    PubMed Central

    Schroeder, Kari B.; Jakobsson, Mattias; Crawford, Michael H.; Schurr, Theodore G.; Boca, Simina M.; Conrad, Donald F.; Tito, Raul Y.; Osipova, Ludmilla P.; Tarskaia, Larissa A.; Zhadanov, Sergey I.; Wall, Jeffrey D.; Pritchard, Jonathan K.; Malhi, Ripan S.; Smith, David G.; Rosenberg, Noah A.

    2009-01-01

    Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these assumptions are satisfied, we genotyped 34 single nucleotide polymorphisms across ∼500 kilobases (kb) around D9S1120 in 21 Native American and Western Beringian populations and 54 other worldwide populations. All chromosomes with the 9-repeat allele share the same haplotypic background in the vicinity of D9S1120, suggesting that all sampled copies of the 9-repeat allele are identical by descent. Ninety-one percent of these chromosomes share the same 76.26 kb haplotype, which we call the “American Modal Haplotype” (AMH). Three observations lead us to conclude that the high frequency and widespread distribution of the 9-repeat allele are unlikely to be the result of positive selection: 1) aside from its association with the 9-repeat allele, the AMH does not have a high frequency in the Americas, 2) the AMH is not unusually long for its frequency compared with other haplotypes in the Americas, and 3) in Latin American mestizo populations, the proportion of Native American ancestry at D9S1120 is not unusual compared with that observed at other genomewide microsatellites. Using a new method for estimating the time to the most recent common ancestor (MRCA) of all sampled copies of an allele on the basis of an estimate of the length of the genealogy descended from the MRCA, we calculate the mean time to the MRCA of the 9-repeat allele to be between 7,325 and 39,900 years, depending on the demographic model used. The results support the hypothesis that all

  19. A novel fluorescent quadruplex STR typing system and the allele frequency distributions in a Thai population.

    PubMed

    Yoshimoto, Takashi; Yamamoto, Toshimichi; Mizutani, Masaki; Uchihi, Rieko; Ohtaki, Hiroyuki; Katsumata, Yoshinao; Waiyawuth, Worawee; Songsivilai, Sirirurg

    2003-01-01

    We have previously reported a new triplex amplification and typing system by silver staining for three short tandem repeat (STR) loci, 9q2h2 (D2S3020), D15S233, and D14S299 without "microvariant" alleles such as .1, .2, and, .3 alleles in the Japanese population. In the present study, we established a new quadruplex system with an additional locus D7S809 using primer sets labeled with fluorescent multi-color dyes. Using this system, we genotyped 183 Thai people, found only one "microvariant" allele (allele 20.2) at D7S809, and calculated allele frequencies and some statistical properties at these four STR loci. From these allele frequencies at four STR loci, we performed three statistical analyses including a homozygosity test, a likelihood ratio test, and an exact test for Hardy-Weinberg equilibrium (HWE). Deviations from HWE (p < 0.05) were observed only in the two tests at the locus D7S809. In the present study, we compared the allele frequencies at these four loci in the Thai population to those in the Japanese population described previously. Consequently, all observed heterozygosities and power of discrimination (PD) at those loci in the Thai population were higher than 0.8 and 0.9, respectively, and all statistical values for discriminating power in the Thai population were slightly higher than those in the Japanese population. The combined paternity exclusion rate (combined PE) in the Thai population (0.978) was almost the same as that in the Japanese population (0.971). Therefore, this novel PCR amplification and typing system for four STR loci would be a convenient and informative DNA profiling system in the forensic field. PMID:12570210

  20. VNTR allele frequency distributions under the stepwise mutation model: A computer simulation approach

    SciTech Connect

    Shriver, M.D.; Jin, L.; Chakraborty, R.; Boerwinkle, E. )

    1993-07-01

    Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size, and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). The authors estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. The authors then compared simulation expectations with actual data reported in the literature. They used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, it is hypothesized that these three classes of loci are subject to different mutational forces.

  1. Frequency of CCR5Δ32 allele in healthy Bosniak population.

    PubMed

    Adler, Grażyna; Valjevac, Amina; Skonieczna-Żydecka, Karolina; Mackic-Djurovic, Mirela; Parczewski, Miłosz; Urbańska, Anna; Salkic, Nermin Nusret

    2014-08-28

    Recent evidence has demonstrated the role of CCR5Δ32 in a variety of human diseases: from infectious and inflammatory diseases to cancer. Several studies have confirmed that genetic variants in chemokine receptor CCR5 gene are correlated with susceptibility and resistance to HIV infection. A 32-nucleotide deletion within the CCR5 reading frame is associated with decreased susceptibility to HIV acquisition and a slower progression to AIDS. Mean frequency of CCR5Δ32 allele in Europe is approximately 10%. The highest allele frequency is observed among Nordic populations (about 12%) and lower in the regions of Southeast Mediterranean (about 5%). Although the frequency of CCR5Δ32 was determined in numerous European populations, there is a lack of studies on this variant in the Bosnia and Hercegovina population. Therefore, the aim of our study was to assess the frequency of CCR5Δ32 allele in the cohort of Bosniaks and compare the results with European reports. CCR5Δ32 was detected by sequence-specific PCR in a sample of 100 healthy subjects from Bosnia and Herzegovina (DNA collected 2011-2013). Mean age of the cohort being 58.8 (± 10.7) years, with 82% of women. We identified 17 heterozygotes and one mutant homozygote in study group, with mean ∆32 allele frequency of 9.5%. CCR5∆32 allele frequency among Bosniaks is comparable to that found in Caucasian populations and follows the pattern of the north-southern gradient observed for Europe. Further studies on larger cohorts with adequate female-to-male ratio are necessary.

  2. Frequency of CCR5Δ32 allele in healthy Bosniak population

    PubMed Central

    Adler, Grażyna; Valjevac, Amina; Skonieczna-Żydecka, Karolina; Mackic-Djurovic, Mirela; Parczewski, Miłosz; Urbańska, Anna; Salkic, Nermin N

    2014-01-01

    Recent evidence has demonstrated the role of CCR5Δ32 in a variety of human diseases: from infectious and inflammatory diseases to cancer. Several studies have confirmed that genetic variants in chemokine receptor CCR5 gene are correlated with susceptibility and resistance to HIV infection. A 32-nucleotide deletion within the CCR5 reading frame is associated with decreased susceptibility to HIV acquisition and a slower progression to AIDS. Mean frequency of CCR5Δ32 allele in Europe is approximately 10%. The highest allele frequency is observed among Nordic populations (about 12%) and the lowest in the regions of Southeast Mediterranean (about 5%). Although the frequency of CCR5Δ32 was determined in numerous European populations, there is a lack of studies on this variant in the Bosnia and Herzegovina population. Therefore, the aim of our study was to assess the frequency of CCR5Δ32 allele in the cohort of Bosniaks and compare the results with European reports. CCR5Δ32 was detected by sequence-specific PCR in a sample of 100 healthy Bosniaks (DNA collected 2011-2013). Mean age of the cohort being 58.8 (±10.7) years, with 82% of women. We identified 17 heterozygotes and one mutant homozygote in study group, with mean ∆32 allele frequency of 9.5%. CCR5∆32 allele frequency among Bosniaks is comparable to that found in Caucasian populations and follows the pattern of the north-southern gradient observed for Europe. Further studies on larger cohorts with adequate female-to-male ratio are necessary. PMID:25172974

  3. 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.

  4. Allele frequency of CODIS 13 in Indonesian population.

    PubMed

    Untoro, Evi; Atmadja, Djaja Surya; Pu, Chang-En; Wu, Fang-Chi

    2009-04-01

    Since the first application of DNA technology in 1985 in forensic cases, and the acceptance of this technology in 1988 at court, the DNA typing is widely used in personal identification, parentage cases and tracing the source of biological samples found in the crime scene. The FBI on 1990 had recommended the forensic labs to used 13 loci of Short Tandem Repeats (STR), known as CODIS 13, as the loci of choice for forensic use. The research on the population DNA database on these loci is extremely important for calculating the Paternity Index as well as Matching Probability for forensic application of DNA technology. As many as 402 unrelated persons, consisted of 322 from western part of Indonesia and 80 from eastern part of Indonesia, were chosen as the respondents of this research, after signing the informed consent. The peripheral blood sample was taken using sterile lancets and dropped onto FTA classic cards. The DNA was extracted by FTA purification solution (3x) and TE(-1) (2x), and amplified by PCR mix, either Cofiler or Profiler Plus (Perkin Elmers), followed by sequencing using ABI Prism type 3100 Avant Genetic Analyzer. The analysis showed that the alleles frequencies of Indonesian is specific, different with the other Asian populations with some specific alleles and microvariant were found. PMID:19261522

  5. Intracellular Population Genetics: Evidence for Random Drift of Mitochondrial Allele Frequencies in SACCHAROMYCES CEREVISIAE and SCHIZOSACCHAROMYCES POMBE

    PubMed Central

    Thrailkill, Kathryn M.; Birky, C. William; Lückemann, Gudrun; Wolf, Klaus

    1980-01-01

    We report evidence for random drift of mitochondrial allele frequencies in zygote clones of Saccharomyces cerevisiae and Schizosaccharomyces pombe. Monofactorial and bifactorial crosses were done, using strains resistant or sensitive to erythromycin (alleles ER, ES), oligomycin (OR, OS), or diuron (DR, DS). The frequencies of resistant and sensitive cells (and thus the frequencies of the resistant and sensitive alleles) were determined for each of a number of clones of diploid cells arising from individual zygotes. Allele frequencies were extremely variable among these zygote clones; some clones were "uniparental," with mitochondrial alleles from only one parent present. These observations suggest random drift of the allele frequencies in the population of mitochondrial genes within an individual zygote and its diploid progeny. Drift would cease when all the cells in a clone become homoplasmic, due to segregation of the mitochondrial genomes during vegetative cell divisions. To test this, we delayed cell division (and hence segregation) for varying times by starving zygotes in order to give drift more time to operate. As predicted, delaying cell division resulted in an increase in the variance of allele frequencies among the zygote clones and an increase in the proportion of uniparental zygote clones. The changes in form of the allele frequency distributions resembled those seen during random drift in finite Mendelian populations. In bifactorial crosses, genotypes as well as individual alleles were fixed or lost in some zygote clones. However, the mean recombination frequency for a large number of clones did not increase when cell division was delayed. Several possible molecular mechanisms for intracellular random drift are discussed. PMID:7009322

  6. Allele frequencies of 14 STR loci in the population of Malta.

    PubMed

    Cassar, M; Farrugia, C; Vidal, C

    2008-05-01

    Allele frequencies of 14 STR loci (D13S317, D16S539, D2S1338, vWA, TPOX, D18S51, D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, TH01 and D3S1358) observed in the population of Malta are being reported. Polymerase chain reaction (PCR) amplification using the AmpFl STR Identifiler kit was performed in a random sample of 157 subjects (314 chromosomes). Markers D2S1338, D18S51 and FGA had the highest power of discrimination (PD) values while TPOX was the least informative marker. Allele frequencies observed in the Maltese population were also compared with those of other populations from the Mediterranean region, Europe and Africa. Our data is useful for anthropological and other comparative studies of populations and is powerful for forensic and paternity testing in the Maltese islands.

  7. Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.)

    PubMed Central

    2013-01-01

    Background New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wide distributed SNPs enabling genome wide association studies (GWAS). However, genotyping significant numbers of individuals with large number of SNPs remains prohibitively expensive for many research groups. A possible solution to this problem is to determine allele frequencies from pooled DNA samples, such ‘allelotyping’ has been presented as a cost-effective alternative to individual genotyping and has become popular in human GWAS. In this article we have tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon (Salmo salar L.) populations using an Illumina SNP-chip. Results In total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an Atlantic salmon SNP-chip containing probes for 5568 SNP markers, 3928 of which were bi-allelic. We developed an efficient quality control filter which enables exclusion of loci showing high error rate and minor allele frequency (MAF) close to zero. After applying multiple quality control filters we obtained allele frequency estimates for 3631 bi-allelic loci. We observed high concordance (r > 0.99) between allele frequency estimates derived from individual genotyping and DNA pools. Our results also indicate that even relatively small DNA pools (35 individuals) can provide accurate allele frequency estimates for a given sample. Conclusions Despite of higher level of variation associated with array replicates compared to pool construction, we suggest that both sources of variation should be taken into account. This study demonstrates that DNA pooling allows fast and high-throughput determination of allele frequencies in Atlantic salmon enabling cost

  8. How-To-Do-It: Multiple Allelic Frequencies in Populations at Equilibrium: Algorithms and Applications.

    ERIC Educational Resources Information Center

    Nussbaum, Francis, Jr.

    1988-01-01

    Presents an algorithm for solving problems related to multiple allelic frequencies in populations at equilibrium. Considers sample problems and provides their solution using this tabular algorithm. (CW)

  9. Frequency and characterization of known and novel RHD variant alleles in 37 782 Dutch D-negative pregnant women.

    PubMed

    Stegmann, Tamara C; Veldhuisen, Barbera; Bijman, Renate; Thurik, Florentine F; Bossers, Bernadette; Cheroutre, Goedele; Jonkers, Remco; Ligthart, Peter; de Haas, Masja; Haer-Wigman, Lonneke; van der Schoot, C Ellen

    2016-05-01

    To guide anti-D prophylaxis, Dutch D- pregnant women are offered a quantitative fetal-RHD-genotyping assay to determine the RHD status of their fetus. This allowed us to determine the frequency of different maternal RHD variants in 37 782 serologically D- pregnant women. A variant allele is present in at least 0·96% of Dutch D- pregnant women The D- serology could be confirmed after further serological testing in only 54% of these women, which emphasizes the potential relevance of genotyping of blood donors. 43 different RHD variant alleles were detected, including 15 novel alleles (11 null-, 2 partial D- and 2 DEL-alleles). Of those novel null alleles, one allele contained a single missense mutation (RHD*443C>G) and one allele had a single amino acid deletion (RHD*424_426del). The D- phenotype was confirmed by transduction of human D- erythroblasts, consolidating that, for the first time, a single amino acid change or deletion causes the D- phenotype. Transduction also confirmed the phenotypes for the two new variant DEL-alleles (RHD*721A>C and RHD*884T>C) and the novel partial RHD*492C>A allele. Notably, in three additional cases the DEL phenotype was observed but sequencing of the coding sequence, flanking introns and promoter region revealed an apparently wild-type RHD allele without mutations. PMID:27018217

  10. HLA class II allele and haplotype frequencies in Ethiopian Amhara and Oromo populations.

    PubMed

    Fort, M; de Stefano, G F; Cambon-Thomsen, A; Giraldo-Alvarez, P; Dugoujon, J M; Ohayon, E; Scano, G; Abbal, M

    1998-04-01

    HLA class II alleles were identified in 181 healthy unrelated Ethiopian children of both sexes and in 350 European controls from the South of France. The Ethiopian individuals belonged to the two major ethnic groups of the country: Oromo (N=83) and Amhara (N=98). In both panels, genetic polymorphism of HLA class II alleles was analysed for the first time by molecular typing of DRB1, DQA1 and DQB1 loci. Allelic and phenotypic frequencies were compared with those of European controls and other African populations. Construction of HLA class II three-locus haplotypes was also performed. The study revealed some differences between the two groups. Characteristic features of Central and North African populations appeared on the Ethiopian HLA genotypes. Surprisingly, DRB1*11 presented one of the lowest gene frequencies in both Ethiopian ethnic groups in contrast to Europeans and West Africans. Furthermore, this decrease was more marked than those observed using serological techniques in other geographically close East African countries. Oromo and Amhara only showed minor differences in spite of their different origins and histories. One significant difference consisted of a lower DRB1*01 gene frequency in Oromo as reported in most West African people. Some new or rare haplotypes were also observed in the Oromo group. Our results underline the distinctive features of the Ethiopian populations among the few HLA genotyping data available for East African groups and emphasise the major interest of such investigations in this region of Africa.

  11. Allele frequency distribution of CYP2C9 2 and CYP2C9 3 polymorphisms in six Mexican populations.

    PubMed

    Castelán-Martínez, Osvaldo D; Hoyo-Vadillo, Carlos; Sandoval-García, Emmanuel; Sandoval-Ramírez, Lucila; González-Ibarra, Miriam; Solano-Solano, Gloria; Gómez-Díaz, Rita A; Parra, Esteban J; Cruz, Miguel; Valladares-Salgado, Adán

    2013-07-10

    Allele frequency differences of functional CYP2C9 polymorphisms are responsible for some of the variation in drug response observed in human populations. The most relevant CYP2C9 functional variants are CYP2C9*2 (rs1799853) and CYP2C9 3 (rs1057910). These polymorphisms show variation in allele frequencies among different population groups. The present study aimed to analyze these polymorphisms in 947 Mexican-Mestizo from Mexico City and 483 individuals from five indigenous Mexican populations: Nahua, Teenek, Tarahumara, Purepecha and Huichol. The CYP2C9*2 allele frequencies in the Mestizo, Nahua and Teenek populations were 0.051, 0.007 and 0.005, respectively. As for CYP2C9 3, the allelic frequencies in the Mestizo, Nahua and Teenek populations were 0.04, 0.005 and 0.005, respectively. The CYP2C9 2 and CYP2C9 3 alleles were not observed in the Tarahumara, Purepecha and Huichol populations. These findings are in agreement with previous studies reporting very low allele frequencies for these polymorphisms in American Indigenous populations.

  12. Phylogenetic relationship analysis of Iranians and other world populations using allele frequencies at 12 polymorphic markers.

    PubMed

    Fazeli, Zahra; Vallian, Sadeq

    2012-12-01

    The estimation of genetic distance between populations could improve our viewpoint about human migration and its genetic origin. In this study, we used allele frequency data of 12 polymorphic markers on 250 individuals (500 alleles) from the Iranian population to estimate genetic distance between the Iranians and other world populations. The phylogenetic trees for three different sets of allele frequency data were constructed. Our results revealed the genetic similarity between the Iranians and European populations. The lowest genetic distance was observed between the Iranians and some populations reside in Russia. Furthermore, the high genetic distance was observed between the Iranians and East Asian populations. The data suggested that the Iranians might have relatively close evolutionary history with Europeans, but historically independent from East Asian populations. The evaluation of genetic distance between Indians populations and Iranians was also performed. The Indian groups showed low genetic distance with others, but high genetic distance with the Iranians. This study could provide a new insight into the evolutionary history of the Iranian population.

  13. Frequencies of Null Alleles at Enzyme Loci in Natural Populations of Ponderosa and Red Pine

    PubMed Central

    Allendorf, Fred W.; Knudsen, Kathy L.; Blake, George M.

    1982-01-01

    Pinus ponderosa and P. resinosa population samples have mean frequencies of enzymatically inactive alleles of 0.0031 and 0.0028 at 29 and 27 enzyme loci, respectively. Such alleles are rare and are apparently maintained by selection-mutation balance. Ponderosa pine have much higher amounts of allozymic and polygenic phenotypic variation than red pine, yet both species have similar frequencies of null alleles. Thus, null alleles apparently do not contribute to polygenic variation, as has been suggested. The concordance between allozymic and polygenic variation adds support to the view that allozyme studies may be valuable in predicting the relative amount of polygenic variation in populations. PMID:17246067

  14. 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.

  15. Global distribution of allele frequencies at the human dopamine D4 receptor locus

    SciTech Connect

    Chang, F.M.; Kidd, J.R.; Livak, K.J.

    1994-09-01

    The dopamine D4 receptor (DRD4) is a candidate gene for schizophrenia because the dopaminergic system has been implicated in this neuropsychiatric disorder. Several research groups have reported an association between allelic variants at DRD4 and schizophrenia, while others have been unable to replicate that finding. Knowledge of the appropriate gene frequencies in the underlying populations may resolve these inconsistencies. We have determined the frequencies of 8 different alleles of the 48 bp imperfect tandem repeat of exon 3 at the DRD4 locus in samples from 33 populations around the world. The frequencies vary considerably in the different populations with the most common allele ranging from 16% to 95%. Frequencies and Fst values will be presented for the 3 most common alleles (4-, 7-, and 2- repeat) by continental groupings, but the individual populations vary significantly around the averages. The populations averaged 4.3 alleles (range 2 to 7).

  16. Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection.

    PubMed

    Hofer, T; Ray, N; Wegmann, D; Excoffier, L

    2009-01-01

    Several studies have found strikingly different allele frequencies between continents. This has been mainly interpreted as being due to local adaptation. However, demographic factors can generate similar patterns. Namely, allelic surfing during a population range expansion may increase the frequency of alleles in newly colonised areas. In this study, we examined 772 STRs, 210 diallelic indels, and 2834 SNPs typed in 53 human populations worldwide under the HGDP-CEPH Diversity Panel to determine to which extent allele frequency differs among four regions (Africa, Eurasia, East Asia, and America). We find that large allele frequency differences between continents are surprisingly common, and that Africa and America show the largest number of loci with extreme frequency differences. Moreover, more STR alleles have increased rather than decreased in frequency outside Africa, as expected under allelic surfing. Finally, there is no relationship between the extent of allele frequency differences and proximity to genes, as would be expected under selection. We therefore conclude that most of the observed large allele frequency differences between continents result from demography rather than from positive selection.

  17. Dombrock genotyping in Brazilian blood donors reveals different regional frequencies of the HY allele

    PubMed Central

    Piassi, Fabiana Chagas Camargos; Santos, Silvana Maria Eloi; de Castilho, Lilian Maria; Baleotti Júnior, Wilson; Suzuki, Rodrigo Buzinaro; da Cunha, Débora Moura

    2013-01-01

    Background Dombrock blood group system genotyping has revealed various rearrangements of the Dombrock gene and identified new variant alleles in Brazil (i.e., DO*A-SH, DO*A-WL and DO*B-WL). Because of the high heterogeneity of the Brazilian population, interregional differences are expected during the investigation of Dombrock genotypes. Objective The present study aims to determine the frequencies of Dombrock genotypes in blood donors from Minas Gerais and compare the frequencies of the HY and JO alleles to those of another population in Brazil. Methods The frequencies of the DO alleles in Minas Gerais, a southeastern state of Brazil, were determined from the genotyping of 270 blood donors. Genotyping involved polymerase chain reaction and restriction fragment length polymorphism analysis to identify the 323G>T, 350C>T, 793A>G, and 898C>G mutations, which are related to the HY, JO, DO*A/DO*B, and DO*A-WL/DO*B-WL alleles, respectively. Moreover, the frequencies of rare HY and JO alleles were statistically compared using the chi-square test with data from another Brazilian region. Results The HY allele frequency in Minas Gerais (2.4%) was almost twice that of the JO allele (1.5%). The frequency of the HY allele was significantly higher (p-value = 0.001) than that in another Brazilian population and includes a rare homozygous donor with the Hy- phenotype. In addition, the DO*A-WL and DO*B-WL alleles, which were first identified in Brazil, were found in the state of Minas Gerais. Conclusions The data confirm that the frequencies of DO alleles differ between regions in Brazil. The population of Minas Gerais could be targeted in a screening strategy to identify the Hy- phenotype in order to develop a rare blood bank. PMID:24478605

  18. Frequency of HLA-A alleles in the Syrian population genotyped by sequence-based typing.

    PubMed

    Madania, A; Ghoury, I; Al-Ashkar, W; Nweder, S; Zarzour, H

    2014-10-01

    HLA-A molecules are highly polymorphic. Their accurate typing at a high-resolution level is crucial for successful organ, bone marrow and cord blood transplantation. Furthermore, several HLA alleles have been involved in susceptibility to autoimmune diseases, allergies, cancers and inflammations. In order to determine common HLA-A alleles in Syria and their frequencies, sequence-based typing (SBT) was used to genotype HLA-A alleles at high resolution (four digit level) among one hundred and thirty randomly selected Syrian individuals. Exons 2, 3 and 4 of the HLA-A gene were amplified by PCR and sequenced. The sbt-engine software was used for allele assignment. Ambiguities were solved using group-specific sequencing primers (GSSPs). We could identify 32 different HLA-A alleles which were divided into 3 groups: high frequency (approximately 10%, A*01:01; A*24:02; A*03:01; A*02:01), moderate frequency (approximately 3%, such as A*02:05, A*31:01 and A*33:01), and low frequency (approximately 1%, such as A*02:11, A*29:01, A*02:02 and A*36:01). Homozygosity rate was higher than expected (11.5% vs. 7.15%). For high frequency alleles, our results show similarity to neighbouring countries. However, 15 alleles (such as A*02:04, A*02:06, A*02:11 and A*02:17) found in our cohort in low frequencies were never reported in some or all neighbouring countries. This is the first report on HLA-A allele frequencies in Syria. In spite of the relatively low number of tested subjects, our results revealed a high degree of diversity, with 32 different alleles, reflecting the high ethnic heterogeneity of the Syrian population. The identification of alleles rarely or never reported in neighbouring countries indicates a higher genetic diversity in Syria.

  19. Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon.

    PubMed

    da Costa Francez, Pablo Abdon; Rodrigues, Elzemar Martins Ribeiro; Frazão, Gleycianne Furtado; Dos Reis Borges, Nathalia Danielly; Dos Santos, Sidney Emanuel Batista

    2011-01-01

    The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (F(ST) coefficients) to the present database ranged from F(ST) = 0.0016 between Macapá and Belém to F(ST) = 0.0036 between Macapá and the Iberian Peninsula.

  20. Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon

    PubMed Central

    da Costa Francez, Pablo Abdon; Rodrigues, Elzemar Martins Ribeiro; Frazão, Gleycianne Furtado; dos Reis Borges, Nathalia Danielly; dos Santos, Sidney Emanuel Batista

    2011-01-01

    The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (FST coefficients) to the present database ranged from FST = 0.0016 between Macapá and Belém to FST = 0.0036 between Macapá and the Iberian Peninsula. PMID:21637540

  1. Allele frequency distributions of D1S80 in the Polish population.

    PubMed

    Ciesielka, M; Kozioł, P; Krajka, A

    1996-08-15

    The polymorphism of the D1S80 locus has been analyzed in a population sample of 208 unrelated individuals in the Southeast Poland and 103 mother/child pairs. PCR amplified alleles were separated by a vertical discontinuous polyacrylamide gel electrophoresis system. Nineteen different alleles and 52 phenotypes could be distinguished. The alleles 18 (f = 0.267) and 24 (f = 0.300) were most common in Poland. D1S80 genotype frequencies of Poland population do not deviate from Hardy-Weinberg equilibrium. All mother/child pairs shared at least one D1S80 allele.

  2. ApoE allele frequencies in Italian sporadic and familial Alzheimer's disease.

    PubMed

    Sorbi, S; Nacmias, B; Forleo, P; Latorraca, S; Gobbini, I; Bracco, L; Piacentini, S; Amaducci, L

    1994-08-15

    Recent studies have provided evidence of association of apolipoprotein E (ApoE) epsilon 4 allele and late onset familial and sporadic Alzheimer's disease (AD). Epidemiological studies have established allelic variation at the ApoE locus. We have analyzed the ApoE gene polymorphism in a sample of 446 Italian subjects. Our data confirm a significant association between epsilon 4 allele and sporadic AD. The frequency of epsilon 4 allele in early onset familial AD patients was comparable to control values suggesting that epsilon 4 allele does not represent a risk factor for early onset familial AD (EOFAD). Moreover, we found a not previously reported association between ApoE epsilon 2 allele and sporadic AD and EOFAD. PMID:7824157

  3. Power of IRT in GWAS: successful QTL mapping of sum score phenotypes depends on interplay between risk allele frequency, variance explained by the risk allele, and test characteristics.

    PubMed

    van den Berg, Stéphanie M; Service, Susan K

    2012-12-01

    As data from sequencing studies in humans accumulate, rare genetic variants influencing liability to disease and disorders are expected to be identified. Three simulation studies show that characteristics and properties of diagnostic instruments interact with risk allele frequency to affect the power to detect a quantitative trait locus (QTL) based on a test score derived from symptom counts or questionnaire items. Clinical tests, that is, tests that show a positively skewed phenotypic sum score distribution in the general population, are optimal to find rare risk alleles of large effect. Tests that show a negatively skewed sum score distribution are optimal to find rare protective alleles of large effect. For alleles of small effect, tests with normally distributed item parameters give best power for a wide range of allele frequencies. The item-response theory framework can help understand why an existing measurement instrument has more power to detect risk alleles with either low or high frequency, or both kinds.

  4. Worldwide allele frequencies of the human apolipoprotein E gene: climate, local adaptations, and evolutionary history.

    PubMed

    Eisenberg, Dan T A; Kuzawa, Christopher W; Hayes, M Geoffrey

    2010-09-01

    The epsilon4 allele of the apolipoprotein E (APOE) gene is associated with increased cholesterol levels and heart disease. Population allele frequencies of APOE have previously been shown to vary, with epsilon4 frequencies generally increasing with latitude. We hypothesize that this trend resulted from natural selection protecting against low-cholesterol levels. In high-latitude cold environments and low-latitude hot environments, metabolic rate is elevated, which could require higher cholesterol levels. To explore this hypothesis, we compiled APOE allele frequencies, latitude, temperature, and elevation from populations around the world. epsilon4 allele frequencies show a curvilinear relationship with absolute latitude, with lowest frequencies found in the mid-latitudes where temperatures generally require less expenditure on cooling/thermogenesis. Controlling for population structure in a subset of populations did not appreciably change this pattern of association, consistent with selection pressures that vary by latitude shaping epsilon4 allele frequencies. Temperature records also predict APOE frequency in a curvilinear fashion, with lowest epsilon4 frequencies at moderate temperatures. The model fit between historical temperatures and epsilon4 is less than between latitude and epsilon4, but strengthened after correcting for estimated temperature differences during the Paleolithic. Contrary to our hypothesis, we find that elevation did not improve predictive power, and an integrated measure of the cholesterol effect of multiple APOE alleles was less related to latitude than was epsilon4 alone. Our results lend mixed support for a link between past temperature and human APOE allele distribution and point to the need to develop better models of past climate in future analyses.

  5. 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.

  6. Allele frequency distribution of 10 MiniSTRs in the Pashtun population of Pakistan.

    PubMed

    Shafique, Muhammad; Shahzad, Muhammad Saqib; Perveen, Uzma; Parveen, Rukhsana; Ali, Azam; Hussain, Manzoor; Rehman, Ziaur; Shahid, Ahmad Ali; Husnain, Tayyab

    2015-05-01

    Two hundred individual samples of Pashtun population from Khyber Pakhtunkhwa province of Pakistan were randomly evaluated through 10 MiniSTR loci (CSF1PO, D7S820, TPOX, D18S51, D2S1338, D13S317, FGA, D5S818, D21S11, and D16S539). The PCR product size was reduced in the range of 65 to 280 bp. A total of 112 alleles were observed containing allelic frequency ranging from 0.0025 to 0.4325. Statistical values for forensic and parentage analysis were calculated including combined power of discrimination (PD), combined power of exclusion (PE), and cumulative probability of matching (PM) and equaled to 0.99999999999768, 0.99984944, and 2.33 × 10(-12), respectively. These MiniSTRs show a high degree of polymorphism information content and discriminatory power which would be helpful to resolve forensic cases and establish DNA database for major population groups of Pakistan. In contrast to different populations, significant differences were also observed on these loci. PMID:25821203

  7. Determination of the allelic frequencies of an L-myc and a p53 polymorphism in human lung cancer.

    PubMed

    Weston, A; Ling-Cawley, H M; Caporaso, N E; Bowman, E D; Hoover, R N; Trump, B F; Harris, C C

    1994-04-01

    The L-myc and p53 genes have been implicated in lung cancer. Both of these genes have restriction fragment length polymorphisms (RFLPs) that could account for differential expression or activity of variant forms. An EcoRI restriction site in the L-myc gene was previously reported to be a predictor of poor prognosis in Japanese lung cancer patients. There are several RFLPs in the p53 gene. In exon 4 there is a polymorphism that codes for either an arginine or proline residue at codon 72. We previously reported the frequency of DNA-RFLPs at these gene loci revealed by EcoRI and AccII respectively. Here we report results from a study comparing lung cancer cases (n = 31) with chronic obstructive pulmonary disease controls (n = 49). No association was found between these RFLPs and disease status. Previous observations that the frequencies of these RFLPs varied by race were confirmed. The p53 arginine allele was found to be more common in Caucasians (0.71) than African-Americans (0.50). The EcoRI restriction site present allele in L-myc was more frequent in African-Americans (0.71) than Caucasians (0.49). Thus, the allelic frequency for L-myc was similar in African-Americans to that reported for Japanese, and the allelic frequency for p53 was similar in Caucasians to that reported for Japanese.

  8. Unequal allelic frequencies at the self-incompatibility locus within local populations of Prunus avium L.: an effect of population structure?

    PubMed

    Stoeckel, S; Castric, V; Mariette, S; Vekemans, X

    2008-05-01

    In this paper, we investigated the genetic structure and distribution of allelic frequencies at the gametophytic self-incompatibility locus in three populations of Prunus avium L. In line with theoretical predictions under balancing selection, genetic structure at the self-incompatibility locus was almost three times lower than at seven unlinked microsatellites. Furthermore, we found that S-allele frequencies in wild cherry populations departed significantly from the expected isoplethic distribution towards which balancing selection is expected to drive allelic frequencies (i.e. identical frequency equal to the inverse of the number of alleles in the population). To assess whether this departure could be caused either by drift alone or by population structure, we used numerical simulations to compare our observations with allelic frequency distributions expected : (1) within a single deme from a subdivided population with various levels of differentiation; and (2) within a finite panmictic population with identical allelic diversity. We also investigated the effects of sample size and degree of population structure on tests of departure from isoplethic equilibrium. Overall, our results showed that the observed allele frequency distributions were consistent with a model of subdivided population with demes linked by moderate migration rate.

  9. Analysis and frequency of bovine lymphocyte antigen DRB3.2 alleles in Jersey cows.

    PubMed

    Gilliespie, B E; Jayarao, B M; Dowlen, H H; Oliver, S P

    1999-09-01

    Jersey cows (n = 172) were genotyped for the bovine lymphocyte antigen (BoLA)-DRB3.2 allele by polymerase chain reaction and restriction fragment length polymorphism analysis. Bovine DNA was isolated from aliquots of whole blood. A two-step polymerase chain reaction followed by digestion with restriction endonucleases RsaI, BstyI, and HaeIII was conducted on the DNA from Jersey cattle. Twenty-four BoLA-DRB3.2 alleles were identified with frequencies ranging from 0.3 to 22.9%. Thirteen allele types were similar to those reported previously; and 11 were new allele types that have not been reported previously. Allele types reported previously include: BoLA-DRB3.2*2, *8, *10, *15, *17, *20, *21, *22, *23, *25, *28, *36, and *37. Their frequencies were 0.3, 11.3, 22.9, 13.6, 5.5, 3.7, 10.7, 3.5, 0.9, 0.3, 4.7, 9.3, and 0.9%, respectively. Of the new allele types detected, *ibe occurred at the highest frequency (6.1%) in Jersey cows from this herd. The six most frequently isolated alleles (BoLA-DRB3.2*8, *10, *15, *21, *36, and *ibe) accounted for 73.9% of the alleles in the population of this herd. Results of this study demonstrate that the BoLA-DRB3.2 locus is highly polymorphic in Jersey cattle.

  10. HLA Allele Frequencies in 5802 Koreans: Varied Allele Types Associated with SJS/TEN According to Culprit Drugs

    PubMed Central

    Park, Hye Jung; Kim, Young Joo; Kim, Dong Hyun; Kim, Junho; Park, Kyung Hee; Park, Jung-Won

    2016-01-01

    Purpose Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are very serious forms of drug-induced cutaneous adverse reaction. SJS/TEN induced by certain drug is well known to be associated with some human leukocyte antigen (HLA) gene type. We aimed to explore HLA allele frequencies and their association with SJS/TEN according to culprit drugs in Korea. Materials and Methods We enrolled 5802 subjects who had results of HLA typing test from August 2005 to July 2014. Total 28 SJS/TEN patients were categorized based on culprit drugs (allopurinol, lamotrigine, carbamazepine) and identified the presence of HLA-B*58:01, HLA-B*44:03, HLA-B*15:02, and HLA-A*31:01. Results HLA-A*24:02 (20.5%), HLA-B*44:03 (10.0%), and HLA-Cw*01:02 (17.1%) were the most frequent type in HLA-A, -B, and -C genes, respectively. Allele frequencies of HLA-B*58:01, HLA-B*44:03, HLA-A*31:01, and HLA-B*15:02 were 7.0%, 10.0%, 5.0%, and 0.3%, respectively. In 958 allopurinol users, 9 subjects (0.9%) were diagnosed with SJS/TEN. Among them, 8 subjects possessed HLA-B*58:01 allele. SJS/TEN induced by allopurinol was more frequently developed in subjects with HLA-B*58:01 than in subjects without it [odds ratio: 57.4; confidence interval (CI) 7.12-463.50; p<0.001]. Allopurinol treatment, based on screening by HLA-B*58:01 genotyping, could be more cost-effective than that not based on screening. HLA-B*44:03 may be associated with lamotrigine-induced SJS/TEN (odds ratio: 12.75; CI 1.03-157.14; p=0.053). Among carbamazepine users, only two patients experienced SJS/TEN and possessed neither HLA-B*15:02 nor HLA-A*31:03. Conclusion HLA gene frequencies varied in Korea. Screening of HLA-B*58:01 before the use of allopurinol might be needed to anticipate probability of SJS/TEN. PMID:26632391

  11. [RHD 1227A allele frequency among Rh negative population and random population].

    PubMed

    Wu, Jun-Jie; Hong, Xiao-Zhen; Xu, Xian-Guo; Ma, Kai-Rong; Zhu, Fa-Ming; Yan, Li-Xing

    2006-12-01

    To investigate the frequency of RHD 1227A allele in Rh negative population and random population, an AS-PCR (allele specific-polymerase chain reaction) method was employed to detect RHD 1227A allele. RHD gene copy was determined by D zygosity test and RHD exon 9 nucleotide sequence analysis. The results showed that among 143 Rh negative donors, forty-one RHD 1227A allele carriers were detected, and 8 (19.51%) out of which were RhCCdee, 32 (78.05%) were RhCcdee, and 1 (2.44%) was RhCcdEe. Thirty-five Rh negative RHD 1227A carriers had RHD gene deletion, and the remaining carriers were RHD 1227A homozygous. Seven (1.43%) individuals were detected with RHD 1227A allele among 489 random donors. They were all G/A heterozygous at RHD 1227 site. Serological test indicated that they were normal Rh positive phenotype. It is concluded that the frequency of RHD 1227A allele is 16.43% among Rh negative population and 0.72% among the random population.

  12. Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly.

    PubMed

    Fountain, Toby; Nieminen, Marko; Sirén, Jukka; Wong, Swee Chong; Hanski, Ilkka

    2016-03-01

    Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction.

  13. Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile.

    PubMed

    Vergara, Ismael A; Villouta, Pamela; Herrera, Sandra; Melo, Francisco

    2012-05-01

    The thirteen autosomal STR loci of the CODIS system were typed from DNA of 732 unrelated male individuals sampled from different locations in Chile. This is the first report of allele frequencies for the thirteen STRs loci defined in the CODIS system from the Chilean population.

  14. Human acetylator polymorphism: estimate of allele frequency in Libya and details of global distribution.

    PubMed Central

    Karim, A K; Elfellah, M S; Evans, D A

    1981-01-01

    Acetylator phenotyping by means of a sulphadimidine tests revealed 65% of Libyan Arabs to be slow acetylators. Hence the frequency of the allele controlling slow acetylation (As) is estimated as q = 0.81 +/- 0.05. This estimate is similar to those previously recorded in European and adjacent Middle Eastern populations. PMID:7328611

  15. Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution

    PubMed Central

    Jónás, Ágnes; Taus, Thomas; Kosiol, Carolin; Schlötterer, Christian; Futschik, Andreas

    2016-01-01

    The effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-seq). Pool-seq is cost-effective and often outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: Additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling, which increases the variance of allele frequency estimates. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide Ne estimates, we extend our method using a recursive partitioning approach to estimate Ne locally along the chromosome. Since the type I error is controlled, our method permits the identification of genomic regions that differ significantly in their Ne estimates. We present an application to Pool-seq data from experimental evolution with Drosophila and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R package at https://github.com/ThomasTaus/Nest. PMID:27542959

  16. Allele frequency data of 15 autosomal STR loci in four major population groups of South Africa.

    PubMed

    Lucassen, Anton; Ehlers, Karen; Grobler, Paul J; Shezi, Adeline L

    2014-03-01

    Allele frequency distributions for 15 tetrameric short tandem repeat (STR) loci were determined using the AmpFlSTR® Identifiler Plus™ PCR amplification kit. There was little evidence of departures from Hardy-Weinberg equilibrium or association of alleles of different loci in the population samples. The probability of identity values for the different populations range from 1/3.3 × 10(17) (White) to 1/1.88 × 10(18) (Coloured). The combined probability of paternal exclusion for the different population groups ranges from 0.9995858 (Coloured) to 0.9997874 (Indian).

  17. DNA-PKcs mutations in dogs and horses: allele frequency and association with neoplasia.

    PubMed

    Ding, Qi; Bramble, Lori; Yuzbasiyan-Gurkan, Vilma; Bell, Thomas; Meek, Katheryn

    2002-01-23

    Previously, spontaneous genetic immunodeficiencies in mice, Arabian foals, and recently in Jack Russell terriers have been ascribed to defects in DNA-PKcs (catalytic subunit of the DNA dependent protein kinase) expression. In severe combined immunodeficiency (SCID) foals, a 5 bp deletion at codon 9480 results in a frameshift and a 967 amino acid deletion from the C terminus (including the entire PI3 kinase domain) and an unstable mutant protein. In SCID mice, a single base pair mutation results in a premature stop codon and deletion of 83 amino acids; as in SCID foals, the mutant protein is unstable. Here, we define the mutation within the canine DNA-PKcs gene that results in SCID. In this case, a point mutation results in a stop codon at nucleotide 10,828 and premature termination at a position 517 amino acids before the normal C terminus resulting in a functionally null allele. Thus, this is the third documentation of a spontaneous germline mutation in the C terminus of DNA-PKcs. Emerging data implicate DNA repair factors as potential tumor suppressors. Here, we have ascertained the carrier frequency of the defective DNA-PKcs genes in Arabian horses and in Jack Russell terriers. Our data indicate (in good agreement with a previous report) that the carrier frequency of the equine SCID allele is approximately 8%; in contrast, the carrier frequency of the canine SCID allele is less than 1.1%. We also assessed the frequency of the equine SCID allele in a series of 295 tumors from Arabian horses. We find a statistically significant correlation between the development of a virally induced tumor (sarcoid) and heterozygosity for the equine SCID allele. These data provide further support for an emerging consensus: that DNA-PK may normally act as a tumor suppressor through its caretaker role in maintaining chromosomal stability. PMID:11867233

  18. Frequency of the CCR5-delta32 allele in Brazilian populations: A systematic literature review and meta-analysis.

    PubMed

    Silva-Carvalho, Wlisses Henrique Veloso; de Moura, Ronald Rodrigues; Coelho, Antonio Victor Campos; Crovella, Sergio; Guimarães, Rafael Lima

    2016-09-01

    The CCR5 is a chemokine receptor widely expressed by several immune cells that are engaged in inflammatory responses. Some populations have individuals exhibiting a 32bp deletion in the CCR5 gene (CCR5-delta32) that produces a truncated non-functional protein not expressed on the cell surface. This polymorphism, known to be associated with susceptibility to infectious and inflammatory diseases, such as osteomyelitis, pre-eclampsia, systemic lupus erythematous, juvenile idiopathic arthritis, rheumatoid arthritis and HIV/AIDS, is more commonly found in European populations with average frequency of 10%. However, it is also possible to observe a significant frequency in other world populations, such as the Brazilian one. We performed a systematic review and meta-analysis of CCR5-delta32 genetic association studies in Brazilian populations throughout the country to estimate the frequency of this polymorphism. We also compared CCR5-delta32 frequencies across Brazilian regions. The systematic literature reviewed studies involving delta32 allele in Brazilian populations published from 1995 to 2015. Among the reviewed literature, 25 studies including 30 Brazilian populations distributed between the North, Northeast, South and Southeast regions were included in our meta-analysis. We observed an overall allelic frequency of 4% (95%-CI, 0.03-0.05), that was considered moderate and, notably, higher than some European populations, such as Cyprus (2.8%), Italy (3%) and Greece (2.4%). Regarding the regional frequency comparisons between North-Northeast (N-NE) and South-Southeast (S-SE) regions, we observed an allelic frequency of 3% (95%-CI, 0.02-0.04) and 4% (95%-CI, 0.03-0.05), respectively. The populations from S-SE regions had a slightly higher CCR5-delta32 frequency than N-NE regions (OR=1.41, p=0.002). Although there are several studies about the CCR5-delta32 polymorphism and its effect on the immune response of some infectious diseases, this report is the first meta

  19. High Resolution Human Leukocyte Antigen Class I Allele Frequencies and HIV-1 Infection Associations in Chinese Han and Uyghur Cohorts

    PubMed Central

    Liu, Yanhou; Zhao, Zhongfang; Li, Tianyi; Liao, Qi; Kushner, Nicholas; Touzjian, Neal Y.; Shao, Yiming; Sun, Yongtao; Strong, Amie J.; Lu, Yichen

    2012-01-01

    Background Host immunogenetic factors such as HLA class I polymorphism are important to HIV-1 infection risk and AIDS progression. Previous studies using high-resolution HLA class I profile data of Chinese populations appeared insufficient to provide information for HIV-1 vaccine development and clinical trial design. Here we reported HLA class I association with HIV-1 susceptibility in a Chinese Han and a Chinese Uyghur cohort. Methodology/Principal Findings Our cohort included 327 Han and 161 Uyghur ethnic individuals. Each cohort included HIV-1 seropositive and HIV-1 seronegative subjects. Four-digit HLA class I typing was performed by sequencing-based typing and high-resolution PCR-sequence specific primer. We compared the HLA class I allele and inferred haplotype frequencies between HIV-1 seropositive and seronegative groups. A neighbor-joining tree between our cohorts and other populations was constructed based on allele frequencies of HLA-A and HLA-B loci. We identified 58 HLA-A, 75 HLA-B, and 32 HLA-Cw distinct alleles from our cohort and no novel alleles. The frequency of HLA-B*5201 and A*0301 was significantly higher in the Han HIV-1 negative group. The frequency of HLA-B*5101 was significantly higher in the Uyghur HIV-1 negative group. We observed statistically significant increases in expectation-maximization (EM) algorithm predicted haplotype frequencies of HLA-A*0201-B*5101 in the Uyghur HIV-1 negative group, and of Cw*0304-B*4001 in the Han HIV-1 negative group. The B62s supertype frequency was found to be significantly higher in the Han HIV-1 negative group than in the Han HIV-1 positive group. Conclusions At the four-digit level, several HLA class I alleles and haplotypes were associated with lower HIV-1 susceptibility. Homogeneity of HLA class I and Bw4/Bw6 heterozygosity were not associated with HIV-1 susceptibility in our cohort. These observations contribute to the Chinese HLA database and could prove useful in the development of HIV-1 vaccine

  20. Increased TNFA*2, but not TNFB*1, allele frequency in Spanish atopic patients.

    PubMed

    Castro, J; Tellería, J J; Linares, P; Blanco-Quirós, A

    2000-01-01

    Tumor necrosis factor (TNF) is a potent proinflammatory cytokine involved in asthma and atopy. Increased TNF-alpha levels have been found in airway biopsies and bronchoalveolar lavage fluids from asthmatic patients. Constitutional variations in the TNF-alpha secretion levels in vitro are associated with molecular polymorphisms located within and around the TNF loci. Our study objective was to investigate the association between atopy and two described di-allelic polymorphisms in the TNF locus: a G to A transition at position -308 in the 5'-promoter region of the TNFA gene (TNFA*1 and TNFA*2 alleles) and an Ncol restriction fragment length polymorphism (RFLP) in the first intron of the TNFB gene (TNFB*1 and TNFB*2 alleles). The genetic study was performed in 65 unrelated atopic patients and 60 healthy controls. The regions of interest were amplified from genomic DNA using specific primers and polymerase chain reaction. SSP-PCR analysis for TNFA -308 polymorphism genotyping and endonuclease digestion analysis for the TNFB Ncol RFLP were used. The frequency of the TNFA*2 allele was significantly higher in atopic subjects compared to the control group (38.5% vs. 10.5%; chi2 = 32.06; p <0.0001). The TNFA*2 allele is associated with a higher risk for the development of atopy (risk ratio = 9.44; EF = 0.65; chi2 = 30.06 p <0.0005). On the other hand, no significant association between the TNFB alleles and atopy was found. In conclusion, the TNFA*2 allele could be also a genetic risk marker for the predisposition to atopy in our population, as has been reported in other studies. Either the TNFA gene itself or a linked gene on chromosome region 6p21, which has yet to be identified, is a candidate gene for susceptibility to atopy. PMID:10923589

  1. Genotype and allele frequency of CYP2C19*17 in a healthy Iranian population

    PubMed Central

    Payan, Maryam; Tajik, Nader; Rouini, Mohammad Reza; Ghahremani, Mohammad Hossein

    2015-01-01

    Background: Cytochrome P450 2C19 (CYP2C19) is important in metabolism of wide range of drugs. CYP2C19*17 is a novel variant allele which increases gene transcription and therefore results in ultra-rapid metabolizer phenotype (URM). Distribution of this variant allele has not been well studied worldwide. The aim of present study was to investigate allele and genotype frequencies of CYP2C19*17 in a healthy Iranian population and compare them with other ethnic groups. Methods: One hundred eighty healthy unrelated Iranian volunteer took part in this study and were genotyped for CYP2C19 *2, *3, *17 (-3402) by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and CYP2C19*17 (-806) by a nested-PCR assays. The distribution of CYP2C19*17 polymorphism in Iranian population was then compared with other ethnic groups. Results: The CYP2C19*17 allele frequency was 21.6% in Iranian population. Among studied subjects 5.5% were homozygous for CYP2C19*17 and phenotyped as ultra-rapid metabolizers; 28.8% were genotyped as CYP2C19*1*17 (extensive metabolizers) and 3.3% as CYP2C19*2*17 (intermediate metabolizers). Conclusion: The CYP2C19*17 genetic distribution in Iranian population is similar to Middle East or European countries. The high frequency of CYP2C19*17 in Iranian population highlights the importance of this new variant allele in metabolism of CYP2C19 substrates. Thus, future association studies are required to reveal clinical consequence of this genetic polymorphism in carrier individuals. PMID:26793660

  2. A method for estimating the intensity of overdominant selection from the distribution of allele frequencies.

    PubMed Central

    Slatkin, M; Muirhead, C A

    2000-01-01

    A method is proposed for estimating the intensity of overdominant selection scaled by the effective population size, S = 2Ns, from allele frequencies. The method is based on the assumption that, with strong overdominant selection, allele frequencies are nearly at their deterministic equilibrium values and that, to a first approximation, deviations depend only on S. Simulations verify that reasonably accurate estimates of S can be obtained for realistic sample sizes. The method is applied to data from several loci in the major histocompatibility complex (Mhc) in numerous human populations. For alleles distinguished by both serological typing and the sequence of the peptide-binding region, our estimates of S are comparable to those obtained by analysis of DNA sequences in showing that selection is strongest on HLA-B and weaker on HLA-A, HLA-DRB1, and HLA-DQA1. The intensity of selection on HLA-B varied considerably among populations. Two populations, Native American and Inuit, showed an excess rather than a deficiency in homozygosity. Comparable estimates of S were obtained for alleles at Mhc class II loci distinguished by serological reactions (serotyping) and by differences in the amino acid sequences of the peptide-binding region (molecular typing). A comparison of two types of data for DQA1 and DRB1 showed that serotyping led to generally lower estimates of S. PMID:11102400

  3. Allele frequency data for 15 autosomal STR loci in eight Indonesian subpopulations.

    PubMed

    Venables, Samantha J; Daniel, Runa; Sarre, Stephen D; Soedarsono, Nurtami; Sudoyo, Herawati; Suryadi, Helena; van Oorschot, Roland A H; Walsh, Simon J; Widodo, Putut T; McNevin, Dennis

    2016-01-01

    Evolutionary and cultural history can affect the genetic characteristics of a population and influences the frequency of different variants at a particular genetic marker (allele frequency). These characteristics directly influence the strength of forensic DNA evidence and make the availability of suitable allele frequency information for every discrete country or jurisdiction highly relevant. Population sub-structure within Indonesia has not been well characterised but should be expected given the complex geographical, linguistic and cultural architecture of the Indonesian population. Here we use forensic short tandem repeat (STR) markers to identify a number of distinct genetic subpopulations within Indonesia and calculate appropriate population sub-structure correction factors. This data represents the most comprehensive investigation of population sub-structure within Indonesia to date using these markers. The results demonstrate that significant sub-structure is present within the Indonesian population and must be accounted for using island specific allele frequencies and corresponding sub-structure correction factors in the calculation of forensic DNA match statistics.

  4. The impact of library preparation protocols on the consistency of allele frequency estimates in Pool-Seq data.

    PubMed

    Kofler, Robert; Nolte, Viola; Schlötterer, Christian

    2016-01-01

    Sequencing pools of individuals (Pool-Seq) is a cost-effective method to determine genome-wide allele frequency estimates. Given the importance of meta-analyses combining data sets, we determined the influence of different genomic library preparation protocols on the consistency of allele frequency estimates. We found that typically no more than 1% of the variation in allele frequency estimates could be attributed to differences in library preparation. Also read length had only a minor effect on the consistency of allele frequency estimates. By far, the most pronounced influence could be attributed to sequence coverage. Increasing the coverage from 30- to 50-fold improved the consistency of allele frequency estimates by at least 27%. We conclude that Pool-Seq data can be easily combined across different library preparation methods, but sufficient sequence coverage is key to reliable results.

  5. Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly

    PubMed Central

    Fountain, Toby; Nieminen, Marko; Sirén, Jukka; Wong, Swee Chong; Lehtonen, Rainer; Hanski, Ilkka

    2016-01-01

    Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction. PMID:26903642

  6. Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly.

    PubMed

    Fountain, Toby; Nieminen, Marko; Sirén, Jukka; Wong, Swee Chong; Hanski, Ilkka

    2016-03-01

    Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction. PMID:26903642

  7. Reducing bias of allele frequency estimates by modeling SNP genotype data with informative missingness.

    PubMed

    Lin, Wan-Yu; Liu, Nianjun

    2012-01-01

    The presence of missing single-nucleotide polymorphism (SNP) genotypes is common in genetic studies. For studies with low-density SNPs, the most commonly used approach to dealing with genotype missingness is to simply remove the observations with missing genotypes from the analyses. This naïve method is straightforward but is valid only when the missingness is random. However, a given assay often has a different capability in genotyping heterozygotes and homozygotes, causing the phenomenon of "differential dropout" in the sense that the missing rates of heterozygotes and homozygotes are different. In practice, differential dropout among genotypes exists in even carefully designed studies, such as the data from the HapMap project and the Wellcome Trust Case Control Consortium. Under the assumption of Hardy-Weinberg equilibrium and no genotyping error, we here propose a statistical method to model the differential dropout among different genotypes. Compared with the naïve method, our method provides more accurate allele frequency estimates when the differential dropout is present. To demonstrate its practical use, we further apply our method to the HapMap data and a scleroderma data set. PMID:22719749

  8. New CODIS core loci allele frequencies for 96,400 Brazilian individuals.

    PubMed

    Aguiar, Vitor R C; de Castro, Amanda M; Almeida, Vanessa C O; Malta, Frederico S V; Ferreira, Alessandro C S; Louro, Iúri D

    2014-11-01

    We have reported the allele frequencies of 15 STR loci, including the original 13 CODIS core loci, in over 100,000 Brazilian individuals. A new CODIS core loci has been proposed, but the recently established Brazilian Integrated Network of DNA Databases made a decision in 2010 to postpone the implementation of this new set of loci due to the lack of allele frequency data for the Brazilian population. We aimed to report allele frequencies of 20 loci, estimated from 96,400 Brazilian individuals undergoing paternity testing during 2011-2013. The percentage of missing data was less than 0.6% for all loci, except for CSF1PO (3.15%) and D7S820 (2.5%). The dropout rates estimated by the MicroDrop software were 0.013 for CSF1PO, 0.000037 for D7S820 and less than 0.000001 for other loci. Small missing data percentages and dropout rates reflect the high quality of the data.

  9. Detection of Allelic Frequency Differences between the Sexes in Humans: A Signature of Sexually Antagonistic Selection

    PubMed Central

    Lucotte, Elise A.; Laurent, Romain; Heyer, Evelyne; Ségurel, Laure; Toupance, Bruno

    2016-01-01

    Sexually antagonistic (SA) selection, a form of selection that can occur when both sexes have different fitness optima for a trait, is a major force shaping the evolution of organisms. A seminal model developed by Rice (Rice WR. 1984. Sex chromosomes and the evolution of sexual dimorphism. Evolution 38:735–742.) predicts that the X chromosome should be a hotspot for the accumulation of loci under SA selection as compared with the autosomes. Here, we propose a methodological framework designed to detect a specific signature of SA selection on viability, differences in allelic frequencies between the sexes. Applying this method on genome-wide single nucleotide polymorphism (SNP) data in human populations where no sex-specific population stratification could be detected, we show that there are overall significantly more SNPs exhibiting differences in allelic frequencies between the sexes on the X chromosome as compared with autosomes, supporting the predictions of Rice’s model. This pattern is consistent across populations and is robust to correction for potential biases such as differences in linkage disequilibrium, sample size, and genotyping errors between chromosomes. Although SA selection is not the only factor resulting in allelic frequency differences between the sexes, we further show that at least part of the identified X-linked loci is caused by such a sex-specific processes. PMID:27189992

  10. HLA-A, -B and -DR allele and haplotype frequencies in Malays.

    PubMed

    Dhaliwal, J S; Shahnaz, M; Too, C L; Azrena, A; Maiselamah, L; Lee, Y Y; Irda, Y A; Salawati, M

    2007-03-01

    One thousand four hundreds and forty-five Malays registered with the Malaysian Marrow Donor Registry were typed for HLA-A, HLA-B and HLA-DR. Fifteen HLA-A, twenty nine HLA-B and fourteen HLA-DR alleles were detected. The most common HLA-A alleles and their frequencies were HLA-A24 (0.35), HLA-A11 (0.21) and HLA-A2 (0.15). The most common HLA-B alleles were HLA-B15 (0.26), HLA-B35 (0.11) and HLA-B18 (0.10) while the most common HLA-DR alleles were HLA-DR15 (0.28), HLA-DR12 (0.27) and HLA-DR7 (0.10). A24-B15-DR12 (0.047), A24-B15-DR15 (0.03) and the A24-B35-DR12 (0.03) were the most frequent haplotypes. This data may be useful in determining the probability of finding a matched donor and for estimating the incidence of HLA associated diseases.

  11. Combining allele frequency uncertainty and population substructure corrections in forensic DNA calculations.

    PubMed

    Cowell, Robert

    2016-07-01

    In forensic DNA calculations of relatedness of individuals and in DNA mixture analyses, at least two sources of uncertainty are present concerning the allele frequencies used for evaluating genotype probabilities when evaluating likelihoods. They are: (i) imprecision in the estimates of the allele frequencies in the population by using an inevitably finite database of DNA profiles to estimate them; and (ii) the existence of population substructure. Green and Mortera [6] showed that these effects may be taken into account individually using a common Dirichlet model within a Bayesian network formulation, but that when taken in combination this is not the case; however they suggested an approximation that could be used. Here we develop a slightly different approximation that is shown to be exact in the case of a single individual. We demonstrate the numerical closeness of the approximation using a published database of allele counts, and illustrate the effect of incorporating the approximation into calculations of a recently published statistical model of DNA mixtures. PMID:27231804

  12. An historical perspective on "The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus".

    PubMed

    Kidd, Kenneth K; Pakstis, Andrew J; Yun, Libing

    2014-04-01

    Human population genetics is a completely different science today compared to two decades ago, at least at the empiric level. Our paper [Chang (Hum Genet 98:91-101, 1996a)] demonstrated that three different alleles were common when one considered many populations although other low frequency alleles occurred. Because previous work had been largely done on European subjects, our findings involved 36 distinct populations and showed that East Asian populations had nearly lost the 7-repeat allele, and that Native American populations had the highest frequencies of that allele globally, was a significant early empiric demonstration of the potential magnitude of population variation at important genes. There are thousands of loci tested on many of the same populations and the gene frequency pattern seen for the DRD4 7-repeat allele is seen at other loci, arguing that this pattern commonly reflects the pattern of divergence of populations and accumulated random genetic drift.

  13. Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

    PubMed Central

    2012-01-01

    Background The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identification of genetic variants underlying complex traits and although technologies are improving rapidly, high-throughput sequencing of large numbers of complete individual genomes remains prohibitively expensive. Therefore using a pooled DNA approach coupled with target enrichment and high-throughput sequencing, the aim of this study was to identify polymorphisms and estimate allele frequency differences across 83 candidate genes of the somatotrophic axis, in 150 Holstein-Friesian dairy bulls divided into two groups divergent for genetic merit for fertility. Results In total, 4,135 SNPs and 893 indels were identified during the resequencing of the 83 candidate genes. Nineteen percent (n = 952) of variants were located within 5' and 3' UTRs. Seventy-two percent (n = 3,612) were intronic and 9% (n = 464) were exonic, including 65 indels and 236 SNPs resulting in non-synonymous substitutions (NSS). Significant (P < 0.01) mean allele frequency differentials between the low and high fertility groups were observed for 720 SNPs (58 NSS). Allele frequencies for 43 of the SNPs were also determined by genotyping the 150 individual animals (Sequenom® MassARRAY). No significant differences (P > 0.1) were observed between the two methods for any of the 43 SNPs across both pools (i.e., 86 tests in total). Conclusions The results of the current study support previous findings of the use of DNA sample pooling and high-throughput sequencing as a viable strategy for polymorphism discovery and allele frequency estimation. Using this approach we have characterised the genetic variation within genes of the somatotrophic axis and related pathways, central to mammalian post

  14. The non-equilibrium allele frequency spectrum in a Poisson random field framework.

    PubMed

    Kaj, Ingemar; Mugal, Carina F

    2016-10-01

    In population genetic studies, the allele frequency spectrum (AFS) efficiently summarizes genome-wide polymorphism data and shapes a variety of allele frequency-based summary statistics. While existing theory typically features equilibrium conditions, emerging methodology requires an analytical understanding of the build-up of the allele frequencies over time. In this work, we use the framework of Poisson random fields to derive new representations of the non-equilibrium AFS for the case of a Wright-Fisher population model with selection. In our approach, the AFS is a scaling-limit of the expectation of a Poisson stochastic integral and the representation of the non-equilibrium AFS arises in terms of a fixation time probability distribution. The known duality between the Wright-Fisher diffusion process and a birth and death process generalizing Kingman's coalescent yields an additional representation. The results carry over to the setting of a random sample drawn from the population and provide the non-equilibrium behavior of sample statistics. Our findings are consistent with and extend a previous approach where the non-equilibrium AFS solves a partial differential forward equation with a non-traditional boundary condition. Moreover, we provide a bridge to previous coalescent-based work, and hence tie several frameworks together. Since frequency-based summary statistics are widely used in population genetics, for example, to identify candidate loci of adaptive evolution, to infer the demographic history of a population, or to improve our understanding of the underlying mechanics of speciation events, the presented results are potentially useful for a broad range of topics.

  15. The non-equilibrium allele frequency spectrum in a Poisson random field framework.

    PubMed

    Kaj, Ingemar; Mugal, Carina F

    2016-10-01

    In population genetic studies, the allele frequency spectrum (AFS) efficiently summarizes genome-wide polymorphism data and shapes a variety of allele frequency-based summary statistics. While existing theory typically features equilibrium conditions, emerging methodology requires an analytical understanding of the build-up of the allele frequencies over time. In this work, we use the framework of Poisson random fields to derive new representations of the non-equilibrium AFS for the case of a Wright-Fisher population model with selection. In our approach, the AFS is a scaling-limit of the expectation of a Poisson stochastic integral and the representation of the non-equilibrium AFS arises in terms of a fixation time probability distribution. The known duality between the Wright-Fisher diffusion process and a birth and death process generalizing Kingman's coalescent yields an additional representation. The results carry over to the setting of a random sample drawn from the population and provide the non-equilibrium behavior of sample statistics. Our findings are consistent with and extend a previous approach where the non-equilibrium AFS solves a partial differential forward equation with a non-traditional boundary condition. Moreover, we provide a bridge to previous coalescent-based work, and hence tie several frameworks together. Since frequency-based summary statistics are widely used in population genetics, for example, to identify candidate loci of adaptive evolution, to infer the demographic history of a population, or to improve our understanding of the underlying mechanics of speciation events, the presented results are potentially useful for a broad range of topics. PMID:27378747

  16. Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST) can evidence environmental selection...

  17. Mamu-DQA1 allele and genotype frequencies in a randomly sampled breeding colony of rhesus macaques (Macaca mulatta).

    PubMed

    Rolfs, B K; Lorenz, J G; Wu, C C; Lerche, N W; Smith, D G

    2001-04-01

    We studied the allelic and genotypic distribution of the major histocompatibility class-II locus DQA1 observed in a random sample of Indian rhesus macaques (Macaca mulatta) from a major breeding facility in the United States. The DNA was isolated from whole blood samples collected between 1991 and 1994 from 65 Indian rhesus monkeys. Polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP), which involves use of specific amplification of DQA1 exon 2 and subsequent restriction digestion of the 242-base pair fragment, was used to genotype the animals for the 20 known macaque (Mamu)-DQA1 alleles. Frequencies for four alleles (DQA1*240x, *2502, *2503 and *0102) differed significantly from those reported in a smaller sample of rhesus macaques from the German Primate Center. The modest genetic survey of Mamu-DQA1 genotypes presented here will be particularly useful in designing epidemiologic studies that investigate associations between immunogenetic background and disease susceptibility in macaque models of human disease.

  18. Inference in two dimensions: allele frequencies versus lengths of shared sequence blocks.

    PubMed

    Barton, N H; Etheridge, A M; Kelleher, J; Véber, A

    2013-08-01

    We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ(2), based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FST) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a 'local scale', κ; the rate of gene flow, σ(2), cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ(2). With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ(2).

  19. Semantic Web-based integration of cancer pathways and allele frequency data.

    PubMed

    Holford, Matthew E; Rajeevan, Haseena; Zhao, Hongyu; Kidd, Kenneth K; Cheung, Kei-Hoi

    2009-01-01

    We demonstrate the use of Semantic Web technology to integrate the ALFRED allele frequency database and the Starpath pathway resource. The linking of population-specific genotype data with cancer-related pathway data is potentially useful given the growing interest in personalized medicine and the exploitation of pathway knowledge for cancer drug discovery. We model our data using the Web Ontology Language (OWL), drawing upon ideas from existing standard formats BioPAX for pathway data and PML for allele frequency data. We store our data within an Oracle database, using Oracle Semantic Technologies. We then query the data using Oracle's rule-based inference engine and SPARQL-like RDF query language. The ability to perform queries across the domains of population genetics and pathways offers the potential to answer a number of cancer-related research questions. Among the possibilities is the ability to identify genetic variants which are associated with cancer pathways and whose frequency varies significantly between ethnic groups. This sort of information could be useful for designing clinical studies and for providing background data in personalized medicine. It could also assist with the interpretation of genetic analysis results such as those from genome-wide association studies.

  20. Comparison of allele frequencies of eight STR loci from Argentinian Amerindian and European populations.

    PubMed

    Sala, A; Penacino, G; Corach, D

    1998-10-01

    Eight STR systems (THO1, FABP, VWA, FES/FPS, HPRTB, F13A1, CSF1PO, and D6S366) were investigated in different ethnic groups of Argentina. Allele and genotype frequencies, power of exclusion, and discriminative power were investigated. Hardy-Weinberg expectations were calculated from heterozygosity levels. FST and G tests demonstrated that significant differences exist among the investigated populations for some of the eight STRs markers. The Wichi Indians are clearly separated from the Mapuche and Tehuelche, who in turn are closer to the European population, suggesting non-Amerindian admixture.

  1. Frequency of CYP2C9 alleles in Koreans and their effects on losartan pharmacokinetics

    PubMed Central

    Bae, Jung-woo; Choi, Chang-ik; Kim, Mi-jeong; Oh, Da-hee; Keum, Seul-ki; Park, Jung-in; Kim, Bo-hye; Bang, Hye-kyoung; Oh, Sung-gon; Kang, Byung-sung; Park, Hyun-joo; Kim, Hae-deun; Ha, Ji-hey; Shin, Hee-jung; Kim, Young-hoon; Na, Han-sung; Chung, Myeon-woo; Jang, Choon-gon; Lee, Seok-yong

    2011-01-01

    Aim: CYP2C9 enzyme metabolizes numerous clinically important drugs. The aim of this study is to investigate the frequencies of CYP2C9 genotypes and the effects of selected alleles on losartan pharmacokinetics in a large sample of the Korean population. Methods: The CYP2C9 gene was genotyped in 1796 healthy Korean subjects. CYP2C9 alleles (CYP2C9*1, *2, *3 and *13 alleles) were measured using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay and direct sequencing assay. The enzymatic activity of each CYP2C9 genotype was evaluated using losartan as the substrate. Results: The frequencies of CYP2C9*1, *3 and *13 allele were 0.952 (95% confidence interval 0.945–0.959), 0.044 (95% CI 0.037–0.051) and 0.005 (95% CI 0.003–0.007), respectively. The frequencies of the CYP2C9*1/*1, *1/*3, *1/*13 and *3/*3 genotypes were 0.904 (95% CI 0.890–0.918), 0.085 (95% CI 0.072–0.098), 0.009 (95% CI 0.005–0.013) and 0.001 (95% CI 0.000–0.002), respectively. In the pharmacokinetics studies, the AUC0–∞ of losartan in CYP2C9*3/*3 subjects was 1.42-fold larger than that in CYP2C9*1/*1 subjects, and the AUC0–∞ of E-3174, a more active metabolite of losartan, in CYP2C9*3/*3 subjects was only 12% of that in CYP2C9*1/*1 subjects. Conclusion: The results confirmed the frequencies of CYP2C9 genotypes in a large cohort of Koreans, and detected the CYP2C9*3/*3 genotype. CYP2C9*3/*3 subjects metabolized much less losartan into E-3174 than CYP2C9*1/*1 subjects. PMID:21841812

  2. Initial frequency of alleles conferring resistance to Bacillus thuringiensis poplar in a field population of Chrysomela tremulae.

    PubMed Central

    Génissel, Anne; Augustin, Sylvie; Courtin, Claudine; Pilate, Gilles; Lorme, Philippe; Bourguet, Denis

    2003-01-01

    Globally, the estimated total area planted with transgenic plants producing Bacillus thuringiensis (Bt) toxins was 12 million hectares in 2001. The risk of target pests becoming resistant to these toxins has led to the implementation of resistance-management strategies. The efficiency and sustainability of these strategies, including the high-dose plus refuge strategy currently recommended for North American maize, depend on the initial frequency of resistance alleles. In this study, we estimated the initial frequencies of alleles conferring resistance to transgenic Bt poplars producing Cry3A in a natural population of the poplar pest Chrysomela tremulae (Coleoptera: Chrysomelidae). We used the F(2) screen method developed for detecting resistance alleles in natural pest populations. At least three parents of the 270 lines tested were heterozygous for a major Bt resistance allele. We estimated mean resistance-allele frequency for the period 1999-2001 at 0.0037 (95% confidence interval = 0.00045-0.0080) with a detection probability of 90%. These results demonstrate that (i) the F(2) screen method can be used to detect major alleles conferring resistance to Bt-producing plants in insects and (ii) the initial frequency of alleles conferring resistance to Bt toxin can be close to the highest theoretical values that are expected prior to the use of Bt plants if considering fitness costs and typical mutation rates. PMID:12737656

  3. D9S1120, a simple STR with a common Native American-specific allele: forensic optimization, locus characterization and allele frequency studies.

    PubMed

    Phillips, C; Rodriguez, A; Mosquera-Miguel, A; Fondevila, M; Porras-Hurtado, L; Rondon, F; Salas, A; Carracedo, A; Lareu, M V

    2008-12-01

    The simple tetrameric STR D9S1120 exhibits a common population-specific allele of 9 repeats (9RA) reported to have an average frequency of 0.36 in Native Americans from both North and South of the continent. Apart from the presence of 9RA in two northeast Siberian populations, D9S1120 shows variability exclusive to, and universal in all American populations studied to date. This STR therefore provides an informative forensic marker applicable in countries with significant proportions of Native American populations or ancestry. We have re-designed PCR primers that reduce the amplified product sizes reported in NCBI UniSTS by more than a third and have characterized the repeat structure of D9S1120. The 9RA allele shares the same repeat structure as the majority of other D9S1120 alleles and so originates from a slippage-diminution mutation rather than an independent deletion. We confirm the previously reported allele frequencies from a range of populations indicating a global heterozygosity range for D9S1120 of 66-75% and estimate the proportion of Native American-diagnostic genotypes to average 53%, underlining the potential usefulness of this STR in both forensic identification and in population genetics studies of the Americas.

  4. Minor Allele Frequency Changes the Nature of Genotype by Environment Interactions.

    PubMed

    Verhulst, Brad; Neale, Michael C

    2016-09-01

    In the classical twin study, phenotypic variation is often partitioned into additive genetic (A), common (C) and specific environment (E) components. From genetical theory, the outcome of genotype by environment interaction is expected to inflate A when the interacting factor is shared (i.e., C) between the members of a twin pair. We show that estimates of both A and C can be inflated. When the shared interacting factor changes the size of the difference between homozygotes' means, the expected sibling or DZ twin correlation is .5 if and only if the minor allele frequency (MAF) is .5; otherwise the expected DZ correlation is greater than this value, consistent (and confounded) with some additional effect of C. This result is considered in the light of the distribution of minor allele frequencies for polygenic traits. Also discussed is whether such interactions take place at the locus level or affect an aggregated biological structure or system. Interactions with structures or endophenotypes that result from the aggregated effects of many loci will generally emerge as part of the A estimate. PMID:27105628

  5. On the Bayesness, minimaxity and admissibility of point estimators of allelic frequencies.

    PubMed

    Martínez, Carlos Alberto; Khare, Kshitij; Elzo, Mauricio A

    2015-10-21

    In this paper, decision theory was used to derive Bayes and minimax decision rules to estimate allelic frequencies and to explore their admissibility. Decision rules with uniformly smallest risk usually do not exist and one approach to solve this problem is to use the Bayes principle and the minimax principle to find decision rules satisfying some general optimality criterion based on their risk functions. Two cases were considered, the simpler case of biallelic loci and the more complex case of multiallelic loci. For each locus, the sampling model was a multinomial distribution and the prior was a Beta (biallelic case) or a Dirichlet (multiallelic case) distribution. Three loss functions were considered: squared error loss (SEL), Kulback-Leibler loss (KLL) and quadratic error loss (QEL). Bayes estimators were derived under these three loss functions and were subsequently used to find minimax estimators using results from decision theory. The Bayes estimators obtained from SEL and KLL turned out to be the same. Under certain conditions, the Bayes estimator derived from QEL led to an admissible minimax estimator (which was also equal to the maximum likelihood estimator). The SEL also allowed finding admissible minimax estimators. Some estimators had uniformly smaller variance than the MLE and under suitable conditions the remaining estimators also satisfied this property. In addition to their statistical properties, the estimators derived here allow variation in allelic frequencies, which is closer to the reality of finite populations exposed to evolutionary forces. PMID:26271891

  6. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China*

    PubMed Central

    Wang, Hong-dan; Shen, Chun-mei; Liu, Wen-juan; Zhang, Yu-dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Zhu, Bo-feng

    2013-01-01

    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population’s genetic background, for individual identification, and for paternity testing in forensic practice. PMID:23733431

  7. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China.

    PubMed

    Wang, Hong-dan; Shen, Chun-mei; Liu, Wen-juan; Zhang, Yu-dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Zhu, Bo-feng

    2013-06-01

    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population's genetic background, for individual identification, and for paternity testing in forensic practice.

  8. Allele and genotype frequencies of metabolic genes in Native Americans from Argentina and Paraguay.

    PubMed

    Bailliet, G; Santos, M R; Alfaro, E L; Dipierri, J E; Demarchi, D A; Carnese, F R; Bianchi, N O

    2007-03-01

    Interethnic differences in the allele frequencies of CYP2D6, NAT2, GSTM1 and GSTT1 deletions have been documented for Caucasians, Asians, and Africans population. On the other hand, data on Amerindians are scanty and limited to a few populations from southern areas of South America. In this report we analyze the frequencies of 11 allele variants of CYP2D6 and 4 allele variants of NAT2 genes, and the frequency of GSTM1 and GSTT1 homozygous deleted genotypes in a sample of 90 donors representing 8 Native American populations from Argentina and Paraguay, identified as Amerindians on the basis of their geographic location, genealogical data, mitochondrial- and Y-chromosome DNA markers. For CYP2D6, 88.6% of the total allele frequency corresponded to *1, *2, *4 and *10 variants. Average frequencies for NAT2 *4, *5, *6 and *7 alleles were 51.2%, 25%, 6.1%, and 20.1%, respectively. GSTM1 deletion ranged from 20% to 66%, while GSTT1 deletion was present in four populations in less than 50%. We assume that CYP2D6 *2, *4, *10, *14; NAT2 *5, *7 alleles and GSTM1 and GSTT1 *0/*0 genotypes are founder variants brought to America by the first Asian settlers. PMID:17194620

  9. GST M1-T1 null allele frequency patterns in geographically assorted human populations: a phylogenetic approach.

    PubMed

    Kasthurinaidu, Senthilkumar Pitchalu; Ramasamy, Thirumurugan; Ayyavoo, Jayachitra; Dave, Dhvani Kirtikumar; Adroja, Divya Anantray

    2015-01-01

    Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME). Among the XMEs, glutathione-S-transferases (GST) gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs). Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs). The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions) and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs.

  10. GST M1-T1 null Allele Frequency Patterns in Geographically Assorted Human Populations: A Phylogenetic Approach

    PubMed Central

    Ramasamy, Thirumurugan; Ayyavoo, Jayachitra

    2015-01-01

    Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME). Among the XMEs, glutathione-S-transferases (GST) gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs). Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs). The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions) and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs. PMID:25867025

  11. GST M1-T1 null allele frequency patterns in geographically assorted human populations: a phylogenetic approach.

    PubMed

    Kasthurinaidu, Senthilkumar Pitchalu; Ramasamy, Thirumurugan; Ayyavoo, Jayachitra; Dave, Dhvani Kirtikumar; Adroja, Divya Anantray

    2015-01-01

    Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME). Among the XMEs, glutathione-S-transferases (GST) gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs). Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs). The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions) and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs. PMID:25867025

  12. Geographical distribution of pyrethroid resistance allele frequency in head lice (Phthiraptera: Pediculidae) from Argentina.

    PubMed

    Toloza, Ariel Ceferino; Ascunce, Marina S; Reed, David; Picollo, María Inés

    2014-01-01

    The human head louse, Pediculus humanus capitis De Geer (Phthiraptera: Pediculidae), is an obligate ectoparasite that causes pediculosis capitis and has parasitized humans since the beginning of humankind. Head louse infestations are widespread throughout the world and have been increasing since the early 1990s partially because of ineffective pediculicides. In Argentina, the overuse of products containing pyrethroids has led to the development of resistant louse populations. Pyrethroid insecticides act on the nervous system affecting voltage-sensitive sodium channels. Three point mutations at the corresponding amino acid sequence positions M815I, T917I, and L920F in the voltage-gated sodium channel gene are responsible for contributing to knockdown resistance (kdr). The management of pyrethroid resistance requires either early detection or the characterization of the mechanisms involved in head louse populations. In the current study, we estimated the distribution of kdr alleles in 154 head lice from six geographical regions of Argentina. Pyrethroid resistance kdr alleles were found in high frequencies ranging from 67 to 100%. Of these, 131 (85.1%) were homozygous resistant, 13 (8.4%) were homozygous susceptible, and 10 (6.5%) were heterozygous. Exact tests for the Hardy-Weinberg equilibrium for each location showed that genotype frequencies differed significantly from expectation in four of the six sites studied. These results show that pyrethroid resistance is well established reaching an overall frequency of 88%, thus close to fixation. With 30 yr of pyrethroid-based pediculicides use in Argentina, kdr resistance has evolved rapidly among these head louse populations. PMID:24605463

  13. Geographical distribution of pyrethroid resistance allele frequency in head lice (Phthiraptera: Pediculidae) from Argentina.

    PubMed

    Toloza, Ariel Ceferino; Ascunce, Marina S; Reed, David; Picollo, María Inés

    2014-01-01

    The human head louse, Pediculus humanus capitis De Geer (Phthiraptera: Pediculidae), is an obligate ectoparasite that causes pediculosis capitis and has parasitized humans since the beginning of humankind. Head louse infestations are widespread throughout the world and have been increasing since the early 1990s partially because of ineffective pediculicides. In Argentina, the overuse of products containing pyrethroids has led to the development of resistant louse populations. Pyrethroid insecticides act on the nervous system affecting voltage-sensitive sodium channels. Three point mutations at the corresponding amino acid sequence positions M815I, T917I, and L920F in the voltage-gated sodium channel gene are responsible for contributing to knockdown resistance (kdr). The management of pyrethroid resistance requires either early detection or the characterization of the mechanisms involved in head louse populations. In the current study, we estimated the distribution of kdr alleles in 154 head lice from six geographical regions of Argentina. Pyrethroid resistance kdr alleles were found in high frequencies ranging from 67 to 100%. Of these, 131 (85.1%) were homozygous resistant, 13 (8.4%) were homozygous susceptible, and 10 (6.5%) were heterozygous. Exact tests for the Hardy-Weinberg equilibrium for each location showed that genotype frequencies differed significantly from expectation in four of the six sites studied. These results show that pyrethroid resistance is well established reaching an overall frequency of 88%, thus close to fixation. With 30 yr of pyrethroid-based pediculicides use in Argentina, kdr resistance has evolved rapidly among these head louse populations.

  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. Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation.

    PubMed

    Racimo, Fernando

    2016-02-01

    A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality and finding which model is most compatible with the data. A previous method based on a cross-population composite likelihood ratio (XP-CLR) uses an outgroup population to detect departures from neutrality that could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method - called "3-population composite likelihood ratio" (3P-CLR) - outperforms XP-CLR when testing for selection that occurred before two populations split from each other and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans, and the ancestors of both populations, after their split from Yoruba. In both cases, we are able to confirm a number of regions identified by previous methods and find several new candidates for selection in recent and ancient times. For some of these, we also find suggestive functional mutations that may have driven the selective events. PMID:26596347

  16. Frequency of null allele of Human Leukocyte Antigen-G (HLA-G) locus in subjects to recurrent miscarriage

    PubMed Central

    Alizadeh, Nazila; Mosaferi, Elnaz; Farzadi, Laya; Majidi, Jafar; Monfaredan, Amir; Yousefi, Bahman; Baradaran, Behzad

    2016-01-01

    Background: Human leukocyte antigen-G (HLA-G) is a non-classical class I molecule highly expressed by extravillous cytotrophoblast cells. Due to a single base pair deletion, its function can be compensated by other isoforms. Investigating the frequency of null allele in Recurrent Miscarriage (RM) subjects could be useful in understanding the relationship between frequency of this allele and RM in a given population. Objective: This study aimed to determine the frequency of HLA-G*0105N null allele and its potential association with down-regulation of HLA-G in subjects with RM. Materials and Methods: Western blotting was used to assess the level of HLA-G protein expression. For investigating the frequency of HLA-G*0105N null allele in RM subjects, PCR-RFLP method was used. Exon 3 of HLA-G gene was amplified by polymerase chain reaction (PCR). Subsequently, PpuM-1 enzyme was employed to digest the PCR products and fragments were analyzed using gel electrophoresis. Results: Digestion using restriction enzyme showed the presence of heterozygous HLA-G*0105N null allele in 10% of the test population. Western blotting results confirmed the decrease in expression of HLA-G in the placental tissue of subjects with RM compared to subjects who could give normal birth. Conclusion: The frequency of heterozygous HLA-G*0105N null allele was high to some extent in subjects with RM. The mutation rate in subjects suggested that there is a significant association between RM and frequency of mutations in this allele. PMID:27525330

  17. Initial frequency of alleles for resistance to Bacillus thuringiensis toxins in field populations of Heliothis virescens

    PubMed Central

    Gould, F.; Anderson, A.; Jones, A.; Sumerford, D.; Heckel, D. G.; Lopez, J.; Micinski, S.; Leonard, R.; Laster, M.

    1997-01-01

    The risk of rapid pest adaptation to an insecticide is highly dependent on the initial frequency of resistance alleles in field populations. Because we have lacked empirical estimates of these frequencies, population–genetic models of resistance evolution have relied on a wide range of theoretical estimates. The recent commercialization of genetically engineered cotton that constitutively produces an insecticidal protein derived from the biocontrol agent, Bacillus thuringiensis (Bt) has raised concern that we lack data needed to quantify the risk of insect pests such as Heliothis virescens rapidly adapting to this ecologically valuable class of toxins. By individually mating over 2,000 male H. virescens moths collected in four states to females of a Bt toxin-resistant laboratory strain, and screening F1 and F2 offspring for tolerance of the toxic protein, we were able to directly estimate the field frequency of alleles for resistance as 1.5 × 10−3. This high initial frequency underscores the need for caution in deploying transgenic cotton to control insect pests. Our single-pair mating technique greatly increases the efficiency of detecting recessive resistance alleles. Because alleles that decrease target site sensitivity to Bt toxins and other insecticides are often recessive, this technique could be useful in estimating resistance allele frequencies in other insects exposed to transgenic insecticidal crops or conventional insecticides. PMID:11038613

  18. Utilizing ethnic-specific differences in minor allele frequency to recategorize reported pathogenic deafness variants.

    PubMed

    Shearer, A Eliot; Eppsteiner, Robert W; Booth, Kevin T; Ephraim, Sean S; Gurrola, José; Simpson, Allen; Black-Ziegelbein, E Ann; Joshi, Swati; Ravi, Harini; Giuffre, Angelica C; Happe, Scott; Hildebrand, Michael S; Azaiez, Hela; Bayazit, Yildirim A; Erdal, Mehmet Emin; Lopez-Escamez, Jose A; Gazquez, Irene; Tamayo, Marta L; Gelvez, Nancy Y; Leal, Greizy Lopez; Jalas, Chaim; Ekstein, Josef; Yang, Tao; Usami, Shin-ichi; Kahrizi, Kimia; Bazazzadegan, Niloofar; Najmabadi, Hossein; Scheetz, Todd E; Braun, Terry A; Casavant, Thomas L; LeProust, Emily M; Smith, Richard J H

    2014-10-01

    Ethnic-specific differences in minor allele frequency impact variant categorization for genetic screening of nonsyndromic hearing loss (NSHL) and other genetic disorders. We sought to evaluate all previously reported pathogenic NSHL variants in the context of a large number of controls from ethnically distinct populations sequenced with orthogonal massively parallel sequencing methods. We used HGMD, ClinVar, and dbSNP to generate a comprehensive list of reported pathogenic NSHL variants and re-evaluated these variants in the context of 8,595 individuals from 12 populations and 6 ethnically distinct major human evolutionary phylogenetic groups from three sources (Exome Variant Server, 1000 Genomes project, and a control set of individuals created for this study, the OtoDB). Of the 2,197 reported pathogenic deafness variants, 325 (14.8%) were present in at least one of the 8,595 controls, indicating a minor allele frequency (MAF) > 0.00006. MAFs ranged as high as 0.72, a level incompatible with pathogenicity for a fully penetrant disease like NSHL. Based on these data, we established MAF thresholds of 0.005 for autosomal-recessive variants (excluding specific variants in GJB2) and 0.0005 for autosomal-dominant variants. Using these thresholds, we recategorized 93 (4.2%) of reported pathogenic variants as benign. Our data show that evaluation of reported pathogenic deafness variants using variant MAFs from multiple distinct ethnicities and sequenced by orthogonal methods provides a powerful filter for determining pathogenicity. The proposed MAF thresholds will facilitate clinical interpretation of variants identified in genetic testing for NSHL. All data are publicly available to facilitate interpretation of genetic variants causing deafness. PMID:25262649

  19. Knockdown Resistance Allele Frequencies in North American Head Louse (Anoplura: Pediculidae) Populations

    PubMed Central

    Yoon, Kyong Sup; Previte, Domenic J.; Hodgdon, Hilliary E.; Poole, Bryan C.; Kwon, Deok Ho; El-Ghar, Gamal E. Abo; Lee, Si Hyeock; Clark, J. Marshall

    2014-01-01

    The study examines the extent and frequency of a knockdown-type resistance allele (kdr type) in North American populations of human head lice. Lice were collected from 32 locations in Canada and the United States. DNA was extracted from individual lice and used to determine their zygosity using the serial invasive signal amplification technique to detect the kdr-type T917I (TI) mutation, which is most responsible for nerve insensitivity that results in the kdr phenotype and permethrin resistance. Previously sampled sites were resampled to determine if the frequency of the TI mutation was changing. The TI frequency was also reevaluated using a quantitative sequencing method on pooled DNA samples from selected sites to validate this population genotyping method. Genotyping substantiated that TI occurs at high levels in North American lice (88.4%). Overall, the TI frequency in U.S. lice was 84.4% from 1999 to 2009, increased to 99.6% from 2007 to 2009, and was 97.1% in Canadian lice in 2008. Genotyping results using the serial invasive signal amplification reaction (99.54%) and quantitative sequencing (99.45%) techniques were highly correlated. Thus, the frequencies of TI in North American head louse populations were found to be uniformly high, which may be due to the high selection pressure from the intensive and widespread use of the pyrethrins- or pyrethroid-based pediculicides over many years, and is likely a main cause of increased pediculosis and failure of pyrethrins- or permethrin-based products in Canada and the United States. Alternative approaches to treatment of head lice infestations are critically needed. PMID:24724296

  20. Haemoglobin polymorphism in atlantic cod (Gadus morhua): Allele frequency variation between yearclasses in a Norwegian fjord stock

    NASA Astrophysics Data System (ADS)

    Mork, J.; Sundnes, G.

    1985-03-01

    A total of 262 specimens (0-, and 1-group) of Atlantic cod (Gadus morhua) representing 4 different yearclasses were caught in Trondheimsfjorden, Norway, during 1977 1984. They were genotyped by agar gel electrophoresis for the polymorphic haemoglobin locus HbI (Sick, 1961). The analyses revealed a highly significant (P=0.0003) heterogeneity of HbI allele frequencies between yearclasses. The difference in the frequency of the HbI-1 allele between the first (1977) and the last (1983) yearclass amounted to 0.18 (±0.07). The results appear to support recent reports on considerable selection effects at HbI, and stress the unreliability of allele frequencies at this locus for use in studies of the genetic population structure of cod.

  1. Frequencies of 23 Functionally Significant Variant Alleles Related with Metabolism of Antineoplastic Drugs in the Chilean Population: Comparison with Caucasian and Asian Populations

    PubMed Central

    Roco, Ángela; Quiñones, Luis; Agúndez, José A. G.; García-Martín, Elena; Squicciarini, Valentina; Miranda, Carla; Garay, Joselyn; Farfán, Nancy; Saavedra, Iván; Cáceres, Dante; Ibarra, Carol; Varela, Nelson

    2012-01-01

    Cancer is a leading cause of death worldwide. The cancer incidence rate in Chile is 133.7/100,000 inhabitants and it is the second cause of death, after cardiovascular diseases. Most of the antineoplastic drugs are metabolized to be detoxified, and some of them to be activated. Genetic polymorphisms of drug-metabolizing enzymes can induce deep changes in enzyme activity, leading to individual variability in drug efficacy and/or toxicity. The present research describes the presence of genetic polymorphisms in the Chilean population, which might be useful in public health programs for personalized treatment of cancer, and compares these frequencies with those reported for Asian and Caucasian populations, as a contribution to the evaluation of ethnic differences in the response to chemotherapy. We analyzed 23 polymorphisms in a group of 253 unrelated Chilean volunteers from the general population. The results showed that CYP2A6*2, CYP2A6*3, CYP2D6*3, CYP2C19*3, and CYP3A4*17 variant alleles are virtually absent in Chileans. CYP1A1*2A allele frequency (0.37) is similar to that of Caucasians and higher than that reported for Japanese people. Allele frequencies for CYP3A5*3(0.76) and CYP2C9*3(0.04) are similar to those observed in Japanese people. CYP1A1*2C(0.32), CYP1A2*1F(0.77), CYP3A4*1B(0.06), CYP2D6*2(0.41), and MTHFR T(0.52) allele frequencies are higher than the observed either in Caucasian or in Japanese populations. Conversely, CYP2C19*2 allelic frequency (0.12), and genotype frequencies for GSTT1 null (0.11) and GSTM1 null (0.36) are lower than those observed in both populations. Finally, allele frequencies for CYP2A6*4(0.04), CYP2C8*3(0.06), CYP2C9*2(0.06), CYP2D6*4(0.12), CYP2E1*5B(0.14), CYP2E1*6(0.19), and UGT2B7*2(0.40) are intermediate in relation to those described in Caucasian and in Japanese populations, as expected according to the ethnic origin of the Chilean population. In conclusion, our findings support the idea that ethnic variability must be

  2. Confidence intervals for population allele frequencies: the general case of sampling from a finite diploid population of any size.

    PubMed

    Fung, Tak; Keenan, Kevin

    2014-01-01

    The estimation of population allele frequencies using sample data forms a central component of studies in population genetics. These estimates can be used to test hypotheses on the evolutionary processes governing changes in genetic variation among populations. However, existing studies frequently do not account for sampling uncertainty in these estimates, thus compromising their utility. Incorporation of this uncertainty has been hindered by the lack of a method for constructing confidence intervals containing the population allele frequencies, for the general case of sampling from a finite diploid population of any size. In this study, we address this important knowledge gap by presenting a rigorous mathematical method to construct such confidence intervals. For a range of scenarios, the method is used to demonstrate that for a particular allele, in order to obtain accurate estimates within 0.05 of the population allele frequency with high probability (> or = 95%), a sample size of > 30 is often required. This analysis is augmented by an application of the method to empirical sample allele frequency data for two populations of the checkerspot butterfly (Melitaea cinxia L.), occupying meadows in Finland. For each population, the method is used to derive > or = 98.3% confidence intervals for the population frequencies of three alleles. These intervals are then used to construct two joint > or = 95% confidence regions, one for the set of three frequencies for each population. These regions are then used to derive a > or = 95%% confidence interval for Jost's D, a measure of genetic differentiation between the two populations. Overall, the results demonstrate the practical utility of the method with respect to informing sampling design and accounting for sampling uncertainty in studies of population genetics, important for scientific hypothesis-testing and also for risk-based natural resource management. PMID:24465792

  3. Distribution of DI*A and DI*B Allele Frequencies and Comparisons among Central Thai and Other Populations

    PubMed Central

    Nathalang, Oytip; Panichrum, Puangpaka; Intharanut, Kamphon; Thattanon, Phatchira; Nathalang, Siriporn

    2016-01-01

    Alloantibodies to the Diego (DI) blood group system, anti-Dia and anti-Dib are clinically significant in causing hemolytic transfusion reactions (HTRs) and hemolytic disease of the fetus and newborn (HDFN), especially in Asian populations with Mongolian ancestry. This study aimed to report the frequency of the DI*A and DI*B alleles in a Central Thai population and to compare them with those of other populations previously published. Altogether, 1,011 blood samples from unrelated healthy blood donors at the National Blood Centre, Thai Red Cross Society, Bangkok were included. Only 391 samples were tested with anti-Dia by conventional tube technique. All samples were genotyped for DI*A and DI*B alleles using an in-house polymerase chain reaction with sequence-specific primer (PCR-SSP) technique. The DI phenotyping and genotyping results were in 100% concordance. The DI*A and DI*B allele frequencies among 1,011 Central Thais were 0.0183 (37/2,022) and 0.9817 (1,985/2,022), respectively. Allele frequencies were compared between Central Thai and other populations. Our data shows that DI*A and DI*B allele frequencies are similar to Southeast Asian, Brazilian, Southern Brazilian and American Native populations; whereas, these frequencies significantly differ from those reported in East Asian, Italian, Alaska Native/Aleut, Hawaiian/Pacific Islander and Filipino populations (P<0.05), corresponding to the results of a matrix of geometric genetic distances. This study confirms that the prevalence of DI*A and DI*B alleles among Central Thais is similar to Southeast Asians and different to others populations of the world. A PCR-based identification of DI genotyping should overcome some of the serological limitations in transfusion medicine and provides a complementary tool for further population-genetic studies. PMID:27764238

  4. Lower frequency of sister chromatid exchanges and altered frequency of HLA B-region alleles among individuals with sporadic dysplastic nevi.

    PubMed

    Illeni, M T; Rovini, D; Di Lernia, M; Cascinelli, N; Ghidoni, A

    1997-01-01

    Sister chromatid exchanges (SCE) were analyzed in peripheral blood lymphocytes of 24 individuals, following diagnosis, and prior to surgical removal, of a sporadic dysplastic nevus (DN). Lower SCE values and variability were found in 23 sporadic DN individuals compared with controls (2.52 +/- 0.12 and 3.76 +/- 0.22 SCE/cell, respectively). These DN individuals, contrarily to healthy controls and some types of tumor patients whose cells are hypersensitive to mutagenic agents, did not show increased SCE rates as a consequence of cigarette smoking, alcohol consumption and diagnostic radiation treatments. These observations are in contrast with clinical evidence that similar lesions are both markers or risk and precursors of malignancy in individuals with multiple nevi, affected by the dysplastic nevus syndrome (DNS) or belonging to FMM (familial malignant melanoma) families. Three HLA class I alleles out of 72 tested were found more frequently in sporadic DN individuals compared with controls: B37 (p < 0.05), B52 (p < 0.01) and B70 (p < 0.01). Whether the greater chromosomal stability (as shown by the SCE analysis), and/or the altered frequency of some HLA alleles could influence the chance of developing cutaneous malignancy in DN individuals is yet to be evaluated.

  5. A note on the change in gene frequency of a selected allele in partial full-sib mating populations

    SciTech Connect

    Caballero, A.

    1996-02-01

    The change in gene frequency of a selected allele in partial full-sib mating populations was analyzed. The implications of these papers is important in terms of the fixation probability of genes because, for the same equilibrium inbreeding coefficient, fixation rates of mutant genes would be larger for partial full-sib mating than for partial selfing. 4 refs.

  6. Frequencies of HKαα and anti-HKαα Alleles in Chinese Carriers of Silent Deletional α-Thalassemia.

    PubMed

    Wu, Man-Yu; Li, Jian; Li, Shu-Chen; Li, Yan; Li, Dong-Zhi

    2015-01-01

    The HKαα (HongKongαα) allele is an unusual rearrangement of the α-globin gene cluster containing both the -α(3.7) (rightward) and ααα(anti 4.2) crossover deletion/duplication. The anti-HKαα (anti-HongKongαα) allele is the reciprocal product containing both the -α(4.2) (leftward) and ααα(anti 3.7) unequal crossover deletion/duplication. In clinical practice of thalassemia screening, gap-polymerase chain reaction (gap-PCR) approaches are used to detect the common -α(3.7) and -α(4.2) deletions of α-thalassemia (α-thal). Because the HKαα and anti-HKαα alleles also contain the single α-globin gene deletion, individuals with these alleles would be misdiagnosed as -α(3.7) or -α(4.2) carriers. This would likely produce misleading or incorrect information in genetic counseling. In this study, we investigated the HKαα and anti-HKαα alleles in Chinese carriers of silent deletional α-thal, and reported their frequencies to be 2.27 and 0.35% in -α(3.7) and -α(4.2) carriers, respectively. Given the rarity of the HKαα and anti-HKαα alleles, a routine screening for these two rearrangements are unlikely to be necessary on most occasions.

  7. PoMo: An Allele Frequency-Based Approach for Species Tree Estimation

    PubMed Central

    De Maio, Nicola; Schrempf, Dominik; Kosiol, Carolin

    2015-01-01

    Incomplete lineage sorting can cause incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data. We extend this model to perform efficient estimation of species trees. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele frequency based. We show that PoMo is well suited for genome-wide species tree estimation and that on such data it is more accurate than previous approaches. PMID:26209413

  8. Exome sequencing can detect pathogenic mosaic mutations present at low allele frequencies.

    PubMed

    Pagnamenta, Alistair T; Lise, Stefano; Harrison, Victoria; Stewart, Helen; Jayawant, Sandeep; Quaghebeur, Gerardine; Deng, Alexander T; Murphy, Valerie Elizabeth; Sadighi Akha, Elham; Rimmer, Andy; Mathieson, Iain; Knight, Samantha J L; Kini, Usha; Taylor, Jenny C; Keays, David A

    2012-01-01

    The development of next generation sequencing (NGS) has radically transformed the scientific landscape, making it possible to sequence the exome of any given individual in a cost-effective way. The power of this approach has been demonstrated by a number of groups who have identified pathogenic mutations in small pedigrees that have been resistant to traditional genetic mapping. Recently it has become clear that exome sequencing has great potential with respect to sporadic disease and the identification of de novo mutations. This is highlighted by studies reporting whole-exome sequencing of patient-parental trios affected by learning disability, autism and schizophrenia. It is widely anticipated that the introduction of this technique into a clinical setting will revolutionise genetic diagnosis. However, the sensitivity of NGS exome sequencing is currently unclear. Here, we describe the exome sequencing of DNA samples from a patient with double cortex syndrome and her parents, resulting in the detection of a mosaic splicing mutation in LIS1. This variant was found at an allele frequency of just 18%, demonstrating that NGS methods have the capacity to identify pathogenic mosaic mutations present at a low level. PMID:22129557

  9. Inference of population splits and mixtures from genome-wide allele frequency data.

    PubMed

    Pickrell, Joseph K; Pritchard, Jonathan K

    2012-01-01

    Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data, we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com. PMID:23166502

  10. Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

    PubMed Central

    Pickrell, Joseph K.; Pritchard, Jonathan K.

    2012-01-01

    Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data, we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and “ancient” Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com. PMID:23166502

  11. HLA allele and haplotype frequencies in the Albanian population and their relationship with the other European populations.

    PubMed

    Sulcebe, G; Sanchez-Mazas, A; Tiercy, J-M; Shyti, E; Mone, I; Ylli, Z; Kardhashi, V

    2009-12-01

    Human leucocyte antigen (HLA) alleles are very interesting markers in identifying population relationships. Moreover, their frequency distribution data are important in the implementation of donor-recipient registry programs for transplantation purposes and also in determining the genetic predisposition for many diseases. For these reasons, we studied the HLA class I and II allele and haplotype frequencies in 160 healthy, unrelated Albanian individuals originating from all regions of the country. The HLA genotyping was performed through a 2-digit resolution SSOP method. The data were analysed with Arlequin and Phylip programs. No deviation was found from the Hardy-Weinberg equilibrium. A total of 17 A*, 30 B*, 12 Cw*, 13 DRB1* and 5 DQB1* alleles were identified. The six most frequent HLA-A-B-DRB1 haplotypes were A*02-B*18-DRB1*11 (5.60%), A*02-B*51-DRB1*16 (4.74%), A*01-B*08-DRB1*03 (3.48%), A*24-B*35-DRB1*11 (2.77%), A*02-B*51-DRB1*13 (2.21%), A*24-B*35-DRB1*14 (1.89%). Interestingly, 12 HLA-A-B-Cw-DRB1-DQB1 haplotypes occurred at a frequency >1%. When compared with the other populations, a close relationship was found with North Greek, Bulgarian, Macedonian, Romanian, Turkish, Cretan, Serbian, Croatian and Italian populations. A higher differentiation in allele frequency level was found with Western Europe populations. These data are the first report of HLA allele and haplotype distribution in an Albanian population inside this country. When compared with other populations, their distribution frequencies show close similarities with neighbouring populations of the entire Balkan area. PMID:19703234

  12. Status of allele frequency and diversity of Plasmodium falciparum msp1, msp2 and glurp before implementation of an artemisinin-based combined therapy in Northwestern Colombia.

    PubMed Central

    Arango, Eliana; Carmona-Fonseca, Jaime

    2013-01-01

    Introduction: The status of msp1, msp2 and glurp allele frequency and the diversity of Plasmodium falciparum in Northwestern Colombia before the implementation of an artemisinin-combined therapy have been explored only by a few authors and in a relatively small number of samples from this highly endemic region. Objective: To evaluate the frequency of msp1, msp2, and glurp alleles and the diversity of P. falciparum in two Colombian regions before the use of an artemisinin-combined therapy. Methods: This study was part of a major anti-malarial efficacy trial designed as a random, clinically-controlled study for which 224 subjects were recruited. Region 2 of msp1 and msp2 (central region) were amplified by a nested PCR; glurp (region R2) was amplified by a semi-nested PCR. Results: For msp1, five genotypes were observed, representing the K1, MAD20, and RO33 allelic families. All samples corresponded to a MAD20 150 bp allele. For msp2 (IC family), two alleles were detected and for glurp, eight were observed. A total 33 haplotypes were detected. Conclusions: Analysis of glurpcan be used to successfully genotype parasite populations in the new studies in Colombia aimed at exploring Plasmodium spp population dynamics. In addition, analysis of msp1 and msp2 can also be of value for comparisons with past studies, but not when the objective is to study parasites obtained from the same patient in a reduced period of time; for instance, during treatment efficacy studies. PMID:24892236

  13. Influence of admixture components on CYP2C9*2 allele frequency in eight indigenous populations from Northwest Mexico.

    PubMed

    Sosa-Macías, M; Lazalde-Ramos, B P; Galaviz-Hernández, C; Rangel-Villalobos, H; Salazar-Flores, J; Martínez-Sevilla, V M; Martínez-Fierro, M L; Dorado, P; Wong, M L; Licinio, J; LLerena, A

    2013-12-01

    We previously documented the lowest frequency of CYP2C9*2 in Mexican indigenous Tepehuanos followed by Mestizos and Mexican-Americans populations, suggesting a negative correlation between the CYP2C9*2 frequency and the degree of Asian ancestry in indigenous Americans. We determined the influence of ethnic admixture components on the CYP2C9 allele distribution in 505 Amerindian from eight indigenous populations through genotyping CYP2C9*2, *3 and *6 alleles by real-time PCR and molecular evaluation of ancestry. The frequencies for CYP2C9*2 were 0.026 in Seris and 0.057 in Mayos, being higher than in Asians (P<0.001). CYP2C9*3 was found in Tarahumaras (0.104), Mayos (0.091), Tepehuanos (0.075), Guarijíos (0.067), Huicholes (0.033) and Coras (0.037), with East Asians having lower frequencies than the former three groups (P<0.001). CYP2C9*6 was not found. The frequency of CYP2C9*2 was lower in Amerindians than in European populations, and higher than their Asian ancestors. The presence of this allele in ethnic groups in Mexico can be explained by European admixture.

  14. Allele Frequencies of the Single Nucleotide Polymorphisms Related to the Body Burden of Heavy Metals in the Korean Population and Their Ethnic Differences

    PubMed Central

    Eom, Sang-Yong; Lim, Ji-Ae; Kim, Yong-Dae; Choi, Byung-Sun; Hwang, Myung Sil; Park, Jung-Duck; Kim, Heon; Kwon, Ho-Jang

    2016-01-01

    This study was performed to select single nucleotide polymorphisms (SNPs) related to the body burden of heavy metals in Koreans, to provide Korean allele frequencies of selected SNPs, and to assess the difference in allele frequencies with other ethnicities. The candidate-gene approach method and genome-wide association screening were used to select SNPs related to the body burden of heavy metals. Genotyping analysis of the final 192 SNPs selected was performed on 1,483 subjects using the VeraCode Goldengate assay. Allele frequencies differences and genetic differentiations between the Korean population and Chinese (CHB), Japanese (JPT), Caucasian (CEU), and African (YIR) populations were tested by Fisher’s exact test and fixation index (FST), respectively. The Korean population was genetically similar to the CHB and JPT populations (FST < 0.05, for all SNPs in both populations). However, a significant difference in the allele frequencies between the Korean and CEU and YIR populations were observed in 99 SNPs (60.7%) and 120 SNPs (73.6%), respectively. Ten (6.1%) and 26 (16.0%) SNPs had genetic differentiation (FST > 0.05) among the Korean-CEU and Korean-YIR comparisons, respectively. The SNP with the largest FST value between the Korean and African populations was cystathionine-β-synthase rs234709 (FST: KOR-YIR, 0.309; KOR-CEU, 0.064). Our study suggests that interethnic differences exist in SNPs associated with heavy metals of Koreans, and it should be considered in future studies that address ethnic differences in heavy-metal concentrations in the body and genetic susceptibility to the body burden of heavy metals. PMID:27437086

  15. Frequency of the apolipoprotein E epsilon 4 allele in a case-control study of early onset Parkinson's disease.

    PubMed Central

    Whitehead, A S; Bertrandy, S; Finnan, F; Butler, A; Smith, G D; Ben-Shlomo, Y

    1996-01-01

    OBJECTIVES: It has been suggested that Parkinson's disease and Alzheimer's disease may share a common or at least overlapping aetiology. The prevalence of dementia among cases of Parkinson's disease is known to be greater than expected in the general population. The frequency of the apolipoprotein epsilon 4 allele in a large case-control study of early onset Parkinson's disease has been examined. METHODS: 215 patients and 212 population based controls were recruited from the Republic of Ireland between 1992 and 1994. Cases had to have disease onset at 55 years or younger and be born after 1925. RESULTS: The frequency of the epsilon 4 allele was almost identical between cases of Parkinson's disease (14.6%) and healthy controls (13.3%). There was no relation between epsilon 4 status and disease onset, disease duration, Hoehn and Yahr score, and disease progression. The frequency of the epsilon 4 allele was not increased among 10 patients with Parkinson's disease with dementia (10.0%) compared with the other patients without dementia (14.8%). There was no association between epsilon 4 allele status and either a history of smoking, family history of dementia, or Parkinson's disease, or being born in a rural area. The odds ratio for the ApoE epsilon 4 allele associated with Parkinson's disease was 1.10 (95% confidence interval (95% CI) 0.68-1.79), adjusting for age group, sex, and residential status. The pooled odds ratio from a meta-analysis of six studies of ApoE epsilon 4 status and Parkinson's disease was 0.94 (95% CI 0.69-1.27). CONCLUSIONS: The results from our study as well as the pooled meta-analysis exclude any important role for ApoE epsilon 4 status in the development of Parkinson's disease. Our results similarly do not support its role either in dementia associated with Parkinson's disease or disease prognosis. PMID:8890771

  16. Prion protein genotype survey confirms low frequency of scrapie-resistant K222 allele in British goat herds.

    PubMed

    Goldmann, W; Marier, E; Stewart, P; Konold, T; Street, S; Langeveld, J; Windl, O; Ortiz-Pelaez, A

    2016-02-13

    Scrapie in goats is a transmissible, fatal prion disease, which is endemic in the British goat population. The recent success in defining caprine PRNP gene variants that provide resistance to experimental and natural classical scrapie has prompted the authors to conduct a survey of PRNP genotypes in 10 goat breeds and 52 herds to find goats with the resistant K222 allele. They report here the frequencies in 1236 tested animals of the resistance-associated K222 and several other alleles by breed and herd. Eight animals were found to be heterozygous QK222 goats (0.64 per cent genotype frequency, 95 per cent CI 0.28 to 1.27 per cent) but no homozygous KK222 goats were detected. The K222 allele was found in Saanen, Toggenburg and Anglo-Nubian goats. The fact that only a few goats with the K222 allele have been identified does not preclude the possibility to design and implement successful breeding programmes at national level.

  17. Prion protein genotype survey confirms low frequency of scrapie-resistant K222 allele in British goat herds

    PubMed Central

    Goldmann, W.; Stewart, P.; Konold, T.; Street, S.; Langeveld, J.; Windl, O.; Ortiz-Pelaez, A.

    2016-01-01

    Scrapie in goats is a transmissible, fatal prion disease, which is endemic in the British goat population. The recent success in defining caprine PRNP gene variants that provide resistance to experimental and natural classical scrapie has prompted the authors to conduct a survey of PRNP genotypes in 10 goat breeds and 52 herds to find goats with the resistant K222 allele. They report here the frequencies in 1236 tested animals of the resistance-associated K222 and several other alleles by breed and herd. Eight animals were found to be heterozygous QK222 goats (0.64 per cent genotype frequency, 95 per cent CI 0.28 to 1.27 per cent) but no homozygous KK222 goats were detected. The K222 allele was found in Saanen, Toggenburg and Anglo-Nubian goats. The fact that only a few goats with the K222 allele have been identified does not preclude the possibility to design and implement successful breeding programmes at national level. PMID:26755614

  18. Case-control study of allele frequencies of 15 short tandem repeat loci in males with impulsive violent behavior

    PubMed Central

    Yang, Chun; Ba, Huajie; Gao, Zhiqin; Zhao, Hanqing; Yu, Haiying; Guo, Wei

    2013-01-01

    Background Analysis of genetic polymorphisms in short tandem repeats (STRs) is an accepted method for detecting associations between genotype and phenotype but it has not previously been used in the study of the genetics of impulsive violent behavior. Objective Compare the prevalence of different polymorphisms in 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) between men with a history of impulsive violence and male control subjects without a history of impulsive violence. Methods The distributions of the alleles of the 15 STR loci were compared between 407 cases with impulsive violent behavior and 415 controls using AmpFlSTR® Identifiler™ kits. Results Compared to controls, the average frequencies of the following alleles were significantly lower in individuals with a history of violent behavior: allele 10 of TH01 (OR=0.29, 95%CI=0.16-0.52, p<0.0001,), allele 8 of TPOX (OR=0.71, 95%CI=0.58-0.86, p=0.0005), allele 9 of TPOX (OR=0.65, 95%CI=0.47-0.89, p=0.0072) and allele 14 of CSF1PO (OR=0.27, 95%CI=0.11-0.68, p=0.0035). One allele was significantly higher in cases than controls: allele 11 of TPOX (OR=1.79, 95%CI=1.45-2.22, p<0.0001). Conclusions To the best of our knowledge, this is the first behavioral genetic study that clearly demonstrates a close relationship between specific genetic markers and impulsive aggression in non-psychiatric offenders. Further prospective work will be needed to determine whether or not the alleles identified can be considered risk factors for impulsive aggression and, if so, the underlying mechanisms that result in this relationship. PMID:24991178

  19. Genetically Determined Amerindian Ancestry Correlates with Increased Frequency of Risk Alleles for Systemic Lupus Erythematosus

    PubMed Central

    Sanchez, E; Webb, R; Rasmussen, A.; Kelly, J.A; Riba, L.; Kaufman, K.M.; Garcia-de la Torre, I.; Moctezuma, J.F.; Maradiaga-Ceceña, M.A.; Cardiel, M.; Acevedo, E.; Cucho-Venegas, M.; Garcia, M.A.; Gamron, S.; Pons-Estel, B.A.; Vasconcelos, C.; Martin, J.; Tusié-Luna, T.; Harley, J.B.; Richardson, B.; Sawalha, A.H.; Alarcón-Riquelme, M.E.

    2011-01-01

    Objectives To analyze if genetically determined Amerindian ancestry predicts the increased presence of risk alleles of known susceptibility genes for systemic lupus erythematosus. Methods Single nucleotide polymorphisms within 16 confirmed genetic susceptibility loci for SLE were genotyped in a set of 804 Mestizo lupus patients and 667 Mestizo normal healthy controls. In addition, 347 admixture informative markers were genotyped. Individual ancestry proportions were determined using STRUCTURE. Association analysis was performed using PLINK, and correlation of the presence of risk alleles with ancestry was done using linear regression. Results A meta-analysis of the genetic association of the 16 SNPs across populations showed that TNFSF4, STAT4, PDCD1, ITGAM, and IRF5 were associated with lupus in a Hispanic-Mestizo cohort enriched for European and Amerindian ancestry. In addition, two SNPs within the MHC region, previously associated in a genome-wide association study in Europeans, were also associated in Mestizos. Using linear regression we predict an average increase of 2.34 risk alleles when comparing a lupus patient with 100% Amerindian ancestry to an SLE patient with 0% American Indian Ancestry (p<0.0001). SLE patients with 43% more Amerindian ancestry are predicted to carry one additional risk allele. Conclusion Amerindian ancestry increased the number of risk alleles for lupus. PMID:20848568

  20. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes

    PubMed Central

    Hornoy, Benjamin; Pavy, Nathalie; Gérardi, Sébastien; Beaulieu, Jean; Bousquet, Jean

    2015-01-01

    Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome. Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs. Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources. PMID:26560341

  1. Low Frequency Interstellar Scattering and Pulsar Observations

    NASA Technical Reports Server (NTRS)

    Cordes, James M.

    1992-01-01

    Radio astronomy at frequencies from 2 to 30 MHz challenges time tested methods for extracting usable information from observations. One fundamental reason for this is that propagation effects due to the magnetoionic ionosphere, interplanetary medium, and interstellar matter (ISM) increase strongly with wavelength. The problems associated with interstellar scattering off of small scale irregularities in the electron density are addressed. What is known about interstellar scattering is summarized on the basis of high frequency observations, including scintillation and temporal broadening of pulsars and angular broadening of various galactic and extragalactic radio sources. Then those high frequency phenomena are addressed that are important or detectable at low frequencies. The radio sky becomes much simpler at low frequencies, most pulsars will not be seen as time varying sources, intensity variations will be quenched or will occur on time scales much longer than a human lifetime, and many sources will be angularly broadened and/or absorbed into the noise. Angular broadening measurements will help delineate the galactic distribution and power spectrum of small scale electron density irregularities.

  2. Allelic frequencies and association with carcass traits of six genes in local subpopulations of Japanese Black cattle.

    PubMed

    Nishimaki, Takahiro; Ibi, Takayuki; Siqintuya; Kobayashi, Naohiko; Matsuhashi, Tamako; Akiyama, Takayuki; Yoshida, Emi; Imai, Kazumi; Matsui, Mayu; Uemura, Keiichi; Eto, Hisayoshi; Watanabe, Naoto; Fujita, Tatsuo; Saito, Yosuke; Komatsu, Tomohiko; Hoshiba, Hiroshi; Mannen, Hideyuki; Sasazaki, Shinji; Kunieda, Tetsuo

    2016-04-01

    Marker-assisted selection (MAS) is expected to accelerate the genetic improvement of Japanese Black cattle. However, verification of the effects of the genes for MAS in different subpopulations is required prior to the application of MAS. In this study, we investigated the allelic frequencies and genotypic effects for carcass traits of six genes, which can be used in MAS, in eight local subpopulations. These genes are SCD, FASN and SREBP1, which are associated with the fatty acid composition of meat, and NCAPG, MC1R and F11, which are associated with carcass weight, coat color and blood coagulation abnormality, respectively. The frequencies of desirable alleles of SCD and FASN were relatively high and that of NCAPG was relatively low, and NCAPG was significantly associated with several carcass traits, including carcass weight. The proportions of genotypic variance explained by NCAPG to phenotypic variance were 4.83 for carcass weight. We thus confirmed that NCAPG is a useful marker for selection of carcass traits in these subpopulations. In addition, we found that the desirable alleles of six genes showed no negative effects on carcass traits. Therefore, selection using these genes to improve target traits should not have negative impacts on carcass traits.

  3. Mytilus galloprovincialis-type foot-protein-1 alleles occur at low frequency among mussels in the Dutch Wadden Sea

    NASA Astrophysics Data System (ADS)

    Luttikhuizen, Pieternella C.; Koolhaas, Anita; Bol, Anneke; Piersma, Theunis

    2002-11-01

    The presence of M. galloprovincialis-type genes among the population of mussels in the Dutch Wadden Sea, historically described as M. edulis, was assessed. We applied the molecular technique in which a fragment of the gene coding for an adhesive protein of the byssus of mussels is amplified by PCR and assayed for length using electrophoresis. Among 321 individual mussels collected in August-October 2001 at 14 sites (5 intertidal, 9 subtidal) widely dispersed over the Dutch Wadden Sea, 6 specimens (collected at 5 sites) were found that showed a heterozygote genotype with both the M. edulis- and the M. galloprovincialis-type alleles being amplified; all others were identified as homozygotes for the M. edulis-type allele. Differentiation in frequencies of heterozygotes among sites was not detected. The fact that the M. galloprovincialis-type allele was present at low frequency (0.0093) may be attributed to one of three possible, and not mutually exclusive, causes: incomplete diagnosticity of this marker, an historically stable introgression zone in the Wadden Sea, or a recent invasion.

  4. Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations

    PubMed Central

    González-Galarza, Faviel F.; Takeshita, Louise Y.C.; Santos, Eduardo J.M.; Kempson, Felicity; Maia, Maria Helena Thomaz; Silva, Andrea Luciana Soares da; Silva, André Luiz Teles e; Ghattaoraya, Gurpreet S.; Alfirevic, Ana; Jones, Andrew R.; Middleton, Derek

    2015-01-01

    It has been 12 years since the Allele Frequency Net Database (AFND; http://www.allelefrequencies.net) was first launched, providing the scientific community with an online repository for the storage of immune gene frequencies in different populations across the world. There have been a significant number of improvements from the first version, making AFND a primary resource for many clinical and scientific areas including histocompatibility, immunogenetics, pharmacogenetics and anthropology studies, among many others. The most widely used part of AFND stores population frequency data (alleles, genes or haplotypes) related to human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors (KIR), major histocompatibility complex class I chain-related genes (MIC) and a number of cytokine gene polymorphisms. AFND now contains >1400 populations from more than 10 million healthy individuals. Here, we report how the main features of AFND have been updated to include a new section on ‘HLA epitope’ frequencies in populations, a new section capturing the results of studies identifying HLA associations with adverse drug reactions (ADRs) and one for the examination of infectious and autoimmune diseases associated with KIR polymorphisms—thus extending AFND to serve a new user base in these growing areas of research. New criteria on data quality have also been included. PMID:25414323

  5. HLA-Cw Allele Frequency in Definite Meniere’s Disease Compared to Probable Meniere’s Disease and Healthy Controls in an Iranian Sample

    PubMed Central

    Dabiri, Sasan; Ghadimi, Fatemeh; Firouzifar, Mohammadreza; Yazdani, Nasrin; Mohammad-Amoli, Mahsa; Vakili, Varasteh; Mahvi, Zahra

    2016-01-01

    Introduction Several lines of evidence support the contribution of autoimmune mechanisms in the pathogenesis of Meniere’s disease. The aim of this study was determining the association between HLA-Cw Alleles in patients with definite Meniere’s disease and patients with probable Meniere’s disease and a control group. Materials and Methods: HLA-Cw genotyping was performed in 23 patients with definite Meniere’s disease, 24 with probable Meniere’s disease, and 91 healthy normal subjects, using sequence specific primers polymerase chain reaction technique. The statistical analysis was performed using stata 8 software. Results: There was a significant association between HLA-Cw*04 and HLA-Cw*16 in both definite and probable Meniere’s disease compared to normal healthy controls. We observed a significant difference in HLA-Cw*12 frequencies between patients with definite Meniere’s disease compared to patients with probable Meniere’s disease (P=0.04). The frequency of HLA-Cw*18 is significantly higher in healthy controls (P=0.002). Conclusion: Our findings support the rule of HLA-Cw Alleles in both definite and probable Meniere’s disease. In addition, differences in HLA-Cw*12 frequency in definite and probable Meniere’s disease in our study’s population might indicate distinct immune and inflammatory mechanisms involved in each condition. PMID:27602337

  6. HLA-Cw Allele Frequency in Definite Meniere’s Disease Compared to Probable Meniere’s Disease and Healthy Controls in an Iranian Sample

    PubMed Central

    Dabiri, Sasan; Ghadimi, Fatemeh; Firouzifar, Mohammadreza; Yazdani, Nasrin; Mohammad-Amoli, Mahsa; Vakili, Varasteh; Mahvi, Zahra

    2016-01-01

    Introduction Several lines of evidence support the contribution of autoimmune mechanisms in the pathogenesis of Meniere’s disease. The aim of this study was determining the association between HLA-Cw Alleles in patients with definite Meniere’s disease and patients with probable Meniere’s disease and a control group. Materials and Methods: HLA-Cw genotyping was performed in 23 patients with definite Meniere’s disease, 24 with probable Meniere’s disease, and 91 healthy normal subjects, using sequence specific primers polymerase chain reaction technique. The statistical analysis was performed using stata 8 software. Results: There was a significant association between HLA-Cw*04 and HLA-Cw*16 in both definite and probable Meniere’s disease compared to normal healthy controls. We observed a significant difference in HLA-Cw*12 frequencies between patients with definite Meniere’s disease compared to patients with probable Meniere’s disease (P=0.04). The frequency of HLA-Cw*18 is significantly higher in healthy controls (P=0.002). Conclusion: Our findings support the rule of HLA-Cw Alleles in both definite and probable Meniere’s disease. In addition, differences in HLA-Cw*12 frequency in definite and probable Meniere’s disease in our study’s population might indicate distinct immune and inflammatory mechanisms involved in each condition.

  7. SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?

    PubMed

    Schunter, C; Garza, J C; Macpherson, E; Pascual, M

    2014-01-01

    Single nucleotide polymorphisms (SNPs) are rapidly becoming the marker of choice in population genetics due to a variety of advantages relative to other markers, including higher genomic density, data quality, reproducibility and genotyping efficiency, as well as ease of portability between laboratories. Advances in sequencing technology and methodologies to reduce genomic representation have made the isolation of SNPs feasible for nonmodel organisms. RNA-seq is one such technique for the discovery of SNPs and development of markers for large-scale genotyping. Here, we report the development of 192 validated SNP markers for parentage analysis in Tripterygion delaisi (the black-faced blenny), a small rocky-shore fish from the Mediterranean Sea. RNA-seq data for 15 individual samples were used for SNP discovery by applying a series of selection criteria. Genotypes were then collected from 1599 individuals from the same population with the resulting loci. Differences in heterozygosity and allele frequencies were found between the two data sets. Heterozygosity was lower, on average, in the population sample, and the mean difference between the frequencies of particular alleles in the two data sets was 0.135 ± 0.100. We used bootstrap resampling of the sequence data to predict appropriate sample sizes for SNP discovery. As cDNA library production is time-consuming and expensive, we suggest that using seven individuals for RNA sequencing reduces the probability of discarding highly informative SNP loci, due to lack of observed polymorphism, whereas use of more than 12 samples does not considerably improve prediction of true allele frequencies.

  8. Allelic frequency of the MCP-1 promoter -2518 polymorphism in the Turkish population and in Turkish patients with juvenile rheumatoid arthritis.

    PubMed

    Ozyürek, A Ruhi; Gürses, Dolunay; Ulger, Zülal; Levent, Ertürk; Bakiler, A Rahmi; Berdeli, Afig

    2007-04-01

    Although genetic and environmental factors contribute to the pathogenesis of juvenile rheumathoid arthritis (JRA), the etiology and pathogenesis remain controversial. The objective of this study was to investigate genotypic and allelic frequencies of monocyte chemoattractant protein-1 (MCP-1) gene -2518 (G/A) polymorphism in the healthy Turkish population and patients with JRA. Genomic DNA was collected from 66 JRA patients and 150 healthy individuals. To evaluate the association of the -2518 (G/A) MCP-1 gene polymorphism with the outcome of JRA, we analyzed the types of JRA and the score on the childhood health assessment questionnaire (C-HAQ score). In the healthy Turkish population, the frequencies of A and G alleles were 71 and 29%, respectively. No significant difference was observed between the JRA patients and healthy subjects in the distribution allelic and genotypic frequencies of the -2518 (G/A) MCP-1 gene polymorphism (p>0.05). However, the AG genotype was found to be higher and the AA genotype was found to be lower in the patients with systemic type JRA compared to those with the other types of JRA (p=0.019). When the JRA patients were evaluated according to the C-HAQ score, we found that the -2518 (G/A) MCP-1 gene polymorphism did not relate the prognosis (p>0.05). AG genotype was found to be higher in the systemic type of JRA. The results indicate that MCP-1 gene polymorphism might slightly associate with patients with systemic JRA. Further studies are needed to elucidate the role of this polymorphism in the pathogenesis of JRA in various populations because this polymorphism has a functional significance and an ethnic difference.

  9. Genetic comparison of lake sturgeon populations: Differentiation based on allelic frequencies at seven microsatellite loci

    USGS Publications Warehouse

    McQuown, E.; Krueger, C.C.; Kincaid, H.L.; Gall, G.A.E.; May, B.

    2003-01-01

    The lake sturgeon (Acipenser fulvescens) has recently become a high priority for restoration management because of the near extinction of the species from many areas of North America. The identification of the level of population differentiation that naturally exists among lake sturgeon populations will be useful in the development of management plans to conserve and restore diversity, and in the choice of donor populations to use for re-introduction. Genetic variation among and within 210 lake sturgeon collected from seven locations (St. Lawrence River, Des Prairies River (tributary to the St. Lawrence River), Mattagami River (Hudson Bay drainage), Menominee River (Lake Michigan drainage), Wolf River (Lake Michigan drainage), Niagara River, and Lake Erie) was examined based on allelic variation at seven microsatellite loci (four disomic and three putative tetrasomic). High levels of variability were detected at these loci. Analyses revealed an average of 8.6 alleles per locus (range 5 to 12 alleles per locus) and heterozygosity values at the four disomic loci ranging from 0.46 to 0.66. Multivariate factor analysis of Nei's genetic distance values produced three distinct population groups that were organized by geography: 1) Mattagami (northern Quebec), 2) Menominee/ Wolf (Lake Michigan - Wisconsin), and 3) St. Lawrence/ Des Prairies/ Niagara/ Erie (lower Great Lakes). Differences based on G-tests summed over all loci occurred between all possible paired comparisons of the collections (P < 0.01). These analyses indicated that lake sturgeon populations are differentiated within the Great Lakes basin. Managers of this species will need to identify individual populations in their jurisdictions and provide separate consideration for their conservation and rehabilitation.

  10. Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans.

    PubMed

    Keinan, Alon; Mullikin, James C; Patterson, Nick; Reich, David

    2007-10-01

    Large data sets on human genetic variation have been collected recently, but their usefulness for learning about history and natural selection has been limited by biases in the ways polymorphisms were chosen. We report large subsets of SNPs from the International HapMap Project that allow us to overcome these biases and to provide accurate measurement of a quantity of crucial importance for understanding genetic variation: the allele frequency spectrum. Our analysis shows that East Asian and northern European ancestors shared the same population bottleneck expanding out of Africa but that both also experienced more recent genetic drift, which was greater in East Asians.

  11. Allele frequencies of BRAFV600 mutations in primary melanomas and matched metastases and their relevance for BRAF inhibitor therapy in metastatic melanoma

    PubMed Central

    Satzger, Imke; Marks, Lena; Kerick, Martin; Klages, Sven; Berking, Carola; Herbst, Rudolf; Völker, Bernward; Schacht, Vivien; Timmermann, Bernd; Gutzmer, Ralf

    2015-01-01

    Background The detection of BRAFV600 mutations in patients with metastatic melanoma is important because of the availability of BRAF inhibitor therapy. However, the clinical relevance of the frequency of BRAFV600 mutant alleles is unclear. Patients and Methods Allele frequencies of BRAFV600 mutations were analyzed by ultra-deep next-generation sequencing in formalin-fixed, paraffin-embedded melanoma tissue (75 primary melanomas and 88 matched metastases). In a second study, pretreatment specimens from 76 patients who received BRAF inhibitors were retrospectively analyzed, and BRAFV600 allele frequencies were correlated with therapeutic results. Results Thirty-five patients had concordantly BRAF-positive and 36 (48%) patients had concordantly BRAF-negative primary melanomas and matched metastases, and four patients had discordant samples with low allele frequencies (3.4–5.2%). Twenty-six of 35 patients with concordant samples had BRAFV600E mutations, three of whom had additional mutations (V600K in two patients and V600R in one) and nine patients had exclusively non-V600E mutations (V600K in eight patients and V600E -c.1799_1800TG > AA- in one patient). The frequency of mutated BRAFV600 alleles was similar in the primary melanoma and matched metastasis in 27/35 patients, but differed by >3-fold in 8/35 of samples. BRAFV600E allele frequencies in pretreatment tumor specimens were not significantly correlated with treatment outcomes in 76 patients with metastatic melanoma who were treated with BRAF inhibitors. Conclusions BRAFV600 mutation status and allele frequency is consistent in the majority of primary melanomas and matched metastases. A small subgroup of patients has double mutations. BRAFV600 allele frequencies are not correlated with the response to BRAF inhibitors. PMID:26498143

  12. Allele and haplotype frequencies for HLA-DQ in Iranian celiac disease patients

    PubMed Central

    Rostami-Nejad, Mohammad; Romanos, Jihane; Rostami, Kamran; Ganji, Azita; Ehsani-Ardakani, Mohammad Javad; Bakhshipour, Ali-Reza; Zojaji, Homayoun; Mohebbi, Seyed Reza; Zali, Mohammad-Reza; Wijmenga, Cisca

    2014-01-01

    AIM: To assess the distribution of human leukocyte antigen (HLA)-DQ2 and -DQ8 in Iranian celiac disease (CD) patients and compare them to healthy Iranian controls. METHODS: To predict the HLA-DQA1 and -DQB1 genes, we used six previously reported HLA-tagging single nucleotide polymorphism to determine HLA genotypes in 59 Iranian patients with ‘biopsy-confirmed’ CD and in 151 healthy Iranian individuals. To test the transferability of the method, 50 cases and controls were also typed using a commercial kit that identifies individual carriers of DQ2, DQ7 and DQ8 alleles. RESULTS: In this pilot study 97% of CD cases (n = 57) and 58% of controls (n = 87) were carriers of HLA-DQ2 and/or HLA-DQ8 heterodimers, either in the homozygous or heterozygous state. The HLA-DQ pattern of these 57 CD patients: heterozygous DQ2.2 (n = 14) and homozygous DQ2.2 (n = 1), heterozygous DQ2.5 (n = 33) and homozygous DQ2.5 (n = 8), heterozygous DQ8 (n = 13) and homozygous DQ8 (n = 2). Two CD patients were negative for both DQ2 and DQ8 (3%). CONCLUSION: The prevalence of DQ8 in our CD population was higher than that reported in other populations (25.4%). As reported in other populations, our results underline the primary importance of HLA-DQ alleles in the Iranian population’s susceptibility to CD. PMID:24876751

  13. Human Leukocyte Antigens-A, -B, -C, -DRB1 allele and haplotype frequencies in Americans originating from Southern Europe: Contrasting patterns of population differentiation between Italian and Spanish Americans

    PubMed Central

    Mack, Steven J.; Tu, Bin; Yang, Ruyan; Masaberg, Carly; Ng, Jennifer; Hurley, Carolyn Katovich

    2010-01-01

    High resolution DNA sequencing was used to identify the HLA-A, -B, -C, and -DRB1 alleles found in 552 individuals from the United States indicating Southern European (Italian or Spanish) heritage. A total of 46 HLA-A, 80 HLA-B, 32 HLA-C, and 50 DRB1 alleles were identified. Frequent alleles included A*02:01:01G (allele frequency = 0.26 in Italian Americans; 0.22 in Spanish Americans); B*07:02:01G (Italian Americans allele frequency = 0.11); B*44:03 (Spanish Americans allele frequency = 0.07); C*04:01:01G and C*07:01:01G (allele frequency = 0.13 and 0.16, respectively, in Italian Americans; 0.15 and 0.12, respectively, in Spanish Americans); and DRB1*07:01:01 (allele frequency = 0.12 in each population). The action of balancing selection was inferred at the HLA-B and -C loci in both populations. The A*01:01:01G-C*07:01:01G-B*08:01:01G-DRB1*03:01:01 haplotype was the most frequent A-C-B-DRB1 haplotype in Italian Americans (haplotype frequency = 0.049), and was the second most frequent haplotype in Spanish Americans (haplotype frequency = 0.021). A*29:02:01-C*16:01:01-B*44:03-DRB1*07:01:01 was the most frequent A-C-B-DRB1 haplotype in Spanish Americans (haplotype frequency = 0.023), and was observed at a frequency of 0.015 in Italian Americans. Pairwise F’st values measuring the degree of differentiation between these Southern European-American populations and European and European-American populations suggest that Spanish Americans constitute a distinct subset of the European-American population, most similar to Mexican Americans, whereas Italian Americans cannot be distinguished from the larger European-American population. PMID:20974205

  14. Allele and haplotype frequencies of HLA-A, B, C, DRB1 and DQB1 genes in polytransfused patients in ethnically diverse populations from Brazil.

    PubMed

    Rodrigues, C; Macedo, L C; Bruder, A V; Quintero, F d C; de Alencar, J B; Sell, A M; Visentainer, J E L

    2015-10-01

    The red blood transfusion is a practice often used in patients with haematological and oncological diseases. However, the investigation of human leucocyte antigen (HLA) system frequency in these individuals is of great importance because multiple transfusions may lead to HLA alloimmunization. Brazil is a country that was colonized by many other ethnicities, leading to a mixed ethnicity and regionalized population. In view of the importance of HLA typing in these patients, the aim of this study was to investigate the allele and haplotype frequencies from polytransfused patients from three different regions from Brazil. HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 genotyping of 366 patients was performed by PCR-SSO, based on the Luminex technology (One Lambda(®) ), and the anti-HLA class I and class II antibodies were analysed using LabScreen Single Antigen Antibody Detection (One Lambda, Inc.). Allele and haplotype frequencies of polytransfused patients of three regions from Brazil were obtained using the Arlequin program. The most frequent allele frequencies observed were HLA-A*02, A*03, B*15, B*35, B*51, C*07, C*04, C*03, DRB1*13, DRB1*11, DRB1*07, DRB1*03, DRB1*01, DQB1*03, DQB1*02, DQB1*06 and DQB1*05. There were differences between the groups for allele variants HLA-B*57 (between Group 1 and Group 2) and HLA-C*12 (between Group 1 and Group 3). The most frequent haplotypes found in the sample were HLA-A*01B*08DRB1*03, DRBI*07DQB1*02, DRB1*01DQB1*05, DRB1*13DQB1*06 and A*02B*35. HLA class I and II antibodies were detected in 77.9% and 63.9% patients, respectively, while the both alloantibodies were detected in 62 (50.9%) patients. In conclusion, the HLA typing for polytransfused patients in each region has a great importance, as seen in this study; individuals from different regions from Brazil have HLA distribution not completely homogeneous.

  15. Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African Buffalo: a plausible new mechanism for a high frequency anomaly.

    PubMed

    van Hooft, Pim; Greyling, Ben J; Getz, Wayne M; van Helden, Paul D; Zwaan, Bas J; Bastos, Armanda D S

    2014-01-01

    Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer) population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite being associated with low body condition, appears to impart a relative reproductive advantage, and which is stably maintained through a sex-ratio suppressor. Apparently, this sex-ratio suppressor prevents fertility reduction that generally accompanies sex-ratio distortion. We hypothesize that this body-condition-associated reproductive advantage increases the fitness of alleles that negatively affect male body condition, causing genome-wide positive selection of these alleles. To investigate this we genotyped 459 buffalo using 17 autosomal microsatellites. By correlating heterozygosity with body condition (heterozygosity-fitness correlations), we found that most microsatellites were associated with one of two gene types: one with elevated frequencies of deleterious alleles that have a negative effect on body condition, irrespective of sex; the other with elevated frequencies of sexually antagonistic alleles that are negative for male body condition but positive for female body condition. Positive selection and a direct association with a Y-chromosomal sex-ratio suppressor are indicated, respectively, by allele clines and by relatively high numbers of homozygous deleterious alleles among sex-ratio suppressor carriers. This study, which employs novel statistical techniques to analyse heterozygosity-fitness correlations, is the first to demonstrate the abundance of sexually-antagonistic genes in a natural mammal population. It also has important

  16. HLA-DRB1 and HLA-DQB1 allele associations in an Albanian patient population with rheumatoid arthritis: correlations with the specific autoantibody markers and inter-population DRB1 allele frequency variability.

    PubMed

    Prifti-Kurti, Margarita; Nunes, José Manuel; Shyti, Erkena; Ylli, Zamira; Sanchez-Mazas, Alicia; Sulcebe, Genc

    2014-08-01

    The prevalence of rheumatoid arthritis and its specific autoantibodies varies in different populations. This variability depends on the genetic polymorphism of the immune response genes among which the HLA system plays a major role. In this context, we studied the HLA-DRB1 and HLA-DQB1 first-level allele frequencies in 100 Albanian patients with rheumatoid arthritis (RA), and taking into account their rheumatoid factor (RF) and anticitrullinated peptide antibodies (ACPA) serologic subgroups, we compared them with the respective frequencies in a population of 191 Albanian individuals without known pathology. No differences were found between the controls and the RA patient group as a whole, but three statistically significant differences were found: an increase in DRB1*04 among ACPA+, RF+ and ACPA+/RF+ patients, a significant decrease in DRB1*11 among ACPA+/RF+ and also a decrease in DRB1*13 among RF+ patient subgroups. Comparing allele frequencies of putatively associated RA alleles in different European populations revealed a significant negative correlation between the RA predisposing DRB1*04 and protective DRB1*11 allele frequencies. A statistically significant correlation was also found between RA prevalence rates and DRB1*04 as well as DRB1*11 frequencies. The relatively low frequencies of DRB1*04 and high DRB1*11 in the Albanian population might explain the rather low positivity rate of ACPA and RF antibodies among the Albanian RA patients. These specific association patterns suggest that this first study of RA in an Albanian population should be followed up to include second level or higher definition of HLA alleles and to compare RA patterns among European populations.

  17. HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies of 10 918 Koreans from bone marrow donor registry in Korea.

    PubMed

    Park, H; Lee, Y-J; Song, E Y; Park, M H

    2016-10-01

    The human leucocyte antigen (HLA) system is the most polymorphic genetic system in humans, and HLA matching is crucial in organ transplantation, especially in hematopoietic stem cell transplantation. We investigated HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies at allelic level in 10 918 Koreans from bone marrow donor registry in Korea. Intermediate resolution HLA typing was performed using Luminex technology (Wakunaga, Japan), and additional allelic level typing was performed using PCR-single-strand conformation polymorphism method and/or sequence-based typing (Abbott Molecular, USA). Allele and haplotype frequencies were calculated by direct counting and maximum likelihood methods, respectively. A total of 39 HLA-A, 66 HLA-B and 47 HLA-DRB1 alleles were identified. High-frequency alleles found at a frequency of ≥5% were 6 HLA-A (A*02:01, *02:06, *11:01, *24:02, *31:01 and *33:03), 6 HLA-B (B*15:01, *35:01, *44:03, *51:01, 54:01 and *58:01) and 8 HLA-DRB1 (DRB1*01:01, *04:05, *04:06, *07:01, *08:03, *09:01, *13:02 and *15:01) alleles. At each locus, A*02, B*15 and DRB1*14 generic groups were most diverse at allelic level, consisting of 9, 12 and 11 different alleles, respectively. A total of 366, 197 and 21 different HLA-A-B-DRB1 haplotypes were estimated with frequencies of ≥0.05%, ≥0.1% and ≥0.5%, respectively. The five most common haplotypes with frequencies of ≥2.0% were A*33:03-B*44:03-DRB1*13:02 (4.97%), A*33:03-B*58:01-DRB1*13:02, A*33:03-B*44:03-DRB1*07:01, A*24:02-B*07:02-DRB1*01:01 and A*24:02-B*52:01-DRB1*15:02. Among 34 serologic HLA-A-B-DR haplotypes with frequencies of ≥0.5%, 17 haplotypes revealed allele-level diversity and majority of the allelic variation was arising from A2, A26, B61, B62, DR4 and DR14 specificities. Haplotype diversity obtained in this study is the most comprehensive data thus far reported in Koreans, and the information will be useful for unrelated stem cell transplantation as well as for disease

  18. Determination of the Allelic Frequency in Smith-Lemli-Opitz Syndrome by Analysis of Massively Parallel Sequencing Data Sets

    PubMed Central

    Cross, Joanna L.; Iben, James; Simpson, Claire; Thurm, Audrey; Swedo, Susan; Tierney, Elaine; Bailey-Wilson, Joan; Biesecker, Leslie G.; Porter, Forbes D.; Wassif, Christopher A.

    2014-01-01

    Data from massively parallel sequencing or “Next Generation Sequencing” of the human exome has reached a critical mass in both public and private databases, in that these collections now allow researchers to critically evaluate population genetics in a manner that was not feasible a decade ago. The ability to determine pathogenic allele frequencies by evaluation of the full coding sequences and not merely a single SNP or series of SNPs will lead to more accurate estimations of incidence. For demonstrative purposes we analyzed the causative gene for the disorder Smith-Lemli-Opitz Syndrome (SLOS), the 7-dehydrocholesterol reductase (DHCR7) gene and determined both the carrier frequency for DHCR7 mutations, and predicted an expected incidence of the disorder. Estimations of the incidence of SLOS have ranged widely from 1:10,000 to 1:70,000 while the carrier frequency has been reported as high as 1 in 30. Using four exome data sets with a total of 17,836 chromosomes, we ascertained a carrier frequency of pathogenic DHRC7 mutations of 1.01%, and predict a SLOS disease incidence of 1/39,215 conceptions. This approach highlights yet another valuable aspect of the exome sequencing databases, to inform clinical and health policy decisions related to genetic counseling, prenatal testing and newborn screening. PMID:24813812

  19. Allele frequency for Cystic fibrosis in Indians vis-a/-vis global populations.

    PubMed

    Bepari, Karnajit Kumar; Malakar, Arup Kumar; Paul, Prosenjit; Halder, Binata; Chakraborty, Supriyo

    2015-01-01

    Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator gene. This gene encodes a protein involved in epithelial anion channel. Cystic fibrosis is the most common life-limiting genetic disorder in Caucasians; it also affects other ethnic groups like the Blacks and the Native Americans. Cystic fibrosis is considered to be rare among individuals from the Indian subcontinent. We analyzed a total of 29 world׳s populations for cystic fibrosis on the basis of gene frequency and heterozygosity. Among 29 countries Switzerland revealed the highest gene frequency and heterozygosity for CF (0.022, 0.043) whereas Japan recorded the lowest values (0.002, 0.004) followed by India (0.004, 0.008). Our analysis suggests that the prevalence of cystic fibrosis is very low in India. PMID:26339151

  20. An Analysis of HLA-A, -B, and -DRB1 Allele and Haplotype Frequencies of 21,918 Residents Living in Liaoning, China

    PubMed Central

    Li, Xiao-Feng; Zhang, Xu; Chen, Yang; Zhang, Kun-Lian; Liu, Xiang-Jun; Li, Jian-Ping

    2014-01-01

    HLA-A, -B and -DRB1 allele frequencies and their haplotype frequencies in 21,918 Chinese residents living in Liaoning Province, who were registered as volunteer donors of China Marrow Donor Registry, were investigated. They are composed of 93.37% Han Chinese, 5.1% Manchus, 0.57% Mongols, 0.46% Hui persons, 0.29% Koreans and 0.14% Xibe ethnic group. In total eighteen different HLA-A alleles, forty-eight different HLA-B alleles and fourteen different HLA-DRB1 alleles have been identified. Their frequencies are in agreement with the Hardy-Weinberg equilibrium. For Han Chinese in Liaoning, 1,534 different HLA-A-B-DRB1 haplotypes were identified, with a frequency of higher than 0.01%. A*30-B*13-DRB1*07, A*02-B*46-DRB1*09 and A*02-B*13-DRB1*12 are the most frequent haplotypes among Liaoning Han. While Liaoning Han, Liaoning Manchu, Liaoning Mongol, Liaoning Hui and Liaoning Korean share the northern Han characteristic haplotypes, all minority ethnic groups with the exception of Liaoning Manchu have developed their own unique HLA profiles. This dataset characterizes the HLA allele and haplotype frequencies in the Liaoning area and suggests that it is different from those in other parts of China and ethnic groups, which implicates transplant donor searching strategies and studies on population genetics. PMID:24691290

  1. POPTREEW: web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities.

    PubMed

    Takezaki, Naoko; Nei, Masatoshi; Tamura, Koichiro

    2014-06-01

    POPTREE software, including the command line (POPTREE) and the Windows (POPTREE2) versions, is available to perform evolutionary analyses of allele frequency data, computing distance measures for constructing population trees and average heterozygosity (H) (measure of genetic diversity within populations) and G(ST) (measure of genetic differentiation among subdivided populations). We have now developed a web version POPTREEW (http://www.med.kagawa-u.ac.jp/∼genomelb/takezaki/poptreew/) to provide cross-platform access to all POPTREE functions including interactive tree editing. Furthermore, new POPTREE software (POPTREE, POPTREE2, and POPTREEW) computes standardized G(ST) and Jost's D, which may be appropriate for data with high variability, and accepts genotype data in GENEPOP format as an input.

  2. Allele frequencies data and statistic parameters for 13 STR loci in a population of the Brazilian Amazon Region.

    PubMed

    Rodrigues, Elzemar Martins Ribeiro; Palha, Teresinha de Jesus Brabo Ferreira; dos Santos, Sidney Emanuel Batista

    2007-05-24

    Allele frequencies for 13 short tandem repeat (D3S1358, vWA, D21S11, D18S51, D5S818, D13S317, D7S820, TH01, TPOX, D16S539, CSF1PO, D8S1179 and FGA) loci were determined in a sample of 325 unrelated individuals from the population of the Amazon of Belém, Brazil. These loci are the most commonly used in forensic and paternity testing. The forensic parameters investigated presented high values. The power of discrimination and the probability of exclusion for these 13 STRs are 99.999999999992% and 99.9998%, respectively. In conclusion, these 13 markers are suitable for forensic analysis and paternity tests of the Amazonian population.

  3. Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies.

    PubMed

    Papadopoulos, Petros; Viennas, Emmanouil; Gkantouna, Vassiliki; Pavlidis, Cristiana; Bartsakoulia, Marina; Ioannou, Zafeiria-Marina; Ratbi, Ilham; Sefiani, Abdelaziz; Tsaknakis, John; Poulas, Konstantinos; Tzimas, Giannis; Patrinos, George P

    2014-01-01

    FINDbase (http://www.findbase.org) aims to document frequencies of clinically relevant genomic variations, namely causative mutations and pharmacogenomic markers, worldwide. Each database record includes the population, ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related databases and the genetic variation together with its frequency in that population. Here, we report, in addition to the regular data content updates, significant developments in FINDbase, related to data visualization and querying, data submission, interrelation with other resources and a new module for genetic disease summaries. In particular, (i) we have developed new data visualization tools that facilitate data querying and comparison among different populations, (ii) we have generated a new FINDbase module, built around Microsoft's PivotViewer (http://www.getpivot.com) software, based on Microsoft Silverlight technology (http://www.silverlight.net), that includes 259 genetic disease summaries from five populations, systematically collected from the literature representing the documented genetic makeup of these populations and (iii) the implementation of a generic data submission tool for every module currently available in FINDbase.

  4. DNA-PCR system FGA (FIBRA)--genotype and allele frequencies in a sample of western Germany (Düsseldorf region).

    PubMed

    Huckenbeck, W; Scheil, H G; Kuntze, K

    1999-12-01

    Frequency data for the STR system FGA (HumFibra) were obtained from a Caucasoid German population sample (Düsseldorf area) of 424 unrelated individuals. PCR products were detected by horizontal polyacrylamid gel electrophoresis and a total of 16 alleles was identified by side-by-side comparison with a commercially available sequenced ladder. The observed genotype distribution showed no significant deviation from the Hardy-Weinberg equilibrium. The high information content (pooled German data: rate of heterozygosity = 0.8626; probability of match = 0.0344; mean exclusion chance = 0.7240) render this system a useful tool not only in forensic casework (criminal and paternity cases) but in population genetics too.

  5. Frequency of BLAD and CVM alleles in sires and elite heifers of Czech Holstein cattle.

    PubMed

    Cítek, J; Rehout, V; Schröffelová, D; Hradecká, E

    2008-12-01

    In this paper, we analyse the occurrence of BLAD and CVM heterozygous animals in Holstein cattle in the Czech Republic in 1993-2005. The occurrence of BLAD heterozygous sires and heifers (BL) during the period 1993-1998 in Czech Holsteins was 13.9% and 10.7%. Radical measures have been taken to restore the population. Evidently, the measures have been efficient, in 2005 one BLAD heterozygous sire of 101 was found. Continuous testing is necessary, because in commercial herds, the eradication process is not short-term. The found occurrence ofCVM heterozygous sires (CV) decreased from 20% in 2001 to 8% (7 positive of 85) in 2005.This is still quite a high frequency. The occurrence in CV females of 20% remains higher. Therefore, the use of CV sires should be restricted thoroughly. Identification of the molecular basis for inherited diseases, should lead to control measures which would enable the quick recovery of the population. PMID:19113030

  6. Could FIV zoonosis responsible of the breakdown of the pathocenosis which has reduced the European CCR5-Delta32 allele frequencies?

    PubMed Central

    Faure, Eric

    2008-01-01

    Background In Europe, the north-south downhill cline frequency of the chemokine receptor CCR5 allele with a 32-bp deletion (CCR5-Δ32) raises interesting questions for evolutionary biologists. We had suggested first that, in the past, the European colonizers, principally Romans, might have been instrumental of a progressively decrease of the frequencies southwards. Indeed, statistical analyses suggested strong negative correlations between the allele frequency and historical parameters including the colonization dates by Mediterranean civilisations. The gene flows from colonizers to native populations were extremely low but colonizers are responsible of the spread of several diseases suggesting that the dissemination of parasites in naive populations could have induced a breakdown rupture of the fragile pathocenosis changing the balance among diseases. The new equilibrium state has been reached through a negative selection of the null allele. Results Most of the human diseases are zoonoses and cat might have been instrumental in the decrease of the allele frequency, because its diffusion through Europe was a gradual process, due principally to Romans; and that several cat zoonoses could be transmitted to man. The possible implication of a feline lentivirus (FIV) which does not use CCR5 as co-receptor is discussed. This virus can infect primate cells in vitro and induces clinical signs in macaque. Moreover, most of the historical regions with null or low frequency of CCR5-Δ32 allele coincide with historical range of the wild felid species which harbor species-specific FIVs. Conclusion We proposed the hypothesis that the actual European CCR5 allelic frequencies are the result of a negative selection due to a disease spreading. A cat zoonosis, could be the most plausible hypothesis. Future studies could provide if CCR5 can play an antimicrobial role in FIV pathogenesis. Moreover, studies of ancient DNA could provide more evidences regarding the implications of

  7. Temporal changes in allele frequencies in a small marble trout Salmo marmoratus population threatened by extreme flood events.

    PubMed

    Pujolar, J M; Vincenzi, S; Zane, L; Crivelli, A J

    2016-03-01

    The effect of extreme floods on the genetic composition of marble trout Salmo marmoratus living in Lipovscek, a tributary of the Soca River in Slovenia, which has been affected by multiple destructive flood events for centuries was investigated. By monitoring genetic variability during the period 2004-2011, apparent signatures of genetic erosion including a decline in observed and expected heterozygosities and allelic richness were observed. Contemporary effective population size was estimated between 11 and 55 individuals, which is congruent with census data. The data suggest asymmetric gene flow between the two sections of the river. The existence of substantial downstream migration (15-19%) was confirmed by paternity analysis. A small (1-3%) upstream migration was also suggested, which was confirmed by tagging data. Overall, low genetic diversity has not prevented the survival of the Lipovscek population, which might be a common feature of salmonid freshwater populations. PMID:26832308

  8. Gene frequencies of ABO and Rh (D) blood group alleles in a healthy infant population in Ibadan, Nigeria.

    PubMed

    Omotade, O O; Adeyemo, A A; Kayode, C M; Falade, S L; Ikpeme, S

    1999-01-01

    The ABO and Rhesus blood group systems remain the most important blood group systems clinically. In order to provide gene frequency values for the ABO and Rh (D) alleles in a healthy infant population in south west Nigeria, 4748 healthy infants were typed for ABO and Rh (D) blood groups over a five year period (1988-1992). Overall, 2575 (54.2%) were blood group O, 1023 (21.6%) were blood group A, 1017 (21.4%) were blood group B and 133 (2.8%) were blood group AB. The distribution of the ABO blood groups did not differ significantly from those expected under the Hardy Weinberg equilibrium (Goodness-of-fit X2 = 6.09, df = 3, p = 0.1075). The proportions of the infants belonging to the various ABO blood groups did not vary significantly over the period of the study (X2 = 14.53, df = 12, p = 0.268). Overall gene frequencies for the O, A and B genes were 0.7398, 0.1305 and 0.1298 respectively. For the Rh (D) gene, 4520 (95.2%) were Rh-positive while 228 (4.8%) were Rh-negative. However, the proportions of Rh (D) negative infants varied significantly over the period of the study, with a particular year (1991) having nearly twice the usual frequency of Rh-negative individuals (X2 = 31.17, df =, p < 0.001). The frequency of the Rh (D) gene was 0.7809. These figures are reported in the hope that they may find some use as reference for studies of ABO blood groups in health and disease, especially since they were obtained in an infant population in which it is expected that selection pressures should not have started to act to any significant extent.

  9. Apolipoprotein E Allelic Frequency Altered in Women with Early-onset Breast Cancer.

    PubMed

    Porrata-Doria, Tirtsa; Matta, Jaime L; Acevedo, Summer F

    2010-05-24

    Among women, the most prevalent type of cancer is breast cancer, affecting 1 out of every 8 women in the United States; in Puerto Rico, 70 out of every 100,000 will develop some type of breast cancer. Therefore, a better understand of the potential risk factors for breast cancer could lead to the development of early detection tools. A gene that has been proposed as a risk factor in several populations around the world is Apolipoprotein E (apoE). ApoE functions as a mechanism of transport for lipoproteins and cholesterol throughout the body, with 3 main isoforms present in humans (apoE2, apoE3, and apoE4). Whether or not apoE4 is a risk factor for breast cancer remains controversial. Previous studies have either included test subjects of all ages (20-80) or have focused on late-onset (after age 50) breast cancer; none has concentrated specifically on early-onset (aged 50 and younger) breast cancer. The objectives of this study was to examine (in a Puerto Rican population) the differences in the relative frequency of occurrence of apoE4 in non-breast cancer versus breast cancer patients and to examine, as well, the potential differences of same in early- versus late-onset patients. We found an increased frequency of apoE4 (odds ratio 2.15) only in early-onset breast cancer survivors, which is similar to the findings of those studies that combined or adjusted for age as well as for an association between apoE4 and decreased tumor size. ApoE is also a potential risk factor for long-term cognitive effects after chemotherapy and affects response to hormone replacement. Our data supports the theory that knowing the apoE genotype of women who are at risk of developing breast cancer may be beneficial, as such knowledge would aid in the prediction of tumor size and the development of treatment regimens.

  10. Frequency requirements for active earth observation sensors

    NASA Technical Reports Server (NTRS)

    1977-01-01

    The foundation and rationale for the selection of microwave frequencies for active remote sensing usage and for subsequent use in determination of sharing criteria and allocation strategies for the WARC-79 are presented.

  11. Variation in Meiotic Recombination Frequencies Between Allelic Transgenes Inserted at Different Sites in the Drosophila melanogaster Genome

    PubMed Central

    McMahan, Susan; Kohl, Kathryn P.; Sekelsky, Jeff

    2013-01-01

    Meiotic crossovers are distributed nonrandomly across the genome. Classic studies in Drosophila suggest that the position of a gene along a chromosome arm can affect the outcome of the recombination process, with proximity to the centromere being associated with lower crossing over. To examine this phenomenon molecularly, we developed an assay that measures meiotic crossovers and noncrossover gene conversions between allelic transgenes inserted into different genomic positions. To facilitate collecting a large number of virgin females, we developed a useful genetic system that kills males and undesired classes of females. We found that the recombination frequency at a site in the middle of the X chromosome, where crossovers are normally frequent, was similar to the frequency at the centromere-proximal end of the euchromatin, where crossovers are normally infrequent. In contrast, we recovered no recombinants—crossovers or noncrossovers—at a site on chromosome 4 and at a site toward the distal end of the X chromosome. These results suggest that local sequence or chromatin features have a stronger impact on recombination rates in this transgene assay than position along the chromosome arm. PMID:23797104

  12. Allele and genotype frequencies of CYP2C9, CYP2C19 and CYP2D6 in an Italian population.

    PubMed

    Scordo, Maria Gabriella; Caputi, Achille P; D'Arrigo, Concetta; Fava, Giuseppina; Spina, Edoardo

    2004-08-01

    The polymorphic cytochrome P450 isoenzymes (CYPs) 2C9, 2C19 and 2D6 metabolise many important drugs, as well as other xenobiotics. Their polymorphism gives rise to important interindividual and interethnic variability in the metabolism and disposition of several therapeutic agents and may cause differences in the clinical response to these drugs. In this study, we determined the genotype profile of a random Italian population in order to compare the CYP2C9, CYP2C19 and CYP2D6 allele frequencies among Italians with previous findings in other Caucasian populations. Frequencies for the major CYP2C9, CYP2C19 and CYP2D6 mutated alleles and genotypes have been evaluated in 360 unrelated healthy Italian volunteers (210 males and 150 females, aged 19-52 years). Genotyping has been carried out on peripheral leukocytes DNA by molecular biology techniques (PCR, RFLP, long-PCR). CYP2C9, CYP2C19 and CYP2D6 allele and genotype frequencies resulted in equilibrium with the Hardy-Weinberg equation. One hundred and fourteen subjects (31.7%) carried one and 23 subjects (6.4%) carried two CYP2C9 mutated alleles. Sixty-eight (18.9%) volunteers were found to be heterozygous and six (1.7%) homozygous for the CYP2C19*2, while no CYP2C19*3 was detected in the evaluated population. Volunteers could be divided into four CYP2D6 genotypes groups: 192 subjects (53.3%) with no mutated alleles (homozygous extensive metabolisers, EM), 126 (35.0%) with one mutated allele (heterozygous EM), 12 (3.4%) with two mutated alleles (poor metabolisers, PM) and 30 (8.3%) with extracopies of a functional gene (ultrarapid metabolisers, UM). Frequencies of both CYP2C9 and CYP2C19 allelic variants, as well as CYP2D6 detrimental alleles, in Italian subjects were similar to those of other Caucasian populations. Conversely, the prevalence of CYP2D6 gene duplication among Italians resulted very high, confirming the higher frequency of CYP2D6 UM in the Mediterranean area compared to Northern Europe. PMID:15177309

  13. Polarimetric Observations at Low Radio Frequencies

    NASA Astrophysics Data System (ADS)

    Farnes, J. S.

    2012-06-01

    Magnetic fields play a fundamental role in the evolution of astrophysical systems. These fields can be studied through wide-field spectropolarimetry, which allows for faint polarised signals to be detected at relatively low radio frequencies. An interferometric polarisation mode has recently become available at the Giant Metrewave Radio Telescope (GMRT). A detailed analysis of the GMRT's instrumental response is presented. The findings are used to create a polarisation pipeline, which in combination with rotation measure (RM) Synthesis is used for the detection of extended linearly polarised emission at 610 MHz. A number of compact sources are detected and their Faraday depth and polarisation fraction are reported. New holography observations of the GMRT's primary beam are presented. Instantaneous off-axis polarisation is substantial and scales with the Stokes I beam. The developed beam models are used to reduce direction-dependent instrumental polarisation, and the Stokes I beam is shown to deviate from circular symmetry. A new technique for electric vector polarisation angle calibration is developed that removes the need for known sources on the sky, eliminates ionospheric effects, and avoids a flaw in current methods which could erroneously yield multiple Faraday components for sources that are well-parameterised by a single RM. A sample of nine galaxies from two Southern Compact Groups are then presented, with constraints being placed on the polarised fraction, RM, spectral index, star formation rate, companion sources, and hydrodynamical state. One galaxy has a displaced peak of radio emission that is extended beyond the disk in comparison to the near-IR disk - suggesting the radio disturbance may be a consequence of ram pressure stripping. Linear polarisation is detected from the core of NGC 7552 at 610 MHz, while another three galaxies ESO 0353-G036, NGC 7590, and NGC 7599 are found to be unpolarised. An analysis of additional extended sources allows for an

  14. High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program.

    PubMed

    Zhou, Xiao-Yang; Zhu, Fa-Ming; Li, Jian-Ping; Mao, Wei; Zhang, De-Mei; Liu, Meng-Li; Hei, Ai-Lian; Dai, Da-Peng; Jiang, Ping; Shan, Xiao-Yan; Zhang, Bo-Wei; Zhu, Chuan-Fu; Shen, Jie; Deng, Zhi-Hui; Wang, Zheng-Lei; Yu, Wei-Jian; Chen, Qiang; Qiao, Yan-Hui; Zhu, Xiang-Ming; Lv, Rong; Li, Guo-Ying; Li, Guo-Liang; Li, Heng-Cong; Zhang, Xu; Pei, Bin; Jiao, Li-Xin; Shen, Gang; Liu, Ying; Feng, Zhi-Hui; Su, Yu-Ping; Xu, Zhao-Xia; Di, Wen-Ying; Jiang, Yao-Qin; Fu, Hong-Lei; Liu, Xiang-Jun; Liu, Xiang; Zhou, Mei-Zhen; Du, Dan; Liu, Qi; Han, Ying; Zhang, Zhi-Xin; Cai, Jian-Ping

    2015-01-01

    Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20th, 31st, and 81sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68th, 79th, and 95th haplotypes), one was predominant in the South and Southwest China regions (the 18th haplotype), one was relatively common in the Northeast and North China regions (the 94th haplotype), and one was common in the Northeast, North and Northwest China (the 40th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis

  15. High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program

    PubMed Central

    Zhou, Xiao-Yang; Zhu, Fa-Ming; Li, Jian-Ping; Mao, Wei; Zhang, De-Mei; Liu, Meng-Li; Hei, Ai-Lian; Dai, Da-Peng; Jiang, Ping; Shan, Xiao-Yan; Zhang, Bo-Wei; Zhu, Chuan-Fu; Shen, Jie; Deng, Zhi-Hui; Wang, Zheng-Lei; Yu, Wei-Jian; Chen, Qiang; Qiao, Yan-Hui; Zhu, Xiang-Ming; Lv, Rong; Li, Guo-Ying; Li, Guo-Liang; Li, Heng-Cong; Zhang, Xu; Pei, Bin; Jiao, Li-Xin; Shen, Gang; Liu, Ying; Feng, Zhi-Hui; Su, Yu-Ping; Xu, Zhao-Xia; Di, Wen-Ying; Jiang, Yao-Qin; Fu, Hong-Lei; Liu, Xiang-Jun; Liu, Xiang; Zhou, Mei-Zhen; Du, Dan; Liu, Qi; Han, Ying; Zhang, Zhi-Xin; Cai, Jian-Ping

    2015-01-01

    Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20th, 31st, and 81sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68th, 79th, and 95th haplotypes), one was predominant in the South and Southwest China regions (the 18th haplotype), one was relatively common in the Northeast and North China regions (the 94th haplotype), and one was common in the Northeast, North and Northwest China (the 40th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis

  16. Frequencies of 32 base pair deletion of the (Delta 32) allele of the CCR5 HIV-1 co-receptor gene in Caucasians: a comparative analysis.

    PubMed

    Lucotte, Gérard

    2002-05-01

    The CCR5 gene encodes for the co-receptor for the major macrophage-tropics strains of human immunodeficiency virus (HIV-1), and a mutant allele of this gene (Delta 32) provide to homozygotes a strong resistance against infection by HIV. The frequency of the Delta 32 allele was investigated in 40 populations of 8842 non-infected subjects coming from Europe, the Middle-East and North Africa. A clear north-south decreasing gradient was evident for Delta 32 frequencies, with a significant correlation coefficient (r=0.83). The main frequency value of Delta 32 for Sweden, Norway, Denmark, Finland and Iceland (0.134) is significantly (chi(2)=63.818, P<0.001) highest than the Delta 32 mean value, indicating that probably the Vikings might have been instrumental in disseminating the Delta 32 allele during the eighth to the tenth centuries during historical times. Possibly variola virus has discriminated the Delta 32 carriers in Europe since the eighth century AD, explaining the high frequency of the Delta 32 allele in Europe today.

  17. Allele frequencies for 40 autosomal SNP loci typed for US population samples using electrospray ionization mass spectrometry

    PubMed Central

    Kiesler, Kevin M.; Vallone, Peter M.

    2013-01-01

    Aim To type a set of 194 US African American, Caucasian, and Hispanic samples (self-declared ancestry) for 40 autosomal single nucleotide polymorphism (SNP) markers intended for human identification purposes. Methods Genotyping was performed on an automated commercial electrospray ionization time-of-flight mass spectrometer, the PLEX-ID. The 40 SNP markers were amplified in eight unique 5plex PCRs, desalted, and resolved based on amplicon mass. For each of the three US sample groups statistical analyses were performed on the resulting genotypes. Results The assay was found to be robust and capable of genotyping the 40 SNP markers consuming approximately 4 nanograms of template per sample. The combined random match probabilities for the 40 SNP assay ranged from 10−16 to 10−21. Conclusion The multiplex PLEX-ID SNP-40 assay is the first fully automated genotyping method capable of typing a panel of 40 forensically relevant autosomal SNP markers on a mass spectrometry platform. The data produced provided the first allele frequencies estimates for these 40 SNPs in a National Institute of Standards and Technology US population sample set. No population bias was detected although one locus deviated from its expected level of heterozygosity. PMID:23771752

  18. A new method for studying population genetics of cyst nematodes based on Pool-Seq and genomewide allele frequency analysis.

    PubMed

    Mimee, Benjamin; Duceppe, Marc-Olivier; Véronneau, Pierre-Yves; Lafond-Lapalme, Joël; Jean, Martine; Belzile, François; Bélair, Guy

    2015-11-01

    Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time- and cost-efficient and could be applied to other cyst nematode species.

  19. Maximum likelihood model based on minor allele frequencies and weighted Max-SAT formulation for haplotype assembly.

    PubMed

    Mousavi, Sayyed R; Khodadadi, Ilnaz; Falsafain, Hossein; Nadimi, Reza; Ghadiri, Nasser

    2014-06-01

    Human haplotypes include essential information about SNPs, which in turn provide valuable information for such studies as finding relationships between some diseases and their potential genetic causes, e.g., for Genome Wide Association Studies. Due to expensiveness of directly determining haplotypes and recent progress in high throughput sequencing, there has been an increasing motivation for haplotype assembly, which is the problem of finding a pair of haplotypes from a set of aligned fragments. Although the problem has been extensively studied and a number of algorithms have already been proposed for the problem, more accurate methods are still beneficial because of high importance of the haplotypes information. In this paper, first, we develop a probabilistic model, that incorporates the Minor Allele Frequency (MAF) of SNP sites, which is missed in the existing maximum likelihood models. Then, we show that the probabilistic model will reduce to the Minimum Error Correction (MEC) model when the information of MAF is omitted and some approximations are made. This result provides a novel theoretical support for the MEC, despite some criticisms against it in the recent literature. Next, under the same approximations, we simplify the model to an extension of the MEC in which the information of MAF is used. Finally, we extend the haplotype assembly algorithm HapSAT by developing a weighted Max-SAT formulation for the simplified model, which is evaluated empirically with positive results. PMID:24491253

  20. Variant allele frequency enrichment analysis in vitro reveals sonic hedgehog pathway to impede sustained temozolomide response in GBM

    PubMed Central

    Biswas, Nidhan K.; Chandra, Vikas; Sarkar-Roy, Neeta; Das, Tapojyoti; Bhattacharya, Rabindra N.; Tripathy, Laxmi N.; Basu, Sunandan K.; Kumar, Shantanu; Das, Subrata; Chatterjee, Ankita; Mukherjee, Ankur; Basu, Pryiadarshi; Maitra, Arindam; Chattopadhyay, Ansuman; Basu, Analabha; Dhara, Surajit

    2015-01-01

    Neoplastic cells of Glioblastoma multiforme (GBM) may or may not show sustained response to temozolomide (TMZ) chemotherapy. We hypothesize that TMZ chemotherapy response in GBM is predetermined in its neoplastic clones via a specific set of mutations that alter relevant pathways. We describe exome-wide enrichment of variant allele frequencies (VAFs) in neurospheres displaying contrasting phenotypes of sustained versus reversible TMZ-responses in vitro. Enrichment of VAFs was found on genes ST5, RP6KA1 and PRKDC in cells showing sustained TMZ-effect whereas on genes FREM2, AASDH and STK36, in cells showing reversible TMZ-effect. Ingenuity pathway analysis (IPA) revealed that these genes alter cell-cycle, G2/M-checkpoint-regulation and NHEJ pathways in sustained TMZ-effect cells whereas the lysine-II&V/phenylalanine degradation and sonic hedgehog (Hh) pathways in reversible TMZ-effect cells. Next, we validated the likely involvement of the Hh-pathway in TMZ-response on additional GBM neurospheres as well as on GBM patients, by extracting RNA-sequencing-based gene expression data from the TCGA-GBM database. Finally, we demonstrated TMZ-sensitization of a TMZ non-responder neurosphere in vitro by treating them with the FDA-approved pharmacological Hh-pathway inhibitor vismodegib. Altogether, our results indicate that the Hh-pathway impedes sustained TMZ-response in GBM and could be a potential therapeutic target to enhance TMZ-response in this malignancy. PMID:25604826

  1. Beyond orchids and dandelions: Testing the 5HTT “risky” allele for evidence of phenotypic capacitance and frequency dependent selection

    PubMed Central

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

    2013-01-01

    The persistence of behaviorally deleterious genes in the human population poses an interesting question for population genetics: If certain alleles at these loci are deleterious, why have they survived in the population? We consider evidence for phenotypic capacitance and/or frequency dependent selection for an allele that has been putatively shown to have negative associations with human behaviors (the “short” 5-HTT promoter region allele) yet which has persisted in human and non-human primate populations. Using National Longitudinal Study of Adolescent Health data, we compare sibling and twin variation in depression by 5-HTT genotype (specified in several ways) and investigate sibship-level cross-person gene-gene interactions. In support of the “orchid / dandelion” hypothesis, we find evidence that the short allele increases variation in phenotypes in response to environmental (or genetic) differences (i.e. acts as a perturbation of a phenotypic capacitor). Further, we also find some evidence that the effects of allelic variation at this locus are moderated by the genetic environment of the sibship unit (i.e. may be susceptible to frequency dependent selection). We discuss implications of these findings for genetic models in general, specifically with respect to stable unit treatment value assumption violations (i.e. non-independence of units of analysis). PMID:23701535

  2. Relationship between allozymes, heterozygosity and morphological characters in red deer (Cervus elaphus), and the influence of selective hunting on allele frequency distribution.

    PubMed

    Hartl, G B; Lang, G; Klein, F; Willing, R

    1991-06-01

    Morphological characters in red deer (Cervus elaphus), which serve as criteria for selective hunting, were examined in relation to electrophoretic variation in three populations from the Vosges in eastern France. From the polymorphic loci examined, certain alleles at Idh-2, Me-1 and Acp-1 showed significant associations with a special development of body and antler characters selected for by hunters. Idh-2(125) was associated with larger hind foot length in females and a higher number of antler points in males. Me-1(90) and Acp-1(100) were associated with small spikes. The populations studied differed from one another in the duration and intensity of selective hunting and the increase or decrease in the respective allele frequencies could be explained by selection for large body size, a high number of antler points and against small spikes in yearlings, rather than by genetic drift. Among other morphological characters examined, the length of the main beam was significantly associated with the allele Acp-2(100). In contrast, no associations could be detected between overall heterozygosity and the development or the degree of asymmetry (in paired structures) of any of the morphological traits in question. Although no obvious differences in the overall values of polymorphism or heterozygosity were found between the populations, selective hunting leads towards a change in allele frequencies and eventually to the loss of one or the other rare allele. PMID:1880046

  3. Population diversity of B-locus alleles observed by high-resolution DNA typing.

    PubMed

    Fernandez-Viña, M; Lazaro, A M; Sun, Y; Miller, S; Forero, L; Stastny, P

    1995-03-01

    HLA B-locus typing by group-specific PCR and hybridization with SSOP was performed in 81 10th IHWS B cell lines and 334 selected subjects of our local panel, from four ethnic groups. Most of the B-locus serological specificities were well defined. However, some antigens like B41, B58, B56, the splits of B14, and some subtypes of B5, were not accurately assigned by serology. In the panel studied, we found 17 hybridization patterns that corresponded to probable new alleles. New patterns occurred in the four ethnic groups examined. Multiple subtypes of B35, B5, B15, B41, B44, B57, B58, B70, B14, B40, B22 were found in subjects of the same ethnic group. In view of the poor serological definition of some alleles, and the occurrence of multiple subtypes in the same ethnic population, it appears that high resolution B-locus typing may be an important addition for detection of potentially relevant HLA incompatibilities in transplantation. It should also be valuable for population studies and for the investigation of HLA associations with diseases.

  4. Real-time PCR genotyping assay for canine progressive rod-cone degeneration and mutant allele frequency in Toy Poodles, Chihuahuas and Miniature Dachshunds in Japan.

    PubMed

    Kohyama, Moeko; Tada, Naomi; Mitsui, Hiroko; Tomioka, Hitomi; Tsutsui, Toshihiko; Yabuki, Akira; Rahman, Mohammad Mahbubur; Kushida, Kazuya; Mizukami, Keijiro; Yamato, Osamu

    2016-03-01

    Canine progressive rod-cone degeneration (PRCD) is a middle- to late-onset, autosomal recessive, inherited retinal disorder caused by a substitution (c.5G>A) in the canine PRCD gene that has been identified in 29 or more purebred dogs. In the present study, a TaqMan probe-based real-time PCR assay was developed and evaluated for rapid genotyping and large-scale screening of the mutation. Furthermore, a genotyping survey was carried out in a population of the three most popular breeds in Japan (Toy Poodles, Chihuahuas and Miniature Dachshunds) to determine the current mutant allele frequency. The assay separated all the genotypes of canine PRCD rapidly, indicating its suitability for large-scale surveys. The results of the survey showed that the mutant allele frequency in Toy Poodles was high enough (approximately 0.09) to allow the establishment of measures for the prevention and control of this disorder in breeding kennels. The mutant allele was detected in Chihuahuas for the first time, but the frequency was lower (approximately 0.02) than that in Toy Poodles. The mutant allele was not detected in Miniature Dachshunds. This assay will allow the selective breeding of dogs from the two most popular breeds (Toy Poodle and Chihuahua) in Japan and effective prevention or control of the disorder. PMID:26549343

  5. Real-time PCR genotyping assay for canine progressive rod-cone degeneration and mutant allele frequency in Toy Poodles, Chihuahuas and Miniature Dachshunds in Japan

    PubMed Central

    KOHYAMA, Moeko; TADA, Naomi; MITSUI, Hiroko; TOMIOKA, Hitomi; TSUTSUI, Toshihiko; YABUKI, Akira; RAHMAN, Mohammad Mahbubur; KUSHIDA, Kazuya; MIZUKAMI, Keijiro; YAMATO, Osamu

    2015-01-01

    Canine progressive rod-cone degeneration (PRCD) is a middle- to late-onset, autosomal recessive, inherited retinal disorder caused by a substitution (c.5G>A) in the canine PRCD gene that has been identified in 29 or more purebred dogs. In the present study, a TaqMan probe-based real-time PCR assay was developed and evaluated for rapid genotyping and large-scale screening of the mutation. Furthermore, a genotyping survey was carried out in a population of the three most popular breeds in Japan (Toy Poodles, Chihuahuas and Miniature Dachshunds) to determine the current mutant allele frequency. The assay separated all the genotypes of canine PRCD rapidly, indicating its suitability for large-scale surveys. The results of the survey showed that the mutant allele frequency in Toy Poodles was high enough (approximately 0.09) to allow the establishment of measures for the prevention and control of this disorder in breeding kennels. The mutant allele was detected in Chihuahuas for the first time, but the frequency was lower (approximately 0.02) than that in Toy Poodles. The mutant allele was not detected in Miniature Dachshunds. This assay will allow the selective breeding of dogs from the two most popular breeds (Toy Poodle and Chihuahua) in Japan and effective prevention or control of the disorder. PMID:26549343

  6. Increased frequency of co-existing JAK2 exon-12 or MPL exon-10 mutations in patients with low JAK2(V617F) allelic burden.

    PubMed

    Nussenzveig, Roberto H; Pham, Ha T; Perkins, Sherrie L; Prchal, Josef T; Agarwal, Archana M; Salama, Mohamed E

    2016-01-01

    The frequency of co-existing JAK2(V617F)/MPL and JAK2(V617F)/JAK2 exon-12 mutations has not been previously investigated in MPNs. Poor survival was reported in primary myelofibrosis with low JAK2(V617F) allelic burden. However, mutational status of JAK2 exon-12 or MPL were not reported in these patients. This study developed a cost-effective multiplex high resolution melt assay that screens for mutations in JAK2 gene exons-12 and -14 ((V617F)) and MPL gene exon-10. Co-existing mutations with JAK2(V617F) were detected in 2.9% (6/208; two JAK2 exon-12 and four MPL exon-10) patient specimens with known JAK2(V617F) (allelic-burden range: 0.1-96.8%). Co-existing mutations were detected in specimens with < 12% JAK2(V617F) allelic burden. Current WHO guidelines do not recommend further testing once JAK2(V617F) mutation is detected in MPNs. The findings, however, indicate that quantification of JAK2(V617F) allele burden may be clinically relevant in MPNs and in those with low allelic burden additional testing for JAK2 exon-12 and MPL exon-10 mutation should be pursued.

  7. A microsatellite polymorphism in the von Willebrand factor gene: comparison of allele frequencies in different population samples and evaluation for forensic medicine.

    PubMed

    Sajantila, A; Pacek, P; Lukka, M; Syvänen, A C; Nokelainen, P; Sistonen, P; Peltonen, L; Budowle, B

    1994-09-16

    The allele frequencies at the tetranucleotide repeat (TCTA) vWA locus in the vWF gene were determined in the general Finnish population, in a population representing an internal isolate of Finland, in the Vologda-Russian population, and in US Black population samples. The allele and genotype frequencies from these population samples were compared with each other and with those reported from Spanish and British population samples. Statistically significant differences were demonstrated between most of the different groups (Finns vs. Vologda-Russians, Finns vs. US Blacks, Finns vs. Spanish, Vologda-Russians vs. US Blacks, Vologda-Russians vs. Spanish, US Blacks vs. Spanish and US Blacks vs. British Caucasians), but not between the two Caucasoid population samples from Finland and Great Britain, nor between or within the subpopulation samples from Finland and those from Vologda-Russia. In addition, the vWA marker was evaluated and demonstrated to be reliable for forensic purposes and paternity testing.

  8. Effects of cigarette smoking on human in vivo somatic mutation: Longitudinal sampling of smokers demonstrates a decrease in glycophorin A (GPA) allele-loss variant cell frequencies following cessation

    SciTech Connect

    Bigbee, W.L.; Langlois, R.G. ); Grant, S.G.; Jensen, R.H. ); Mooney, L.M.; Perera, F.P. )

    1993-01-01

    The human in vivo glycophorin A (GPA) assay uses immunolabeling and flow cytometry to quantitate somatic variation in erythrocytes expressing GPA allele loss and allele-loss and duplication phenotypes in peripheral blood samples. The frequency of these variant erythrocytes (V[sub f]) presumably reflects the level of somatic mutation at this locus in the nucleated hematopoietic precursor cells of the bone marrow. We have previously shown that the GPA assay is a cumulative, integrating biodosimeter of accidental, medical, and occupational exposure to chemical mutagens and ionizing radiation. Surveys of otherwise unexposed populations point to an increased GPA allele loss V[sub f] in cigarette smokers compared to nonsmokers consistent with the induction of somatic mutation by mutagenic components of tobacco smoke. To further test this association, blood samples from active heavy smokers who entered a multi-endpoint Smokender study were obtained at enrollment and at 10 wks and 6 and 12 mo following smoking cessation. Results from the first 109 individuals reveal a decrease in the mean GPA allele loss V[sub f] ranging from 9.0 [+-] 1.0 [times] 10[sup [minus]6] (n = 109) for the active smoking samples, to 9.1 [+-] 1.8 [times] 10[sup [minus]6] (n = 46), 6.0 [+-] 0.7 [times] 10[sup [minus]6] (n = 15), and 5.8 [+-] 1.6 [times] 10[sup [minus]6] (n = 8) for the three postcessation samples, respectively. No change in the GPA allele loss and duplication V[sub f] was observed, thus confining the spectrum of mutational events induced by exposure to cigarette smoke. The observed decrease in the level of somatic mutation in smokers following cessation suggests limited persistence and/or repair of tobacco-smoke-induced genetic alterations consistent with epidemiologic findings of decreased cancer risk in smokers following cessation.

  9. Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER).

    PubMed

    Bodner, Martin; Bastisch, Ingo; Butler, John M; Fimmers, Rolf; Gill, Peter; Gusmão, Leonor; Morling, Niels; Phillips, Christopher; Prinz, Mechthild; Schneider, Peter M; Parson, Walther

    2016-09-01

    The statistical evaluation of autosomal Short Tandem Repeat (STR) genotypes is based on allele frequencies. These are empirically determined from sets of randomly selected human samples, compiled into STR databases that have been established in the course of population genetic studies. There is currently no agreed procedure of performing quality control of STR allele frequency databases, and the reliability and accuracy of the data are largely based on the responsibility of the individual contributing research groups. It has been demonstrated with databases of haploid markers (EMPOP for mitochondrial mtDNA, and YHRD for Y-chromosomal loci) that centralized quality control and data curation is essential to minimize error. The concepts employed for quality control involve software-aided likelihood-of-genotype, phylogenetic, and population genetic checks that allow the researchers to compare novel data to established datasets and, thus, maintain the high quality required in forensic genetics. Here, we present STRidER (http://strider.online), a publicly available, centrally curated online allele frequency database and quality control platform for autosomal STRs. STRidER expands on the previously established ENFSI DNA WG STRbASE and applies standard concepts established for haploid and autosomal markers as well as novel tools to reduce error and increase the quality of autosomal STR data. The platform constitutes a significant improvement and innovation for the scientific community, offering autosomal STR data quality control and reliable STR genotype estimates. PMID:27352221

  10. Allele frequencies of the major milk proteins in the Finnish Ayrshire and detection of a new kappa-casein variant.

    PubMed

    Ikonen, T; Ruottinen, O; Erhardt, G; Ojala, M

    1996-06-01

    A total of 20990 Finnish Ayrshire cows were phenotyped for the major milk proteins by isoelectric focusing in polyacrylamide gels. The predominant alleles in the Finnish Ayrshire were alpha S1-casein B (0.999), alpha S2-casein A (0.991), beta-casein A1 (0.509) and alpha 2 (0.490), kappa-casein A (0.612) and beta-lactoglobulin B (0.716). The kappa-casein E allele (0.307) was also rather common in the Finnish Ayrshire. A new kappa-casein variant (kappa-casein F) was demonstrated in two Finnish Ayrshire cows, a dam and a daughter.

  11. Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the...

  12. The frequency of the mitochondrial aldehyde dehydrogenase I2 (atypical) allele in Caucasian, Oriental and African black populations determined by the restriction profile of PCR-amplified DNA.

    PubMed

    Dandré, F; Cassaigne, A; Iron, A

    1995-06-01

    The aldehyde dehydrogenase I (ALDH I) gene codes for a mitochondrial enzyme which plays a major role in hepatic alcohol detoxication. It has been related to alcohol flushing in Orientals bearing the atypical ALDH I2 gene. The variant protein results from a lysine for glutamate substitution at position 487 (G-->A change in exon 12). A procedure for ALDH I2 detection consisting in a differentiation between the 'atypical' allele and the 'wild' allele has been improved through PCR and subsequent MboII digestion. Blood samples collected on anticoagulant or directly absorbed on blotting paper were used for DNA amplification in the presence of two specific oligonucleotidic primers, each one able to incorporate a restriction site in the amplimer. After MboII digestion, PCR products were separated by polyacrylamide gel electrophoresis and then visualized with ethidium bromide. This technique permits a rapid and non-radioactive detection of atypical ALDH I2 on a PCR product without the use of allele specific oligonucleotides. It was applied to the study of ALDH I2 allele frequency in random population samples of three ethnic groups: Caucasians, Orientals and African blacks.

  13. Inosine triphosphatase allele frequency and association with ribavirin-induced anaemia in Brazilian patients receiving antiviral therapy for chronic hepatitis C

    PubMed Central

    Delvaux, Nathália; da Costa, Vanessa Duarte; da Costa, Maristella Matos; Villar, Livia Melo; Coelho, Henrique Sérgio Moraes; Esberard, Eliane Bordalo Cathalá; Flores, Priscila Pollo; Brandão-Mello, Carlos Eduardo; Villela-Nogueira, Cristiane Alves; de Almeida, Adilson José; Lampe, Elisabeth

    2015-01-01

    Inosine triphosphatase (ITPA) single nucleotide polymorphisms (SNPs) are strongly associated with protection against ribavirin (RBV)-induced anaemia in European, American and Asian patients; however, there is a paucity of data for Brazilian patients. The aim of this study was to evaluate the ITPA SNP (rs7270101/rs1127354) frequency in healthy and hepatitis C virus (HCV)-infected patients from Brazil and the association with the development of severe anaemia during antiviral therapy. ITPA SNPs were determined in 200 HCV infected patients and 100 healthy individuals by sequencing. Biochemical parameters and haemoglobin (Hb) levels were analysed in 97 patients who underwent antiviral therapy. A combination of AArs7270101+CCrs1127354 (100% ITPase activity) was observed in 236/300 individuals. Anaemia was observed in 87.5% and 86.2% of treated patients with AA (rs7270101) and CC genotypes (rs1127354), respectively. Men with AA (rs7270101) showed a considerable reduction in Hb at week 12 compared to those with AC/CC (p = 0.1475). In women, there was no influence of genotype (p = 0.5295). For rs1127354, men with the CC genotype also showed a sudden reduction in Hb compared to those with AC. Allelic distribution of rs7270101 and rs1127354 shows high rates of the genotypes AA and CC, respectively, suggesting that the study population had a great propensity for developing RBV-induced anaemia. A progressive Hb reduction during treatment was observed; however, this reduction was greater in men at week 12 than in women. PMID:26154744

  14. High Susceptibility to Cry1Ac and Low Resistance Allele Frequency Reduce the Risk of Resistance of Helicoverpa armigera to Bt Soybean in Brazil

    PubMed Central

    Bacalhau, Fabiana B.; Amado, Douglas; Carvalho, Renato A.; Martinelli, Samuel; Head, Graham P.; Omoto, Celso

    2016-01-01

    The Old World bollworm, Helicoverpa armigera (Hübner), was recently introduced into Brazil, where it has caused extensive damage to cotton and soybean crops. MON 87701 × MON 89788 soybean, which expresses the Bt protein Cry1Ac, was recently deployed in Brazil, providing high levels of control against H. armigera. To assess the risk of resistance to the Cry1Ac protein expressed by MON 87701 × MON 89788 soybean in Brazil, we conducted studies to evaluate the baseline susceptibility of H. armigera to Cry1Ac, in planta efficacy including the assessment of the high-dose criterion, and the initial resistance allele frequency based on an F2 screen. The mean Cry1Ac lethal concentration (LC50) ranged from 0.11 to 1.82 μg·mL−1 of diet among all H. armigera field populations collected from crop seasons 2013/14 to 2014/15, which indicated about 16.5-fold variation. MON 87701 × MON 89788 soybean exhibited a high level of efficacy against H. armigera and most likely met the high dose criterion against this target species in leaf tissue dilution bioassays up to 50 times. A total of 212 F2 family lines of H. armigera were established from field collections sampled from seven locations across Brazil and were screened for the presence of MON 87701 × MON 89788 soybean resistance alleles. None of the 212 families survived on MON 87701 × MON 89788 soybean leaf tissue (estimated allele frequency = 0.0011). The responses of H. armigera to Cry1Ac protein, high susceptibility to MON 87701 × MON 89788 soybean, and low frequency of resistance alleles across the main soybean-producing regions support the assumptions of a high-dose/refuge strategy. However, maintenance of reasonable compliance with the refuge recommendation will be essential to delay the evolution of resistance in H. armigera to MON 87701 × MON 89788 soybean in Brazil. PMID:27532632

  15. High Susceptibility to Cry1Ac and Low Resistance Allele Frequency Reduce the Risk of Resistance of Helicoverpa armigers to Bt Soybean in Brazil

    PubMed Central

    Bacalhau, Fabiana B.; Amado, Douglas; Carvalho, Renato A.; Martinelli, Samuel; Head, Graham P.; Omoto, Celso

    2016-01-01

    The Old World bollworm, Helicoverpa armigera (Hübner), was recently introduced into Brazil, where it has caused extensive damage to cotton and soybean crops. MON 87701 × MON 89788 soybean, which expresses the Bt protein Cry1Ac, was recently deployed in Brazil, providing high levels of control against H. armigera. To assess the risk of resistance to the Cry1Ac protein expressed by MON 87701 × MON 89788 soybean in Brazil, we conducted studies to evaluate the baseline susceptibility of H. armigera to Cry1Ac, in planta efficacy including the assessment of the high-dose criterion, and the initial resistance allele frequency based on an F2 screen. The mean Cry1Ac lethal concentration (LC50) ranged from 0.11 to 1.82 μg·mL−1 of diet among all H. armigera field populations collected from crop seasons 2013/14 to 2014/15, which indicated about 16.5-fold variation. MON 87701 × MON 89788 soybean exhibited a high level of efficacy against H. armigera and most likely met the high dose criterion against this target species in leaf tissue dilution bioassays up to 50 times. A total of 212 F2 family lines of H. armigera were established from field collections sampled from seven locations across Brazil and were screened for the presence of MON 87701 × MON 89788 soybean resistance alleles. None of the 212 families survived on MON 87701 × MON 89788 soybean leaf tissue (estimated allele frequency = 0.0011). The responses of H. armigera to Cry1Ac protein, high susceptibility to MON 87701 × MON 89788 soybean, and low frequency of resistance alleles across the main soybean-producing regions support the assumptions of a high-dose/refuge strategy. However, maintenance of reasonable compliance with the refuge recommendation will be essential to delay the evolution of resistance in H. armigera to MON 87701 × MON 89788 soybean in Brazil. PMID:27532632

  16. High Susceptibility to Cry1Ac and Low Resistance Allele Frequency Reduce the Risk of Resistance of Helicoverpa armigers to Bt Soybean in Brazil.

    PubMed

    Dourado, Patrick M; Bacalhau, Fabiana B; Amado, Douglas; Carvalho, Renato A; Martinelli, Samuel; Head, Graham P; Omoto, Celso

    2016-01-01

    The Old World bollworm, Helicoverpa armigera (Hübner), was recently introduced into Brazil, where it has caused extensive damage to cotton and soybean crops. MON 87701 × MON 89788 soybean, which expresses the Bt protein Cry1Ac, was recently deployed in Brazil, providing high levels of control against H. armigera. To assess the risk of resistance to the Cry1Ac protein expressed by MON 87701 × MON 89788 soybean in Brazil, we conducted studies to evaluate the baseline susceptibility of H. armigera to Cry1Ac, in planta efficacy including the assessment of the high-dose criterion, and the initial resistance allele frequency based on an F2 screen. The mean Cry1Ac lethal concentration (LC50) ranged from 0.11 to 1.82 μg·mL-1 of diet among all H. armigera field populations collected from crop seasons 2013/14 to 2014/15, which indicated about 16.5-fold variation. MON 87701 × MON 89788 soybean exhibited a high level of efficacy against H. armigera and most likely met the high dose criterion against this target species in leaf tissue dilution bioassays up to 50 times. A total of 212 F2 family lines of H. armigera were established from field collections sampled from seven locations across Brazil and were screened for the presence of MON 87701 × MON 89788 soybean resistance alleles. None of the 212 families survived on MON 87701 × MON 89788 soybean leaf tissue (estimated allele frequency = 0.0011). The responses of H. armigera to Cry1Ac protein, high susceptibility to MON 87701 × MON 89788 soybean, and low frequency of resistance alleles across the main soybean-producing regions support the assumptions of a high-dose/refuge strategy. However, maintenance of reasonable compliance with the refuge recommendation will be essential to delay the evolution of resistance in H. armigera to MON 87701 × MON 89788 soybean in Brazil. PMID:27532632

  17. Imaging Observations of a Very High Frequency Type II Burst

    NASA Astrophysics Data System (ADS)

    White, S. M.; Mercier, C.; Bradley, R.; Bastian, T.; Kerdraon, A.; Pick, M.

    2006-05-01

    A remarkable Type II burst was detected by the high-frequency system of the Green Bank Solar Radio Burst Spectrometer on 2005 November 14. The harmonic branch of the Type II extended up to 800 MHz, making it one of the highest frequency Type II bursts ever detected, but it failed to propagate to heights corresponding to frequencies below 100 MHz. At such high frequencies, it implies the formation of a shock relatively low in the corona. No coronal mass ejection was evident in the LASCO data for this east limb event. It is one of the few Type II bursts to be observable at every frequency of observation of the Nancay Radio Heliograph (164-432 MHz). Here we present analysis of images of the event, including simultaneous imaging of the fundamental and harmonic branches.

  18. Allele frequencies and population data for 17 Y-STR loci (The AmpFlSTR® Y-filer™) in Casablanca resident population.

    PubMed

    Laouina, Adil; El Houate, Brahim; Yahia, Hakima; Azeddoug, Houssine; Boulouiz, Redouane; Chbel, Faiza

    2011-01-01

    Allele frequencies and population data for 17 Y-STR loci included in the AmpFlSTR® Y-filer™ PCR amplification kit (Applied Biosystems, Foster City, USA), that permit the simultaneous amplification of all the markers included in the actually used European "extended haplotype", DYS19, DYS189I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II, DYS438, DYS439 and also DYS437, DYS448, DYS456, DYS458, DYS635 and Y GATA H4, were obtained from a sample of 166 healthy unrelated males resident in Casablanca (from Morocco). A total of 166 haplotypes were identified, of which 142 were unique. The overall haplotype diversity for the 17 Y-STR loci reached 0.9974, and a discrimination capacity was 0.855. We report some non-standard situations, including duplications and microvariant alleles. PMID:21126935

  19. HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies in a population of 432 healthy unrelated individuals from Albania.

    PubMed

    Sulcebe, Genc; Shyti, Erkena

    2016-08-01

    This paper reports the HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype polymorphism in a population of 432 healthy individuals from Albania. First-field HLA genotyping was performed by polymerase chain reaction sequence-specific priming and/or oligonucleotide methods. The data were analyzed statistically using gene counting and Arlequin software packages. No deviation from Hardy Weinberg Equilibrium was detected at any of the loci studied. The HLA genotypic data of the population sample reported here are available publicly in the Allele Frequencies Net Database and they can serve as a reference database for further HLA-based population genetics studies including the Albanian population. PMID:27262454

  20. Allele and Haplotype Frequencies of Human Leukocyte Antigen-A, -B, -C, -DRB1, and -DQB1 From Sequence-Based DNA Typing Data in Koreans

    PubMed Central

    In, Ji Won; Roh, Eun Youn; Oh, Sohee; Shin, Sue; Park, Kyoung Un

    2015-01-01

    Background Data on allele frequencies (AFs) and haplotype frequencies (HFs) of HLA-C and -DQB1 are limited in Koreans. We investigated AFs and HFs of HLA-A, -B, -C, -DRB1, and -DQB1 in Koreans by high-resolution sequence-based typing (SBT). Methods Hematopoietic stem cells were obtained from 613 healthy, unrelated donors to analyze HLA-A, -B, -C, -DRB1, and -DQB1 genotypes by using AlleleSEQR HLA-A, -B, -C, -DRB1, and -DQB1 SBT kits (Abbott Molecular, USA), respectively. Alleles belonging to HLA-C*07:01/07:06 group were further discriminated by using PCR-sequence specific primer analysis. AFs and HFs were calculated by direct counting and maximum likelihood method, respectively. Results In all, 24 HLA-A, 46 HLA-B, 24 HLA-C, 29 HLA-DRB1, and 15 HLA-DQB1 alleles were identified. AFs and HFs of HLA-A, -B, and -DRB1 were similar to those reported previously. For the HLA-C locus, C*01:02 was the most common allele, followed by C*03:03, C*03:04, C*14:02, C*03:02, and C*07:02 (AF ≥7%). AFs of C*07:01 and C*07:06 were 0.16% and 3.18%, respectively. For the HLA-DQB1 locus, DQB1*03:01 was the most common allele, followed by DQB1*03:03, *03:02, *06:01, *05:01, *04:01, and *06:02 (AF ≥7%). AFs of DQB1*02:01 and DQB1*02:02 were 2.12% and 6.69%, respectively. HFs of A*33:03-C*07:06 and C*07:06-B*44:03 were 3.09% and 3.10%, respectively, while those of DRB1*07:01-DQB1*02:02 and DRB1*03:01-DQB1*02:01 were 6.61% and 2.04%, respectively. Conclusions This study reported AFs and HFs of HLA, including HLA-C and -DQB1, in Koreans by using high-resolution SBT. These data can be used to resolve ambiguous results of HLA typing for organ and hematopoietic stem cell transplantations. PMID:26131415

  1. Observed emotion frequency versus intensity as predictors of socioemotional maladjustment.

    PubMed

    Hernández, Maciel M; Eisenberg, Nancy; Valiente, Carlos; Spinrad, Tracy L; VanSchyndel, Sarah K; Diaz, Anjolii; Berger, Rebecca H; Silva, Kassondra M; Southworth, Jody; Piña, Armando A

    2015-12-01

    The purpose of this study was to assess whether observed emotional frequency (the proportion of instances an emotion was observed) and intensity (the strength of an emotion when it was observed) uniquely predicted kindergartners' (N = 301) internalizing and externalizing problems. Analyses were tested in a structural equation modeling (SEM) framework with data from multireporters (reports of problem behaviors from teachers and parents) and naturalistic observations of emotion in the fall semester. For observed positive emotion, both frequency and intensity negatively predicted parent- or teacher-reported internalizing symptoms. Anger frequency positively predicted parent- and teacher-reported externalizing symptoms, whereas anger intensity positively predicted parent- and teacher-reported externalizing and parent-reported internalizing symptoms. The findings support the importance of examining both aspects of emotion when predicting maladjustment.

  2. Frequency of Cry1F Non-Recessive Resistance Alleles in North Carolina Field Populations of Spodoptera frugiperda (Lepidoptera: Noctuidae).

    PubMed

    Li, Guoping; Reisig, Dominic; Miao, Jin; Gould, Fred; Huang, Fangneng; Feng, Hongqiang

    2016-01-01

    Fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is a target species of transgenic corn (Zea mays L.) that expresses single and pyramided Bacillus thuringiensis (Bt) toxin. In 2014, S. frugiperda were collected from a light trap in North Carolina, and a total of 212 F1/F2 isofemale lines of S. frugiperda were screened for resistance to Bt and non-Bt corn. All of the 212 isolines were susceptible to corn tissue expressing Cry1A.105 + Cry2Ab, Cry1F + Cry1A.105 + Cry2Ab, and Cry1F + Cry1Ab + Vip3Aa20. Growth rate bioassays were performed to isolate non-recessive Bt resistance alleles. Seven individuals out of the 212 isofemale lines carried major non-recessive alleles conferring resistance to Cry1F. A pooled colony was created from the seven individuals. This colony was 151.21 times more resistant to Cry1F than a known-susceptible population and was also resistant to Cry1A.105, but was not resistant to Cry2Ab and Vip3Aa20. The results demonstrate that field populations of S. frugiperda collected from North Carolina are generally susceptible to Cry1F, but that some individuals carry resistant alleles. The data generated in this study can be used as baseline data for resistance monitoring. PMID:27119741

  3. Frequency of Cry1F Non-Recessive Resistance Alleles in North Carolina Field Populations of Spodoptera frugiperda (Lepidoptera: Noctuidae)

    PubMed Central

    Li, Guoping; Reisig, Dominic; Miao, Jin; Gould, Fred; Huang, Fangneng; Feng, Hongqiang

    2016-01-01

    Fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is a target species of transgenic corn (Zea mays L.) that expresses single and pyramided Bacillus thuringiensis (Bt) toxin. In 2014, S. frugiperda were collected from a light trap in North Carolina, and a total of 212 F1/F2 isofemale lines of S. frugiperda were screened for resistance to Bt and non-Bt corn. All of the 212 isolines were susceptible to corn tissue expressing Cry1A.105 + Cry2Ab, Cry1F + Cry1A.105 + Cry2Ab, and Cry1F + Cry1Ab + Vip3Aa20. Growth rate bioassays were performed to isolate non-recessive Bt resistance alleles. Seven individuals out of the 212 isofemale lines carried major non-recessive alleles conferring resistance to Cry1F. A pooled colony was created from the seven individuals. This colony was 151.21 times more resistant to Cry1F than a known-susceptible population and was also resistant to Cry1A.105, but was not resistant to Cry2Ab and Vip3Aa20. The results demonstrate that field populations of S. frugiperda collected from North Carolina are generally susceptible to Cry1F, but that some individuals carry resistant alleles. The data generated in this study can be used as baseline data for resistance monitoring. PMID:27119741

  4. Solution of high frequency variations of ERP from VLBI observations

    NASA Astrophysics Data System (ADS)

    Zhang, B.; Li, J. L.; Wang, G. L.; Zhao, M.

    2005-01-01

    In the astrometric and geodetic VLBI data analysis software CALC/SOLVE, the high frequency variations of the Earth Rotation Parameters (ERP) are determined by a constrained continuous piecewise linear model. The ERP rate within two epoch nodes is constrained to be smaller than a limitation setting, and the ERP is forced to be continuous at epoch nodes. Observation analysis shows that when the data points are not very dense the constraint and the continuation requirement are helpful to the improvement in the stability of the solution, but degrade the independence of ERP solutions at epoch nodes as well. By using the Userpartial entry of CALC/SOLVE a direct solution module of the high frequency variations of ERP is realized without any constraint on the rate nor the requirement of continuation at nodes. It is shown from real observation reduction that the direct solution mode is feasible. In the solution of high frequency variations of ERP from VLBI observations with long period coverage, the model errors of the precession and nutation (celestial pole offset) should be taken into consideration. A corresponding module is realized and global solutions of the high frequency variation of ERP are successfully performed on the VLBI observations from 1979 to 2003. Comparison of the solutions shows that with the consideration of the pole offsets the precision of parameters could be improved obviously. In the solution of high frequency variation of ERP from VLBI observations, the direct solution mode with the consideration of the pole offsets is accordingly recommended.

  5. Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re-introduced Asiatic wild ass.

    PubMed

    Renan, Sharon; Greenbaum, Gili; Shahar, Naama; Templeton, Alan R; Bouskila, Amos; Bar-David, Shirli

    2015-04-01

    Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re-introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re-introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re-introduced population's genetic diversity could have significant consequences for the long-term persistence of the population in the Negev. The stochastic modelling approach and the use of allele-frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited. PMID:25728575

  6. Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re-introduced Asiatic wild ass.

    PubMed

    Renan, Sharon; Greenbaum, Gili; Shahar, Naama; Templeton, Alan R; Bouskila, Amos; Bar-David, Shirli

    2015-04-01

    Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re-introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re-introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re-introduced population's genetic diversity could have significant consequences for the long-term persistence of the population in the Negev. The stochastic modelling approach and the use of allele-frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited.

  7. Real-Time PCR Genotyping Assay for GM2 Gangliosidosis Variant 0 in Toy Poodles and the Mutant Allele Frequency in Japan

    PubMed Central

    RAHMAN, Mohammad Mahbubur; YABUKI, Akira; KOHYAMA, Moeko; MITANI, Sawane; MIZUKAMI, Keijiro; UDDIN, Mohammad Mejbah; CHANG, Hye-Sook; KUSHIDA, Kazuya; KISHIMOTO, Miori; YAMABE, Remi; YAMATO, Osamu

    2013-01-01

    ABSTRACT GM2 gangliosidosis variant 0 (Sandhoff disease, SD) is a fatal, progressive neurodegenerative lysosomal storage disease caused by mutations of the HEXB gene. In canine SD, a pathogenic mutation (c.283delG) of the canine HEXB gene has been identified in toy poodles. In the present study, a TaqMan probe-based real-time PCR genotyping assay was developed and evaluated for rapid and large-scale genotyping and screening for this mutation. Furthermore, a genotyping survey was carried out in a population of toy poodles in Japan to determine the current mutant allele frequency. The real-time PCR assay clearly showed all genotypes of canine SD. The assay was suitable for large-scale survey as well as diagnosis, because of its high throughput and rapidity. The genotyping survey demonstrated a carrier frequency of 0.2%, suggesting that the current mutant allele frequency is low in Japan. However, there may be population stratification in different places, because of the founder effect by some carriers. Therefore, this new assay will be useful for the prevention and control of SD in toy poodles. PMID:24161966

  8. Quantitative Sequencing for the Determination of Kdr-type Resistance Allele (V419L, L925I, I936F) Frequencies in Common Bed Bug (Hemiptera: Cimicidae) Populations Collected from Israel.

    PubMed

    Palenchar, Daniel J; Gellatly, Kyle J; Yoon, Kyong Sup; Mumcuoglu, Kosta Y; Shalom, Uri; Clark, J Marshall

    2015-09-01

    Human bed bug infestations have dramatically increased worldwide since the mid-1990s. A similar phenomenon was also observed in Israel since 2005, when infestations were reported from all over the country. Two single nucleotide polymorphisms (V419L and L925I) in the bed bug voltage-sensitive sodium channel confer kdr-type resistance to pyrethroids. Using quantitative sequencing (QS), the resistance allele frequencies of Israeli bed bug populations from across the country were determined. Genomic DNA was extracted from samples of 12 populations of bed bugs collected from Israel and DNA fragments containing the V419L or L925I and I936F mutations sites were PCR amplified. The PCR products were analyzed by QS and the nucleotide signal ratios calculated and used to predict the resistance allele frequencies of the unknown populations. Results of the genetic analysis show that resistant nucleotide signals are highly correlated to resistance allele frequencies for both mutations. Ten of the 12 tested populations had 100% of the L925I mutation and 0% of the V419L mutation. One population was heterogeneous for the L925I mutation and had 0% of the V419L mutation and another population was heterogeneous for the V419L mutation and had 100% of the L925I mutation. I936F occurred only at low levels. These results indicate that bed bugs in Israel are genetically resistant to pyrethroids. Thus, pyrethroids should only be used for bed bug management with caution using effective application and careful monitoring procedures. Additionally, new and novel-acting insecticides and nonchemical means of controlling bed bugs should be explored. PMID:26336243

  9. Quantitative Sequencing for the Determination of Kdr-type Resistance Allele (V419L, L925I, I936F) Frequencies in Common Bed Bug (Hemiptera: Cimicidae) Populations Collected from Israel.

    PubMed

    Palenchar, Daniel J; Gellatly, Kyle J; Yoon, Kyong Sup; Mumcuoglu, Kosta Y; Shalom, Uri; Clark, J Marshall

    2015-09-01

    Human bed bug infestations have dramatically increased worldwide since the mid-1990s. A similar phenomenon was also observed in Israel since 2005, when infestations were reported from all over the country. Two single nucleotide polymorphisms (V419L and L925I) in the bed bug voltage-sensitive sodium channel confer kdr-type resistance to pyrethroids. Using quantitative sequencing (QS), the resistance allele frequencies of Israeli bed bug populations from across the country were determined. Genomic DNA was extracted from samples of 12 populations of bed bugs collected from Israel and DNA fragments containing the V419L or L925I and I936F mutations sites were PCR amplified. The PCR products were analyzed by QS and the nucleotide signal ratios calculated and used to predict the resistance allele frequencies of the unknown populations. Results of the genetic analysis show that resistant nucleotide signals are highly correlated to resistance allele frequencies for both mutations. Ten of the 12 tested populations had 100% of the L925I mutation and 0% of the V419L mutation. One population was heterogeneous for the L925I mutation and had 0% of the V419L mutation and another population was heterogeneous for the V419L mutation and had 100% of the L925I mutation. I936F occurred only at low levels. These results indicate that bed bugs in Israel are genetically resistant to pyrethroids. Thus, pyrethroids should only be used for bed bug management with caution using effective application and careful monitoring procedures. Additionally, new and novel-acting insecticides and nonchemical means of controlling bed bugs should be explored.

  10. Allele frequencies of combined DNA index system (CODIS) and non-CODIS short tandem repeat loci in Goiás, Central Brazil.

    PubMed

    Rodovalho, R G; Santos, G S; Cavalcanti, L M; Moura, B F S M; Rodrigues, E L; Lima, P R; Gigonzac, M A D; Vieira, T C

    2015-07-03

    In studies of human identification, obtaining a high standard of outcomes and satisfactory conclusions are directly related to the use of highly polymorphic molecular markers. In addition to the combined DNA index system (CODIS) group, it is also important to implement non-CODIS markers into the analysis, as they increase the power of discrimination. During the identification process, it is essential to consider the genetic variation among distinct groups of populations, as the allele frequencies are directly associated with the power of discrimination. However, the population of Goiás, a State located in Central Brazil, is characterized by a highly mixed population due to its diverse ethnic origins. In this study, a survey of the allelic frequencies in the Goiás population was carried out using a molecular assembly composed of 21 autosomal loci both from and external to the CODIS group. The new data, for some of the markers used, were statistically similar to those from previous studies. This consistency means that the use of these markers might serve as a parameter for future population comparisons. The results from these analyses further our knowledge of the study of human identification.

  11. The Behavior Observation Scale for Autism (BOS): Frequency Analyses.

    ERIC Educational Resources Information Center

    Freeman, B. J.; And Others

    Frequency data are reported from a research project aimed at developing the Behavior Observation Scale (BOS), an objective assessment tool for establishing the diagnosis of autism. The goals of the BOS are to differentiate autistic, normal, and mentally retarded children (ages 30 to 60 months) along objective symptom axes involving 67 behaviors.…

  12. Observation of frequency doubling in tantalum doped silica fibres

    NASA Technical Reports Server (NTRS)

    Driscoll, T. J.; Lawandy, N. M.; Killian, A.; Rienhart, L.; Morse, T. F.

    1991-01-01

    Second harmonic conversion efficients of 3 x 0,0001 in tantalum-doped silica fibers prepared by the seeding technique are reported. A series of experiments were conducted to characterize the frequency doubling in this fiber and to compare the results to the behavior observed in germanosilicate and rare earth-doped aluminosilicate fibers.

  13. Observations of High Frequency Harmonics of the Ionospheric Alfven Resonator

    NASA Astrophysics Data System (ADS)

    Mann, Ian; Usanova, Maria; Bortnik, Jacob; Milling, David; Kale, Andy; Shao, Leo; Miles, David; Rae, I. Jonathan

    We present observations of high frequency harmonics of the ionospheric Alfven Resonator (IAR). These are seen in the form of spectral resonance structures (SRS) recorded by a ground-based search coil magnetometer sampling at 100 samples/s at the Ministik Lake station at L=4.2 within the expanded CARISMA magnetometer array. Previous observational studies have indicated that such SRS are typically confined to frequencies <~5 Hz with only several SRS harmonics being observed. We report the first observations of clear and discrete SRS, which we believe are harmonics of the IAR, and which extend to around 20 Hz in at least 10-12 clear SRS harmonics. We additionally demonstrate the utility of the Bortnik et al. (2007) auto-detection algorithm, designed for Pc1 wavepackets, for characterising the properties of the IAR. Our results also indicate that the cavity supporting SRS in the IAR at this time must be structured to support and trap much higher frequency IAR harmonics than previously assumed. This impacts the potential importance of the IAR for magnetosphere-ionosphere coupling, especially in relation to the impacts of incident Alfven waves on the ionosphere including Alfvenic aurora. Our observations also highlight the potential value of IAR observations for diagnosing the structure of the topside ionosphere, not least using the observed structure of the SRS. These are the first mid-latitude observations demonstrating that the IAR can extend to frequencies beyond those of the lowest few harmonics of the Schumann resonances - significantly suggesting the possibility that the Schumann resonance modes and the IAR may be coupled. The in-situ structure of the IAR is also examined by combining satellite data with conjugate measurements from the ground, and the impacts of the IAR for magnetosphere-ionosphere-thermosphere coupling examined.

  14. The frequency dependence of scattering imprints on pulsar observations

    NASA Astrophysics Data System (ADS)

    Geyer, M.; Karastergiou, A.

    2016-11-01

    Observations of pulsars across the radio spectrum are revealing a dependence of the characteristic scattering time (τ) on frequency, which is more complex than the simple power law with a theoretically predicted power-law index. In this paper, we investigate these effects using simulated pulsar data at frequencies below 300 MHz. We investigate different scattering mechanisms, namely isotropic and anisotropic scattering, by thin screens along the line of sight, and the particular frequency-dependent impact on pulsar profiles and scattering time-scales of each. We also consider how the screen shape, location and offset along the line of sight lead to specific observable effects. We evaluate how well forward fitting techniques perform in determining τ. We investigate the systematic errors in τ associated with the use of an incorrect fitting method and with the determination of an off-pulse baseline. Our simulations provide examples of average pulse profiles at various frequencies. Using these, we compute spectra of τ and mean flux for different scattering setups. We identify setups that lead to deviations from the simple theoretical picture. This work provides a framework for interpretation of upcoming low-frequency data, both in terms of modelling the interstellar medium and understanding intrinsic emission properties of pulsars.

  15. Radio frequency interference affecting type III solar burst observations

    NASA Astrophysics Data System (ADS)

    Anim, N. M.; Hamidi, Z. S.; Abidin, Z. Z.; Monstein, C.; Rohizat, N. S.

    2013-05-01

    The solar burst extinguish from the Sun's corona atmosphere and it dynamical structure of the magnetic field in radio wavelength are studied. Observation of solar radio burst with Compact Astronomical Low cost Low frequency Instrument for Spectroscopy and Transportable Observatory (CALLISTO) from ETH, Zurich in frequency range of 45 until 870 MHz. Observation done at Pusat Angkasa Negara, Banting, Selangor and successfully detected the solar burst type III on 9th March 2012 from 4:22:00 UT until 4:28:00 UT. The solar burst emission is associated with M6.3 solar flare which occurred at sunspot AR1429 at 03:58UT were observed by NOAA. Frequency ranges chosen as the best ranges for solar monitoring in Malaysia is 150 MHz until 400 MHz. The highest signal amplitude within this frequency ranges is 1.7619 dB at 153.188 MHz (Government Use) have potential to influence the detection of solar radio burst type III within 20 until 400 MHz.

  16. Observations of frequency shift associated with schooling fish

    NASA Astrophysics Data System (ADS)

    Diachok, Orest

    2003-04-01

    The number of sardines per school, N, is nominally 10000 and the separation between sardines in school, s, is nominally 1 fish length, L.s is much smaller than the wavelength at f (the resonance frequency of individuals), which suggests that schools may exhibit acoustic properties of bubble clouds. Long-term, broadband transmission loss measurements at a shallow-water site in the Gulf of Lion revealed absorption lines due to dispersed sardines at 1.3 kHz at 20 m at night and 2.7 kHz at 65 m at dawn. Temporal changes in observed values of f were consistent with concurrent echo sounder observations of the vertical migration of sardines, and theoretical computations based on laboratory measurements of swim bladder dimensions. The measured resonance frequency of sardines in schools during daytime, 1.7 kHz at 65 m, was 0.6f at the same depth at dawn. The observed frequency shift is consistent with a hybrid model of the fundamental resonance frequency of a bubble cloud, which is based on theories developed by Feuillade, Nero, and Love (1996) and dAgostino and Brennan (1988), and s=0.8 L and N=5000 fish per school. [Work supported by ONR.

  17. Allelic frequencies of the HLA-B17 antigen group: comparative analysis by serology, IEF and PCR-SSOP typing.

    PubMed

    Levine, J E; Yang, S Y

    1995-11-01

    Current typing technology for class I HLA antigens uses serological and/or isoelectric focusing gel electrophoresis. DNA typing for the HLA class I antigens can accurately identify the class I genotype of individuals and cell lines. Here, we report correlation of DNA typing results with serological and IEF results for the B17 group. The B17 antigens are relatively common, being carried by almost 9% of Caucasians and 28% of blacks. In this study, five 10th International Histocompatibility Workshop cell lines carrying B17 and 106 individuals in 61 families carrying B17 were DNA typed for B17 using B17-allele-specific amplification and sequence specific oligonucleotide probe hybridization pattern analysis. 38 (55.07%) out of 69 unrelated haplotypes had B*5701, 23 (33.33%) had B*5801, 6 (8.70%) had B*5702, and 2 (2.90%) had B*5802. DNA typing results correlated well with serological and isoelectric focusing results. In general, there was high degree of agreement between all three methods, although heterozygosity for B17 poses a particular problem for serological and IEF methodology. Both B*5701 and B*5801 have the same electrophoretic mobility on IEF gel, corresponding to B17.2, B*5702 corresponds to B17.1, while B*5802 corresponds to B17.3.

  18. Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach.

    PubMed Central

    Berthier, Pierre; Beaumont, Mark A; Cornuet, Jean-Marie; Luikart, Gordon

    2002-01-01

    A new genetic estimator of the effective population size (N(e)) is introduced. This likelihood-based (LB) estimator uses two temporally spaced genetic samples of individuals from a population. We compared its performance to that of the classical F-statistic-based N(e) estimator (N(eFk)) by using data from simulated populations with known N(e) and real populations. The new likelihood-based estimator (N(eLB)) showed narrower credible intervals and greater accuracy than (N(eFk)) when genetic drift was strong, but performed only slightly better when genetic drift was relatively weak. When drift was strong (e.g., N(e) = 20 for five generations), as few as approximately 10 loci (heterozygosity of 0.6; samples of 30 individuals) are sufficient to consistently achieve credible intervals with an upper limit <50 using the LB method. In contrast, approximately 20 loci are required for the same precision when using the classical F-statistic approach. The N(eLB) estimator is much improved over the classical method when there are many rare alleles. It will be especially useful in conservation biology because it less often overestimates N(e) than does N(eLB) and thus is less likely to erroneously suggest that a population is large and has a low extinction risk. PMID:11861575

  19. Low-frequency heliographic observations of the quiet Sun corona

    NASA Astrophysics Data System (ADS)

    Stanislavsky, A. A.; Koval, A. A.; Konovalenko, A. A.

    2013-12-01

    We present new results of heliographic observations of quiet-Sun radio emission fulfilled by the UTR-2 radio telescope. The solar corona investigations have been made close to the last solar minimum (Cycle 23) in the late August and early September of 2010 by means of the two-dimensional heliograph within 16.5-33 MHz. Moreover, the UTR-2 radio telescope was used also as an 1-D heliograph for one-dimensional scanning of the Sun at the beginning of September 2010 as well as in short-time observational campaigns in April and August of 2012. The average values of integral flux density of the undisturbed Sun continuum emission at different frequencies have been found. Using the data, we have determined the spectral index of quiet-Sun radio emission in the range 16.5-200 MHz. It is equal to -2.1±0.1. The brightness distribution maps of outer solar corona at frequencies 20.0 MHz and 26.0 MHz have been obtained. The angular sizes of radio Sun were estimated. It is found that the solar corona at these frequencies is stretched-out along equatorial direction. The coefficient of corona ellipticity varies slightly during above period. Its mean magnitudes are equal to ≈ 0.75 and ≈ 0.73 at 20.0 MHz and 26.0 MHz, respectively. The presented results for continuum emission of solar corona conform with being ones at higher frequencies.

  20. Solar observations with a low frequency radio telescope

    NASA Astrophysics Data System (ADS)

    Myserlis, I.; Seiradakis, J.; Dogramatzidis, M.

    2012-01-01

    We have set up a low frequency radio monitoring station for solar bursts at the Observatory of the Aristotle University in Thessaloniki. The station consists of a dual dipole phased array, a radio receiver and a dedicated computer with the necessary software installed. The constructed radio receiver is based on NASA's Radio Jove project. It operates continuously, since July 2010, at 20.1 MHz (close to the long-wavelength ionospheric cut-off of the radio window) with a narrow bandwidth (~5 kHz). The system is properly calibrated, so that the recorded data are expressed in antenna temperature. Despite the high interference level of an urban region like Thessaloniki (strong broadcasting shortwave radio stations, periodic experimental signals, CBs, etc), we have detected several low frequency solar radio bursts and correlated them with solar flares, X-ray events and other low frequency solar observations. The received signal is monitored in ordinary ASCII format and as audio signal, in order to investigate and exclude man-made radio interference. In order to exclude narrow band interference and calculate the spectral indices of the observed events, a second monitoring station, working at 36 MHz, is under construction at the village of Nikiforos near the town of Drama, about 130 km away of Thessaloniki. Finally, we plan to construct a third monitoring station at 58 MHz, in Thessaloniki. This frequency was revealed to be relatively free of interference, after a thorough investigation of the region.

  1. Contrail Frequency over the United States from Surface Observations.

    NASA Astrophysics Data System (ADS)

    Minnis, Patrick; Ayers, J. Kirk; Nordeen, Michele L.; Weaver, Steven P.

    2003-11-01

    Contrails have the potential for affecting climate because they impact the radiation budget and the vertical distribution of moisture. Estimating the effect requires additional knowledge about the temporal and spatial variations of contrails. The mean hourly, monthly, and annual frequencies of daytime contrail occurrence are estimated using 2 yr of observations from surface observers at military installations scattered over the continental United States. During both years, persistent contrails are most prevalent in the winter and early spring and are seen least often during the summer. They co-occur with cirrus clouds 85% of the time. The annual mean persistent contrail frequencies in unobscured skies dropped from 0.152 during 1993-94 to 0.124 in 1998-99 despite a rise in air traffic. Mean hourly contrail frequencies reflect the pattern of commercial air traffic, with a rapid increase from sunrise to midmorning followed by a very gradual decrease during the remaining daylight hours. Although highly correlated with air traffic fuel use, contrail occurrence is governed by meteorological conditions. It is negatively and positively correlated with the monthly mean 300-hPa temperature and 300-hPa relative humidity, respectively, from the National Centers for Environmental Prediction (NCEP) reanalyses. A simple empirical model employing the fuel use and the monthly mean 300-hPa temperatures and relative humidities yields a reasonable representation of the seasonal variation in contrail frequency. The interannual drop in contrail frequency coincides with a decrease in mean 300-hPa relative humidities from 45.8% during the first period to 38.2% in 1998-99, one of the driest periods in the NCEP record.

  2. Technologies for low radio frequency observations of the Cosmic Dawn

    NASA Astrophysics Data System (ADS)

    Jones, D. L.

    2014-03-01

    The Jet Propulsion Laboratory (JPL) is developing concepts and technologies for low frequency radio astronomy space missions aimed at observing highly redshifted neutral Hydrogen from the Dark Ages. This is the period of cosmic history between the recombination epoch when the microwave background radiation was produced and the re-ionization of the intergalactic medium by the first generation of stars (Cosmic Dawn). This period, at redshifts z > ~20, is a critical epoch for the formation and evolution of large-scale structure in the universe. The 21-cm spectral line of Hydrogen provides the most promising method for directly studying the Dark Ages, but the corresponding frequencies at such large redshifts are only tens of MHz and thus require space-based observations to avoid terrestrial RFI and ionospheric absorption and refraction. This paper reports on the status of several low frequency technology development activities at JPL, including deployable bi-conical dipoles for a planned lunar-orbiting mission, and both rover-deployed and inflation-deployed long dipole antennas for use on the lunar surface. In addition, recent results from laboratory testing of low frequency receiver designs are presented. Finally, several concepts for space-based imaging interferometers utilizing deployable low frequency antennas are described. Some of these concepts involve large numbers of antennas and consequently a large digital cross-correlator will be needed. JPL has studied correlator architectures that greatly reduce the DC power required for this step, which can dominate the power consumption of real-time signal processing. Strengths and weaknesses of each mission concept are discussed in the context of the additional technology development required.

  3. Life satisfaction in the new country: a multilevel longitudinal analysis of effects of culture and 5-HTT allele frequency distribution in country of origin.

    PubMed

    Kashima, Emiko S; Kent, Stephen; Kashima, Yoshihisa

    2015-01-01

    Life satisfaction of migrants to Australia from 17 countries, assessed at 4-5 months, 16-17 months and 3½ years after arrival, was analyzed with a longitudinal, multilevel analysis. The results indicated that migrants were more satisfied, if the national average life satisfaction was higher in their country of origin, after adjustment for individual-level income, age, and sex and a linear temporal trend. Simultaneously, the migrants were also happier if people in their country of origin had a higher frequency of 5-HTT long allele, a genotype known to be associated with resilience under life stresses. These two relationships were independent, suggesting that both culture and gene matter in international transitions.

  4. Life satisfaction in the new country: a multilevel longitudinal analysis of effects of culture and 5-HTT allele frequency distribution in country of origin.

    PubMed

    Kashima, Emiko S; Kent, Stephen; Kashima, Yoshihisa

    2015-01-01

    Life satisfaction of migrants to Australia from 17 countries, assessed at 4-5 months, 16-17 months and 3½ years after arrival, was analyzed with a longitudinal, multilevel analysis. The results indicated that migrants were more satisfied, if the national average life satisfaction was higher in their country of origin, after adjustment for individual-level income, age, and sex and a linear temporal trend. Simultaneously, the migrants were also happier if people in their country of origin had a higher frequency of 5-HTT long allele, a genotype known to be associated with resilience under life stresses. These two relationships were independent, suggesting that both culture and gene matter in international transitions. PMID:24532702

  5. Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection

    PubMed Central

    2012-01-01

    Background Next generation sequencing provides clinical research scientists with direct read out of innumerable variants, including personal, pathological and common benign variants. The aim of resequencing studies is to determine the candidate pathogenic variants from individual genomes, or from family-based or tumor/normal genome comparisons. Whilst the use of appropriate controls within the experimental design will minimize the number of false positive variations selected, this number can be reduced further with the use of high quality whole genome reference data to minimize false positives variants prior to candidate gene selection. In addition the use of platform related sequencing error models can help in the recovery of ambiguous genotypes from lower coverage data. Description We have developed a whole genome database of human genetic variations, Huvariome, determined by whole genome deep sequencing data with high coverage and low error rates. The database was designed to be sequencing technology independent but is currently populated with 165 individual whole genomes consisting of small pedigrees and matched tumor/normal samples sequenced with the Complete Genomics sequencing platform. Common variants have been determined for a Benelux population cohort and represented as genotypes alongside the results of two sets of control data (73 of the 165 genomes), Huvariome Core which comprises 31 healthy individuals from the Benelux region, and Diversity Panel consisting of 46 healthy individuals representing 10 different populations and 21 samples in three Pedigrees. Users can query the database by gene or position via a web interface and the results are displayed as the frequency of the variations as detected in the datasets. We demonstrate that Huvariome can provide accurate reference allele frequencies to disambiguate sequencing inconsistencies produced in resequencing experiments. Huvariome has been used to support the selection of candidate cardiomyopathy

  6. Life satisfaction in the new country: a multilevel longitudinal analysis of effects of culture and 5-HTT allele frequency distribution in country of origin

    PubMed Central

    Kent, Stephen; Kashima, Yoshihisa

    2015-01-01

    Life satisfaction of migrants to Australia from 17 countries, assessed at 4–5 months, 16–17 months and 3½ years after arrival, was analyzed with a longitudinal, multilevel analysis. The results indicated that migrants were more satisfied, if the national average life satisfaction was higher in their country of origin, after adjustment for individual-level income, age, and sex and a linear temporal trend. Simultaneously, the migrants were also happier if people in their country of origin had a higher frequency of 5-HTT long allele, a genotype known to be associated with resilience under life stresses. These two relationships were independent, suggesting that both culture and gene matter in international transitions. PMID:24532702

  7. Distribution of HLA-B alleles in Mexican Amerindian populations.

    PubMed

    Vargas-Alarcón, Gilberto; Hernández-Pacheco, Guadalupe; Zuñiga, Joaquín; Rodríguez-Pérez, José Manuel; Pérez-Hernández, Nonanzit; Rangel, Carlos; Villarreal-Garza, Cynthia; Martínez-Laso, Jorge; Granados, Julio; Arnaiz-Villena, Antonio

    2003-02-01

    In the present study we analyzed by PCR-SSO technique the HLA-B gene frequencies in 281 healthy individuals from four Mexican Amerindian populations (66 Mayos, 90 Mazatecans, 72 Nahuas and 53 Teenek). The most frequent alleles in all studied populations were HLA-B35, HLA-B39, and HLA-B40; however, some differences were observed between populations. The HLA-B35 allele was the most frequent in three of the four populations studied (Mayos, Nahuas and Teenek), whereas in Mazatecans the most frequent allele was HLA-B39. HLA-B40 presented frequencies higher than 10% in all groups. On the other hand, only Mayos presented an HLA-B51 gene frequency higher than 10%. When comparisons were made, important differences between groups were observed. The Teenek group presented an increased frequency of HLA-B35 when compared to Mazatecans and the HLA-B52 allele was increased in Nahuas and Teenek when compared to Mayos. An increased frequency of HLA-B39 was observed in Mazatecans when compared to Nahuas, Mayos and Teenek. Also, an increased frequency of HLA-B51 was observed in Mayos when compared to Mazatecans and Nahuas. These data corroborate the restricted polymorphism of HLA-B alleles and the high frequency of HLA-B35, HLA-B39 and HLA-B40 alleles in autochthonous American populations. In spite of the restriction in this polymorphism, differences in frequencies of HLA-B alleles could be helpful in distinguishing each of these populations.

  8. Technologies for Low Frequency Radio Observations of the Cosmic Dawn

    NASA Technical Reports Server (NTRS)

    Jones, Dayton L.

    2014-01-01

    The Jet Propulsion Laboratory (JPL) is developing concepts and technologies for low frequency radio astronomy space missions aimed at observing highly redshifted neutral Hydrogen from the Dark Ages. This is the period of cosmic history between the recombination epoch when the microwave background radiation was produced and the re-ionization of the intergalactic medium by the first generation of stars (Cosmic Dawn). This period, at redshifts greater than about 20, is a critical epoch for the formation and evolution of large-scale structure in the universe. The 21-cm spectral line of Hydrogen provides the most promising method for directly studying the Dark Ages, but the corresponding frequencies at such large redshifts are only tens of MHz and thus require space-based observations to avoid terrestrial RFI and ionospheric absorption and refraction. This paper reports on the status of several low frequency technology development activities at JPL, including deployable bi-conical dipoles for a planned lunar-orbiting mission, and both rover-deployed and inflation-deployed long dipole antennas for use on the lunar surface.

  9. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central europe.

    PubMed

    Krüttli, Annina; Bouwman, Abigail; Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

    Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary

  10. Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe

    PubMed Central

    Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

    Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71–80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary

  11. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central europe.

    PubMed

    Krüttli, Annina; Bouwman, Abigail; Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

    Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary

  12. Prevalence and allele frequency estimation of bovine leukocyte adhesion deficiency (BLAD) in Holstein-Friesian cattle in Japan.

    PubMed

    Nagahata, H; Miura, T; Tagaki, K; Ohtake, M; Noda, H; Yasuda, T; Nioka, K

    1997-04-01

    Blood samples from 796 Holstein dairy cows in 20 herds from 6 districts in Japan from June 1994 to August 1995 were examined to determine whether they were BLAD-free, BLAD carriers, or BLAD-affected by use of DNA-polymerase chain reaction (PCR) analysis. The usage of semen of confirmed BLAD-carriers for artificial insemination in the Hokkaido district and two selected dairy farms was examined to estimate the gene frequency of BLAD carriers of sires. BLAD-carrier prevalence in 20 herds (796 cows, over 2.5 years old) ranged from 0 to 23.5%, and the mean BLAD-carrier prevalence was 8.1%. The BLAD-carrier prevalence in 10 herds (363 cows) in which the occurrence of BLAD was not detected by the DNA-PCR test ranged from 0 to 12.5% with a mean of 5.4%. The BLAD-carrier prevalence in 10 herds (433 cows) in which the occurrence of BLAD was confirmed by DNA-PCR analysis ranged from 2.6 to 23.5% with a mean of 10.8%, and these values were significantly (P < 0.05) higher than those of dairy herds in which the occurrence of BLAD was not detected. The age distribution in BLAD carriers in these cows ranged from 2.5 to 11 years. The mean gene frequencies of BLAD among 796 cows from 20 herds and 433 cows from 10 herds in which the occurrence of BLAD was detected were 0.041 and 0.054, respectively. The proportional usage of semen of BLAD carriers for artificial insemination in the Hokkaido district in 1992 was 12.6%, and its gene frequency was 0.058. On two selected farms in which higher BLAD-carrier rates were detected, the prevalences were 35.5% and 25.8%, and their gene frequencies were 0.177 and 0.129, respectively. The occurrence of BLAD-affected in Holstein dairy cattle was estimated to be 0.16-0.31% at birth in Japan without genetic control. PMID:9152929

  13. Natural frequency identification of smart washer by using adaptive observer

    NASA Astrophysics Data System (ADS)

    Ito, Hitoshi; Okugawa, Masayuki

    2014-04-01

    Bolted joints are used in many machines/structures and some of them have been loosened during long time use, and unluckily these bolt loosening may cause a great accident of machines/structures system. These bolted joint, especially in important places, are main object of maintenance inspection. Maintenance inspection with human- involvement is desired to be improved owing to time-consuming, labor-intensive and high-cost. By remote and full automation monitoring of the bolt loosening, constantly monitoring of bolted joint is achieved. In order to detect loosening of bolted joints without human-involvement, applying a structural health monitoring technique and smart structures/materials concept is the key objective. In this study, a new method of bolt loosening detection by adopting a smart washer has been proposed, and the basic detection principle was discussed with numerical analysis about frequency equation of the system, was confirmed experimentally. The smart washer used in this study is in cantilever type with piezoelectric material, which adds the washer the self-sensing and actuation function. The principle used to detect the loosening of the bolts is a method of a bolt loosening detection noted that the natural frequency of a smart washer system is decreasing by the change of the bolt tightening axial tension. The feature of this proposed method is achieving to identify the natural frequency at current condition on demand by adopting the self-sensing and actuation function and system identification algorithm for varying the natural frequency depending the bolt tightening axial tension. A novel bolt loosening detection method by adopting adaptive observer is proposed in this paper. The numerical simulations are performed to verify the possibility of the adaptive observer-based loosening detection. Improvement of the detection accuracy for a bolt loosening is confirmed by adopting initial parameter and variable adaptive gain by numerical simulation.

  14. Observation of upper drift modes in radio frequency produced magnetized plasmas with frequency above ion cyclotron frequency

    NASA Astrophysics Data System (ADS)

    Ghosh, Abhijit; Saha, S. K.; Chowdhury, S.; Janaki, M. S.

    2015-12-01

    In a RF produced magnetized argon plasma expanding into a larger expansion chamber, electrostatic modes propagating azimuthally in the direction of the electron diamagnetic drift and frequency greater than the ion cyclotron frequency are observed. In the radial direction, the mode amplitude peaks at a location where the radial density gradient is maximum. The modes are detected at axial locations up to 16 cm away from the entrance aperture. For fixed values of the neutral pressure and magnetic field, the mode frequency is found to be independent of the location at which it is measured. The modes exhibit drift wave characteristics revealing a radial structure with the azimuthal mode number m = 1 at the lower radial locations (r ˜ 3.0 cm) while the m = 2 mode is located in the outer region. Theoretical modeling using a local dispersion relation based on the fluid equations predicts destabilization of the modes with frequency greater than the ion-cyclotron frequency by electron-neutral collisions and exhibiting other drift wave features.

  15. Observation of upper drift modes in radio frequency produced magnetized plasmas with frequency above ion cyclotron frequency

    SciTech Connect

    Ghosh, Abhijit; Saha, S. K.; Chowdhury, S.; Janaki, M. S.

    2015-12-15

    In a RF produced magnetized argon plasma expanding into a larger expansion chamber, electrostatic modes propagating azimuthally in the direction of the electron diamagnetic drift and frequency greater than the ion cyclotron frequency are observed. In the radial direction, the mode amplitude peaks at a location where the radial density gradient is maximum. The modes are detected at axial locations up to 16 cm away from the entrance aperture. For fixed values of the neutral pressure and magnetic field, the mode frequency is found to be independent of the location at which it is measured. The modes exhibit drift wave characteristics revealing a radial structure with the azimuthal mode number m = 1 at the lower radial locations (r ∼ 3.0 cm) while the m = 2 mode is located in the outer region. Theoretical modeling using a local dispersion relation based on the fluid equations predicts destabilization of the modes with frequency greater than the ion-cyclotron frequency by electron-neutral collisions and exhibiting other drift wave features.

  16. In situ observations of medium frequency auroral radio emissions

    NASA Astrophysics Data System (ADS)

    Broughton, M.; Labelle, J. W.; Pfaff, R. F.; Parrot, M.; Yan, X.; Burchill, J. K.

    2013-12-01

    The auroral ionosphere is a region rich with plasma waves that can be studied both in space and on the ground. These waves may mediate energy exchange between particle populations and provide information about the local plasma properties and boundaries. Auroral medium frequency (MF) burst is an impulsive radio emission observed at ground-level from 1.3-4.5 MHz that is associated with local substorm onset. There have been two recent reports of impulsive, broadband, MF waves at high latitudes. Burchill and Pfaff [2005] reported observations from the FAST satellite of impulsive, broadband, MF and low frequency (LF) radio waves. Using data from the DEMETER satellite, Parrot et al. [2009] surveyed MF waves caused by lightning. This study did show a high-latitude population of MF waves. We investigate whether the waves observed by these two satellites are related to auroral MF burst. Using FAST satellite burst mode electric field data from high-latitude (> 60 degrees magnetic), low-altitude (< 1000 km) intervals of moderate to large geomagnetic activity (Kp > 3) from 1996-2002, we have found forty-four examples of impulsive MF waves, all of which are associated with impulsive LF waves. Although MF burst and the waves observed by FAST have similar spectral signatures, they have different magnetic local time dependencies, which suggests that they may be unrelated. A study of MF waves observed at high latitude by DEMETER is ongoing. In situ observations of MF burst could provide crucial information about this heretofore unexplained natural radio emission.

  17. Low frequency radio observations of coronal magnetic field

    NASA Astrophysics Data System (ADS)

    Ramesh, R.; Kathiravan, C.

    2012-07-01

    Magnetic fields play an important role in the dynamics as well as the formation of the structures in the solar corona. Despite its fundamental importance, only a few direct measurements of the coronal magnetic field are available. The existing direct estimates using optical/infrared and radio emissions are limited to the inner corona, i.e., r < 1.2 R , where R is the radius of the Sun. In the outer corona beyond r > 3 R , Faraday rotation observations are used to derive the magnetic field. But due to lack of observational techniques, measurements in the range 1.2 R < r > 3 R (middle corona) are not available until now. As the photosphere, chromosphere, and corona are coupled by the solar magnetic field, the magnetic field strength at these distances is generally obtained by mathematical extrapolation of the observed line-of-sight component of the photospheric magnetic field assuming a potential or force-free model. The Indian Institute of Astrophysics has recently commissioned a radio polarimeter (based on inteferometer techniques) for dedicated obervations of the polarized radio emission from the solar corona. The frequency range of observation is 120-30 MHz which corresponds to a radial distance range of about 1.2-1.8 R. Estimates of weak magnetic fields in the 'undisturbed' Sun (non-flaring sunspot active regions, coronal streamers, etc.) obtained from observations with the above instrument will be presented.

  18. Allelic Diversity and Its Implications for the Rate of Adaptation

    PubMed Central

    Caballero, Armando; García-Dorado, Aurora

    2013-01-01

    Genetic variation is usually estimated empirically from statistics based on population gene frequencies, but alternative statistics based on allelic diversity (number of allelic types) can provide complementary information. There is a lack of knowledge, however, on the evolutionary implications attached to allelic-diversity measures, particularly in structured populations. In this article we simulated multiple scenarios of single and structured populations in which a quantitative trait subject to stabilizing selection is adapted to different fitness optima. By forcing a global change in the optima we evaluated which diversity variables are more strongly correlated with both short- and long-term adaptation to the new optima. We found that quantitative genetic variance components for the trait and gene-frequency-diversity measures are generally more strongly correlated with short-term response to selection, whereas allelic-diversity measures are more correlated with long-term and total response to selection. Thus, allelic-diversity variables are better predictors of long-term adaptation than gene-frequency variables. This observation is also extended to unlinked neutral markers as a result of the information they convey on the demographic population history. Diffusion approximations for the allelic-diversity measures in a finite island model under the infinite-allele neutral mutation model are also provided. PMID:24121776

  19. High-frequency radar observations of ocean surface currents.

    PubMed

    Paduan, Jeffrey D; Washburn, Libe

    2013-01-01

    This article reviews the discovery, development, and use of high-frequency (HF) radio wave backscatter in oceanography. HF radars, as the instruments are commonly called, remotely measure ocean surface currents by exploiting a Bragg resonant backscatter phenomenon. Electromagnetic waves in the HF band (3-30 MHz) have wavelengths that are commensurate with wind-driven gravity waves on the ocean surface; the ocean waves whose wavelengths are exactly half as long as those of the broadcast radio waves are responsible for the resonant backscatter. Networks of HF radar systems are capable of mapping surface currents hourly out to ranges approaching 200 km with a horizontal resolution of a few kilometers. Such information has many uses, including search and rescue support and oil-spill mitigation in real time and larval population connectivity assessment when viewed over many years. Today, HF radar networks form the backbone of many ocean observing systems, and the data are assimilated into ocean circulation models.

  20. 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.

  1. Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases

    PubMed Central

    Chen, Rong; Corona, Erik; Sikora, Martin; Dudley, Joel T.; Morgan, Alex A.; Moreno-Estrada, Andres; Nilsen, Geoffrey B.; Ruau, David; Lincoln, Stephen E.; Bustamante, Carlos D.; Butte, Atul J.

    2012-01-01

    Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed

  2. Electromagnetic Waves near the Proton Cyclotron Frequency: STEREO Observations

    NASA Astrophysics Data System (ADS)

    Jian, L. K.; Wei, H. Y.; Russell, C. T.; Luhmann, J. G.; Klecker, B.; Omidi, N.; Isenberg, P. A.; Goldstein, M. L.; Figueroa-Viñas, A.; Blanco-Cano, X.

    2014-05-01

    Transverse, near-circularly polarized, parallel-propagating electromagnetic waves around the proton cyclotron frequency were found sporadically in the solar wind throughout the inner heliosphere. They could play an important role in heating and accelerating the solar wind. These low-frequency waves (LFWs) are intermittent but often occur in prolonged bursts lasting over 10 minutes, named "LFW storms." Through a comprehensive survey of them from Solar Terrestrial Relations Observatory A using dynamic spectral wave analysis, we have identified 241 LFW storms in 2008, present 0.9% of the time. They are left-hand (LH) or right-hand (RH) polarized in the spacecraft frame with similar characteristics, probably due to Doppler shift of the same type of waves or waves of intrinsically different polarities. In rare cases, the opposite polarities are observed closely in time or even simultaneously. Having ruled out interplanetary coronal mass ejections, shocks, energetic particles, comets, planets, and interstellar ions as LFW sources, we discuss the remaining generation scenarios: LH ion cyclotron instability driven by greater perpendicular temperature than parallel temperature or by ring-beam distribution, and RH ion fire hose instability driven by inverse temperature anisotropy or by cool ion beams. The investigation of solar wind conditions is compromised by the bias of the one-dimensional Maxwellian fit used for plasma data calibration. However, the LFW storms are preferentially detected in rarefaction regions following fast winds and when the magnetic field is radial. This preference may be related to the ion cyclotron anisotropy instability in fast wind and the minimum in damping along the radial field.

  3. Electromagnetic waves near the proton cyclotron frequency: Stereo observations

    SciTech Connect

    Jian, L. K.; Wei, H. Y.; Russell, C. T.; Luhmann, J. G.; Klecker, B.; Omidi, N.; Isenberg, P. A.; Goldstein, M. L.; Figueroa-Viñas, A.; Blanco-Cano, X.

    2014-05-10

    Transverse, near-circularly polarized, parallel-propagating electromagnetic waves around the proton cyclotron frequency were found sporadically in the solar wind throughout the inner heliosphere. They could play an important role in heating and accelerating the solar wind. These low-frequency waves (LFWs) are intermittent but often occur in prolonged bursts lasting over 10 minutes, named 'LFW storms'. Through a comprehensive survey of them from Solar Terrestrial Relations Observatory A using dynamic spectral wave analysis, we have identified 241 LFW storms in 2008, present 0.9% of the time. They are left-hand (LH) or right-hand (RH) polarized in the spacecraft frame with similar characteristics, probably due to Doppler shift of the same type of waves or waves of intrinsically different polarities. In rare cases, the opposite polarities are observed closely in time or even simultaneously. Having ruled out interplanetary coronal mass ejections, shocks, energetic particles, comets, planets, and interstellar ions as LFW sources, we discuss the remaining generation scenarios: LH ion cyclotron instability driven by greater perpendicular temperature than parallel temperature or by ring-beam distribution, and RH ion fire hose instability driven by inverse temperature anisotropy or by cool ion beams. The investigation of solar wind conditions is compromised by the bias of the one-dimensional Maxwellian fit used for plasma data calibration. However, the LFW storms are preferentially detected in rarefaction regions following fast winds and when the magnetic field is radial. This preference may be related to the ion cyclotron anisotropy instability in fast wind and the minimum in damping along the radial field.

  4. Frequencies of allele groups HLA-A, HLA-B and HLA-DRB1 in a population from the northwestern region of São Paulo State, Brazil.

    PubMed

    Ayo, C M; da Silveira Camargo, A V; Xavier, D H; Batista, M F; Carneiro, O A; Brandão de Mattos, C C; Ricci, O; de Mattos, L C

    2015-02-01

    The aim of this study was to estimate the HLA-A, HLA-B and HLA-DRB1 allele groups frequencies in a population of 1559 volunteer bone marrow donors from the northwestern region of São Paulo State grouped according to ethnicity. An additional objective was to compare the allele frequencies of the current study with data published for other Brazilian populations. The allele groups were characterized by the PCR-rSSO method using Luminex(®) technology. Twenty HLA-A, 32 HLA-B and 13 HLA-DRB1 allele groups were identified. The most common allele groups in European descent and mixed African and European descent samples were HLA-A*02, HLA-B*35 and HLA-DRB1*13, while HLA-A*02, HLA-B*35 and HLA-DRB1*11 were more common in African descent samples. The HLA-A*23, HLA-A*36, HLA-B*58 and HLA-B*81 allele groups were more common in sample from African descent than European descent, and the HLA-DRB1*08 was more common in mixed African and European descent than in European descent. Allele group frequencies were compared with samples from other Brazilian regions. The HLA-A*30 and HLA-A*23 were more common in this study than in the populations of Rio Grande do Sul and Paraná; and the HLA-A*01, HLA-B*18, HLA-B*57 and HLA-DRB1*11 were more common in this study than in the population of Piauí. The least frequent allele groups were HLA-A*31, HLA-B*15, HLA-B*40 and HLA-DRB1*08 for the population of Piauí, HLA-A*01 and HLA-A*11 for Parana, HLA-A*02 and -A*03 for Rio Grande do Sul and HLA-DRB1*04 for Paraná, Rio Grande do Sul and Piauí. These data provide an overview on the knowledge on HLA diversity in the population of the northwestern region of São Paulo State and show that the genes of this system are useful to distinguish different ethnic groups.

  5. Quantitative resistance affects the speed of frequency increase but not the diversity of the virulence alleles overcoming a major resistance gene to Leptosphaeria maculans in oilseed rape.

    PubMed

    Delourme, R; Bousset, L; Ermel, M; Duffé, P; Besnard, A L; Marquer, B; Fudal, I; Linglin, J; Chadœuf, J; Brun, H

    2014-10-01

    Quantitative resistance mediated by multiple genetic factors has been shown to increase the potential for durability of major resistance genes. This was demonstrated in the Leptosphaeria maculans/Brassica napus pathosystem in a 5year recurrent selection field experiment on lines harboring the qualitative resistance gene Rlm6 combined or not with quantitative resistance. The quantitative resistance limited the size of the virulent isolate population. In this study we continued this recurrent selection experiment in the same way to examine whether the pathogen population could adapt and render the major gene ineffective in the longer term. The cultivars Eurol, with a susceptible background, and Darmor, with quantitative resistance, were used. We confirmed that the combination of qualitative and quantitative resistance is an effective approach for controlling the pathogen epidemics over time. This combination did not prevent isolates virulent against the major gene from amplifying in the long term but the quantitative resistance significantly delayed for 5years the loss of effectiveness of the qualitative resistance and disease severity was maintained at a low level on the genotype with both types of resistance after the fungus population had adapted to the major gene. We also showed that diversity of AvrLm6 virulence alleles was comparable in isolates recovered after the recurrent selection on lines carrying either the major gene alone or in combination with quantitative resistance: a single repeat-induced point mutation and deletion events were observed in both situations. Breeding varieties which combine qualitative and quantitative resistance can effectively contribute to disease control by increasing the potential for durability of major resistance genes.

  6. Recommended Rest Frequencies for Observed Interstellar Molecular Microwave Transitions - 2002 Revision

    National Institute of Standards and Technology Data Gateway

    SRD 116 NIST Recommended Rest Frequencies for Observed Interstellar Molecular Microwave Transitions - 2002 Revision (Web, free access)   Critically evaluated transition frequencies for the molecular transitions detected in interstellar and circumstellar clouds are presented.

  7. Distribution of allele frequencies at TTN g.231054C > T, RPL27A g.3109537C > T and AKIRIN2 c.*188G > A between Japanese Black and four other cattle breeds with differing historical selection for marbling

    PubMed Central

    2011-01-01

    Background Marbling defined by the amount and distribution of intramuscular fat, so-called Shimofuri, is an economically important trait of beef cattle in Japan. Our previous study detected 3 single nucleotide polymorphisms (SNPs), g.231054C > T, g.3109537C > T and c.*188G > A, respectively, in the 5' flanking region of the titin (TTN), the 5' flanking region of the ribosomal protein L27a (RPL27A) and the 3' untranslated region of the akirin 2 genes (AKIRIN2), which have been considered as positional functional candidates for the genes responsible for marbling, and showed association of these SNPs with marbling in Japanese Black beef cattle. In the present study, we investigated the allele frequency distribution of the 3 SNPs among the 5 cattle breeds, Japanese Black, Japanese Brown, Japanese Shorthorn, Holstein and Brown Swiss breeds. Findings We genotyped the TTN g.231054C > T, RPL27A g.3109537C > T and AKIRIN2 c.*188G > A SNPs by polymerase chain reaction-restriction fragment length polymorphism method, using 101 sires and 1,705 paternal half sib progeny steers from 8 sires for Japanese Black, 86 sires and 27 paternal half sib progeny steers from 3 sires for Japanese Brown, 79 sires and 264 paternal half sib progeny steers from 14 sires for Japanese Shorthorn, 119 unrelated cows for Holstein, and 118 unrelated cows for Brown Swiss breeds. As compared to the frequencies of the g.231054C > T T, g.3109537C > T T and c.*188G > A A alleles, associated with high marbling, in Japanese Black breed that has been subjected to a strong selection for high marbling, those in the breeds, Japanese Shorthorn, Holstein and Brown Swiss breeds, that have not been selected for high marbling were null or lower. The Japanese Brown breed selected slightly for high marbling showed lower frequency than Japanese Black breed in the g.3109537C > T T allele, whereas no differences were detected between the 2 breeds in the frequencies of the g.231054C > T T and c.*188G > A A alleles

  8. Low-Frequency Radio Observations of Galaxy Cluster Merger Shocks

    NASA Astrophysics Data System (ADS)

    van Weeren, Reinout

    2014-10-01

    In a few dozen merging galaxy clusters diffuse extended radio emission has been found, implying the presence of relativistic particles and magnetic fields in the intracluster medium. A major question is how these particles are accelerated up to such extreme energies. In this talk I will present LOFAR and JVLA radio observations of the Toothbrush galaxy cluster. The Toothbrush cluster hosts diffuse 2 Mpc extended radio emission in the form of a radio relic and halo. Our deep LOFAR and JVLA observations allow a radio spectral study to test the shock origin of the relic and underlying particle acceleration mechanisms.

  9. High Frequency Variations in Earth Orientation Derived From GNSS Observations

    NASA Astrophysics Data System (ADS)

    Weber, R.; Englich, S.; Snajdrova, K.; Boehm, J.

    2006-12-01

    Current observations gained by the space geodetic techniques, especially VLBI, GPS and SLR, allow for the determination of Earth Orientation Parameters (EOPs - polar motion, UT1/LOD, nutation offsets) with unprecedented accuracy and temporal resolution. This presentation focuses on contributions to the EOP recovery provided by satellite navigation systems (primarily GPS). The IGS (International GNSS Service), for example, currently provides daily polar motion with an accuracy of less than 0.1mas and LOD estimates with an accuracy of a few microseconds. To study more rapid variations in polar motion and LOD we established in a first step a high resolution (hourly resolution) ERP-time series from GPS observation data of the IGS network covering the period from begin of 2005 till March 2006. The calculations were carried out by means of the Bernese GPS Software V5.0 considering observations from a subset of 79 fairly stable stations out of the IGb00 reference frame sites. From these ERP time series the amplitudes of the major diurnal and semidiurnal variations caused by ocean tides are estimated. After correcting the series for ocean tides the remaining geodetic observed excitation is compared with variations of atmospheric excitation (AAM). To study the sensitivity of the estimates with respect to the applied mapping function we applied both the widely used NMF (Niell Mapping Function) and the VMF1 (Vienna Mapping Function 1). In addition, based on computations covering two months in 2005, the potential improvement due to the use of additional GLONASS data will be discussed. Finally, satellite techniques are also able to provide nutation offset rates with respect to the most recent nutation model. Based on GPS observations from 2005 we established nutation rate time series and subsequently derived the amplitudes of several nutation waves with periods less than 30 days. The results are compared to VLBI estimates processed by means of the OCCAM 6.1 software.

  10. Exact break point of a 50 kb deletion 8 kb centromeric of the HLA-A locus with HLA-A*24:02: the same deletion observed in other A*24 alleles and A*23:01 allele.

    PubMed

    Mitsunaga, Shigeki; Okudaira, Yuko; Kunii, Nanae; Cui, Tailin; Hosomichi, Kazuyoshi; Oka, Akira; Suzuki, Yasuo; Homma, Yasuhiko; Sato, Shinji; Inoue, Ituro; Inoko, Hidetoshi

    2011-08-01

    In a structural aberration analysis of patients with arthritis mutilans, a 50 kb deletion near the HLA-A locus with HLA-A*24:02 allele was detected. It was previously reported that HLA-A*24:02 haplotype harbored a large-scale deletion telomeric of the HLA-A gene in healthy individuals. In order to confirm that the deletion are the same in patients with arthritis mutilans and in healthy individuals, and to identify the break point of this deletion, the boundary sequences across the deletion in A*24:02 was amplified by polymerase chain reaction (PCR) as a 3.7 kb genomic fragment and subjected to nucleotide sequence determination. A comparison of these genomic sequences with those of the non-A*24:02 haplotype revealed that the deleted genomic region spanning 50 kb was flanked by 3.7 kb repetitive element-rich segments homologous to each other on both sides in non-A*24. The nucleotide sequences of the PCR products were identical in patients with arthritis mutilans and in healthy individuals, revealing that the deletion linked to A*24:02 is irrelevant to the onset of arthritis mutilans. The deletion was detected in all other A*24 alleles so far examined but not in other HLA-A alleles, except A*23:01. This finding, along with the phylogenic tree of HLA-A alleles and the presence of the 3.7 kb highly homologous segments at the boundary of the deleted genomic region in A*03 and A*32, may suggest that this HLA-A*24:02-linked deletion was generated by homologous recombination within two 3.7 kb homologous segments situated 50 kb apart in the ancestral A*24 haplotype after divergence from the A*03 and A*32 haplotypes.

  11. Low-frequency radio observations of poor clusters of galaxies

    NASA Astrophysics Data System (ADS)

    Hanisch, R. J.; White, R. A.

    1981-06-01

    Observations have been made at the Clark Lake Radio Observatory of 16 poor clusters of galaxies at 34.3 MHz. Four of the poor clusters were detected at flux densities greater than 20 Jy. The spectra of the four detected clusters are all rather steep. Two of the detected clusters, AWM 4 and AWM 5, are also known to be X-ray sources. The possibility that the X-ray-emitting gas is heated by Coulomb interactions with the relativistic electrons responsible for the radio emission is investigated, and it is found that the observed X-ray luminosities can be accounted for if the electron energy spectrum extends to very low energies (gamma approximately 1-10). Collective plasma effects may increase the heating efficiency and eliminate the need to extrapolate the electron energy spectrum to such low values.

  12. Low-frequency radio observations of poor clusters of galaxies

    NASA Technical Reports Server (NTRS)

    Hanisch, R. J.; White, R. A.

    1981-01-01

    Observations have been made at the Clark Lake Radio Observatory of 16 poor clusters of galaxies at 34.3 MHz. Four of the poor clusters were detected at flux densities greater than 20 Jy. The spectra of the four detected clusters are all rather steep. Two of the detected clusters, AWM 4 and AWM 5, are also known to be X-ray sources. The possibility that the X-ray-emitting gas is heated by Coulomb interactions with the relativistic electrons responsible for the radio emission is investigated, and it is found that the observed X-ray luminosities can be accounted for if the electron energy spectrum extends to very low energies (gamma approximately 1-10). Collective plasma effects may increase the heating efficiency and eliminate the need to extrapolate the electron energy spectrum to such low values.

  13. Low frequency waves associated with PSBL ion beams. Cluster observations.

    NASA Astrophysics Data System (ADS)

    Grigorenko, Elena; Sauvaud, Jean-Andre; Zeleniy, Lev; Burinskaya, T.

    The processes of non-adiabatic ion acceleration occurring in the Current Sheet of the Earth's magnetotail produce highly accelerated (up to 2500km/s) field-aligned ion beams (beamlets) with transient appearance streaming earthward in the Plasma Sheet Boundary Layer (PSBL). Multipoint Cluster observations have led to a new understanding of these phenomena with a spatial rather than a temporal structure. Comparison of data from different Cluster spacecraft allows to evaluate the duration of beamlets to be, at least, 5-15 min and confirms their welldefined localization along Y and/or Z directions, i.e. across the lobe magnetic field. Earlier results reporting shorter duration of beamlet observations could be understood by the invoking of an additional effect revealed by Cluster: earthward propagation of magnetic perturbations along the beamlet filaments. Phase velocity of these perturbations is of the order of the local Alfven velocity (V 600-1000km/s) and related fast flappings of localized beamlet structures in Y-Z direction significantly decreases the time of their observation at a given spacecraft. Statistical studies of 90 beamlets have shown that the typical wave length of the related disturbances is about tens RE and typical period is about several minutes. Such Alfvenic-type disturbances may be caused by Kelvin-Helmholtz instability triggered by a flow shear between the highvelocity plasma beam streaming at the PSBL boundary and the slowly moving plasma of the outer lobe. Our analysis revealed that for the majority of accelerated ion beams observed in the PSBL of magnetotail the conditions for the development of Kelvin-Helmholtz instability are satisfied. This work was supported by RFBR grants 07-02-00319; 06-02-72561

  14. Association of the HLA-B*52 allele with non-progression to AIDS in Brazilian HIV-1-infected individuals.

    PubMed

    Teixeira, S L M; de Sá, N B R; Campos, D P; Coelho, A B; Guimarães, M L; Leite, T C N F; Veloso, V G; Morgado, M G

    2014-04-01

    Several human leukocyte antigen (HLA) class I alleles are associated with the susceptibility to human immunodeficiency virus-1 (HIV-1) infection and/or AIDS progression. Of these, the HLA-B alleles are considered the strongest genetic determinant of disease outcome. We evaluated the influence of the HLA-B alleles on AIDS progression among HIV-1-positive individuals from Rio de Janeiro, Brazil, who were categorized as rapid progressors (RPs), typical progressors (TPs) or long-term non-progressors (LTNPs). In this study, significant differences in HLA-B allele frequencies were observed among the three progression groups for the B*48, B*49 and B*52 alleles. After controlling for other factors associated with AIDS progression, the presence of the B*52 allele was shown to be a significant protective factor (hazard ratio (HR) 0.49 (95% confidence interval (CI) 0.27-0.90) P<0.03). Although no direct association was observed between the presence of the B*27 or B*57 allele and the LTNP profile compared with the TP or RP groups, the adjusted model confirmed that these alleles are protective factors against AIDS progression (HR 0.62 (95% CI 0.38-0.99) P<0.05), as previously described. These data corroborate the existence of significant differences in HLA-B allele frequencies among the distinct AIDS progression profiles and further elucidate the role of HLA alleles in the outcome of HIV infections in diverse populations.

  15. Dual frequency observations of flares with the VLA

    NASA Technical Reports Server (NTRS)

    Dulk, G. A.; Bastian, T. S.; Hurford, G. J.

    1983-01-01

    Observations are presented of two subflares near the limb on 21 and 22 November 1981 and an M7.7 flare on 8 May 1981 made at 5 and 15 GHz using the VLA. One of the November flares produced no 5 GHz radiation, while the 15 GHz radiation in the other flare emanated from a source which was smaller, lower, and displaced from the 5 GHz source. The flare occurring on 8 May was intense and complex, and contained two or more sources at both 5 and 15 GHz. Prior to the peak of the flare, the sources were found to grow in size, after which time only weak subsources were visible to the VLA. These subsources were found to be located between or at the edge of the H-alpha ribbons and the two hard X-ray sources imaged by the Hinotori satellite. Highly polarized, bursty radiation was observed at 1 and 2 GHz, which indicated that an electron-cyclotron maser operated during the flare. The maximum field strength in flaring loops is estimated to be 360-600 gauss.

  16. 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...

  17. Frequencies of immune hypersensitivity reaction-associated HLA class I alleles in healthy South African Indian and mixed ancestry populations determined by a novel real-time PCR assay.

    PubMed

    Loubser, S; Paximadis, M; Gentle, N; Puren, A; Gray, C M; Tiemessen, C T

    2014-10-01

    We have determined the frequencies of human leucocyte antigen (HLA)-B*57:01, HLA-B*35:05, HLA-C*04 and HLA-C*08 in healthy individuals of South African Indian (SAI) ethnicity (n = 50) and South African mixed (SAM) ancestry (n = 50) using real-time allele-specific polymerase chain reaction (AS-PCR) assay. HLA-B*57:01 associates with immune hypersensitivity reaction (IHR) in individuals exposed to abacavir (ABC), while nevirapine (NVP) IHR associates with HLA-B*35:05, HLA-C*04 and HLA-C*08. Real-time AS-PCR assays typically use less DNA, are more cost-effective and rapid compared with conventional genotyping methods, such as sequence-based typing (SBT). The assay was developed using samples of known HLA class I genotype and subsequently applied to the SAI and SAM samples. HLA-B*57:01 was detected in SAM and SAI populations at frequencies of 8.0% and 12.0%, respectively, while HLA-B*35:05 was not found in SAI individuals, but was present in 6.0% of SAM individuals. HLA-C*04 was detected in 22.0% and 24.0% of SAM and SAI individuals, respectively, while 10.0% and 8.0% of SAM and SAI individuals, respectively, were HLA-C*08 positive. This study reports the development of a novel real-time AS-PCR assay to identify HLA class I alleles associated with ABC and NVP IHR and has established the frequencies of these alleles present in healthy SAI and SAM populations. Using South African demographic data, our hypothetical analysis suggests that a substantial number of individuals would benefit from the assay.

  18. High frequency and founder effect of the CYP3A4*20 loss-of-function allele in the Spanish population classifies CYP3A4 as a polymorphic enzyme.

    PubMed

    Apellániz-Ruiz, M; Inglada-Pérez, L; Naranjo, M E G; Sánchez, L; Mancikova, V; Currás-Freixes, M; de Cubas, A A; Comino-Méndez, I; Triki, S; Rebai, A; Rasool, M; Moya, G; Grazina, M; Opocher, G; Cascón, A; Taboada-Echalar, P; Ingelman-Sundberg, M; Carracedo, A; Robledo, M; Llerena, A; Rodríguez-Antona, C

    2015-06-01

    Cytochrome P450 3A4 (CYP3A4) is a key drug-metabolizing enzyme. Loss-of-function variants have been reported as rare events, and the first demonstration of a CYP3A4 protein lacking functional activity is caused by CYP3A4*20 allele. Here we characterized the world distribution and origin of CYP3A4*20 mutation. CYP3A4*20 was determined in more than 4000 individuals representing different populations, and haplotype analysis was performed using CYP3A polymorphisms and microsatellite markers. CYP3A4*20 allele was present in 1.2% of the Spanish population (up to 3.8% in specific regions), and all CYP3A4*20 carriers had a common haplotype. This is compatible with a Spanish founder effect and classifies CYP3A4 as a polymorphic enzyme. This constitutes the first description of a CYP3A4 loss-of-function variant with high frequency in a population. CYP3A4*20 results together with the key role of CYP3A4 in drug metabolism support screening for rare CYP3A4 functional alleles among subjects with adverse drug events in certain populations. PMID:25348618

  19. Van Allen Probes observations of unusually low frequency whistler mode waves observed in association with moderate magnetic storms: Statistical study

    PubMed Central

    Breneman, A. W.; Thaller, S. A.; Wygant, J. R.; Kletzing, C. A.; Kurth, W. S.

    2015-01-01

    Abstract We show the first evidence for locally excited chorus at frequencies below 0.1 f ce (electron cyclotron frequency) in the outer radiation belt. A statistical study of chorus during geomagnetic storms observed by the Van Allen Probes found that frequencies are often dramatically lower than expected. The frequency at peak power suddenly stops tracking the equatorial 0.5 f ce and f/f ce decreases rapidly, often to frequencies well below 0.1 f ce (in situ and mapped to equator). These very low frequency waves are observed both when the satellites are close to the equatorial plane and at higher magnetic latitudes. Poynting flux is consistent with generation at the equator. Wave amplitudes can be up to 20 to 40 mV/m and 2 to 4 nT. We conclude that conditions during moderate to large storms can excite unusually low frequency chorus, which is resonant with more energetic electrons than typical chorus, with critical implications for understanding radiation belt evolution. PMID:27667871

  20. Data on IL-6 c.-174 G>C genotype and allele frequencies in patients with coronary heart disease in dependence of cardiovascular outcome.

    PubMed

    Reichert, Stefan; Schlitt, Axel; Benten, Ann-Christin; Hofmann, Britt; Schaller, Hans-Günter; Schulz, Susanne

    2016-09-01

    In this data article we present data on the distribution of alleles and genotypes of the interleukin (IL)-6 c.-174 G>C polymorphism (rs 1800795) in patients with coronary heart disease (CHD) in dependence of the incidence of new cardiovascular events (combined endpoint: myocardial infarction, stroke/TIA, cardiac death, death according to stroke) within three years follow-up. Moreover, we investigated putative associations between individual expression of IL-6 genotypes and IL-6 serum level. This investigation is a subanalysis of the article entitled "The Interleukin 6 c.-174 CC genotype is a predictor for new cardiovascular events in patients with coronary heart disease within three years follow-up" (ClinicalTrials.gov identifier: NCT01045070) (Reichert et al., 2016) [1]. PMID:27570807

  1. LOW-FREQUENCY OBSERVATIONS OF THE MOON WITH THE MURCHISON WIDEFIELD ARRAY

    SciTech Connect

    McKinley, B.; Briggs, F.; Kaplan, D. L.; Greenhill, L. J.; Bernardi, G.; De Oliveira-Costa, A.; Bowman, J. D.; Tingay, S. J.; Gaensler, B. M.; Oberoi, D.; Johnston-Hollitt, M.; Arcus, W.; Emrich, D.; Barnes, D.; Bunton, J. D.; Cappallo, R. J.; Corey, B. E.; Deshpande, A.; DeSouza, L.; Goeke, R.; and others

    2013-01-01

    A new generation of low-frequency radio telescopes is seeking to observe the redshifted 21 cm signal from the epoch of reionization (EoR), requiring innovative methods of calibration and imaging to overcome the difficulties of wide-field low-frequency radio interferometry. Precise calibration will be required to separate the expected small EoR signal from the strong foreground emission at the frequencies of interest between 80 and 300 MHz. The Moon may be useful as a calibration source for detection of the EoR signature, as it should have a smooth and predictable thermal spectrum across the frequency band of interest. Initial observations of the Moon with the Murchison Widefield Array 32 tile prototype show that the Moon does exhibit a similar trend to that expected for a cool thermally emitting body in the observed frequency range, but that the spectrum is corrupted by reflected radio emission from Earth. In particular, there is an abrupt increase in the observed flux density of the Moon within the internationally recognized frequency modulated (FM) radio band. The observations have implications for future low-frequency surveys and EoR detection experiments that will need to take this reflected emission from the Moon into account. The results also allow us to estimate the equivalent isotropic power emitted by the Earth in the FM band and to determine how bright the Earth might appear at meter wavelengths to an observer beyond our own solar system.

  2. RHD allele distribution in Africans of Mali

    PubMed Central

    Wagner, Franz F; Moulds, Joann M; Tounkara, Anatole; Kouriba, Bourema; Flegel, Willy A

    2003-01-01

    Background Aberrant and non-functional RHD alleles are much more frequent in Africans than in Europeans. The DAU cluster of RHD alleles exemplifies that the alleles frequent in Africans have evaded recognition until recently. A comprehensive survey of RHD alleles in any African population was lacking. Results We surveyed the molecular structure and frequency of RHD alleles in Mali (West Africa) by evaluating 116 haplotypes. Only 69% could be attributed to standard RHD (55%) or the RHD deletion (14%). The aberrant RHD allele DAU-0 was predicted for 19%, RHDΨ for 7% and Ccdes for 4% of all haplotypes. DAU-3 and the new RHD allele RHD(L207F), dubbed DMA, were found in one haplotype each. A PCR-RFLP for the detection of the hybrid Rhesus box diagnostic for the RHD deletion in Europeans was false positive in 9 individuals, including all carriers of RHDΨ . Including two silent mutations and the RHD deletion, a total of 9 alleles could be differentiated. Conclusion Besides standard RHD and the RHD deletion, DAU-0, RHDΨ and Ccdes are major alleles in Mali. Our survey proved that the most frequent alleles of West Africans have been recognized allowing to devise reliable genotyping and phenotyping strategies. PMID:14505497

  3. High frequency and allele-specific differences of BRCA1 founder mutations in breast cancer and ovarian cancer patients from Belarus.

    PubMed

    Bogdanova, N V; Antonenkova, N N; Rogov, Y I; Karstens, J H; Hillemanns, P; Dörk, T

    2010-10-01

    Breast cancer and ovarian cancer are common malignancies in Belarus accounting for about 3500 and 800 new cases per year, respectively. For breast cancer, the rates and age of onset appear to vary significantly in regions differentially affected by the Chernobyl accident. We assessed the frequency and distribution of three BRCA1 founder mutations 5382insC, 4153delA and Cys61Gly in two hospital-based series of 1945 unselected breast cancer patients and of 201 unselected ovarian cancer patients from Belarus as well as in 1019 healthy control females from the same population. Any of these mutations were identified in 4.4% of the breast cancer patients, 26.4% of the ovarian cancer patients and 0.5% of the controls. In the breast cancer patients, BRCA1 mutations were strongly associated with earlier age at diagnosis, with oestrogen receptor (ER) negative tumours and with a first-degree family history of breast cancer, although only 35% of the identified BRCA1 mutation carriers had such a family history. There were no marked differences in the regional distribution of BRCA1 mutations, so that the significant differences in age at diagnosis and family history of breast cancer patients from areas afflicted by the Chernobyl accident could not be explained by BRCA1. We next observed a higher impact and a shifted mutational spectrum of BRCA1 in the series of Byelorussian ovarian cancer patients where the three founder mutations accounted for 26.4% (53/201). While the Cys61Gly mutation appeared underrepresented in ovarian cancer as compared with breast cancer cases from the same population (p = 0.01), the 4153delA mutation made a higher contribution to ovarian cancer than to breast cancer (p < 0.01). BRCA1 mutations were significantly enriched among ovarian cancer cases with a first-degree family history of breast or ovarian cancer, whereas the median age at ovarian cancer diagnosis was not different between mutation carriers and non-carriers. Taken together, these results

  4. Morphology of human sweat ducts observed by optical coherence tomography and their frequency of resonance in the terahertz frequency region

    PubMed Central

    Tripathi, Saroj R.; Miyata, Eisuke; Ishai, Paul Ben; Kawase, Kodo

    2015-01-01

    It is crucial to understand the various biological effects induced by terahertz (THz) electromagnetic waves with the rapid development of electronic and photonic devices operating in the THz frequency region. The presence of sweat glands plays an important role in THz wave interactions with human skin. We investigated the morphological features of sweat ducts using optical coherence tomography (OCT) to further understand such phenomena. We observed remarkable features of the ducts, such as their clear helical structure. The intersubject and intrasubject variations in the diameter of sweat ducts were considerably smaller than the variations in other structural parameters, such as length and number of turns. Based on the sweat duct dimensions and THz dielectric properties of skin measured using terahertz time-domain spectroscopy (THz-TDS), we calculated the resonating frequency of the sweat duct under the assumption of it functioning as a helical antenna. Here, we show that the resonance frequency in the axial mode of operation lies in the THz wave region with a centre frequency of 0.44 ± 0.07 THz. We expect that these findings will further our understanding of the various health consequences of the interaction of THz waves with human beings. PMID:25766116

  5. Morphology of human sweat ducts observed by optical coherence tomography and their frequency of resonance in the terahertz frequency region

    NASA Astrophysics Data System (ADS)

    Tripathi, Saroj R.; Miyata, Eisuke; Ishai, Paul Ben; Kawase, Kodo

    2015-03-01

    It is crucial to understand the various biological effects induced by terahertz (THz) electromagnetic waves with the rapid development of electronic and photonic devices operating in the THz frequency region. The presence of sweat glands plays an important role in THz wave interactions with human skin. We investigated the morphological features of sweat ducts using optical coherence tomography (OCT) to further understand such phenomena. We observed remarkable features of the ducts, such as their clear helical structure. The intersubject and intrasubject variations in the diameter of sweat ducts were considerably smaller than the variations in other structural parameters, such as length and number of turns. Based on the sweat duct dimensions and THz dielectric properties of skin measured using terahertz time-domain spectroscopy (THz-TDS), we calculated the resonating frequency of the sweat duct under the assumption of it functioning as a helical antenna. Here, we show that the resonance frequency in the axial mode of operation lies in the THz wave region with a centre frequency of 0.44 +/- 0.07 THz. We expect that these findings will further our understanding of the various health consequences of the interaction of THz waves with human beings.

  6. Comparison between theory and observation of the frequency sweep rates of equatorial rising tone chorus

    NASA Astrophysics Data System (ADS)

    Tao, X.; Li, W.; Bortnik, J.; Thorne, R. M.; Angelopoulos, V.

    2012-04-01

    Theoretical predictions for chorus frequency sweep rates by Helliwell and Trakhtengerts are compared with observations from the THEMIS satellites and a previously published dataset from the Cluster satellites. We first extend the theories to use a general magnetic field model to include the effects of magnetic local time and geomagnetic activity, and then show that both theories give the same dependence of the frequency sweep rate on background plasma parameters. The theoretical scaling of frequency sweep rates are shown to agree very well with observations. We demonstrate that for a given equatorial magnetic field strength, nightside and dawnside chorus waves have higher frequency sweep rates because of the stretching of the magnetic field, while dayside chorus waves have lower frequency sweep rates because of the compression of the field. Increasing geomagnetic activity will enhance the asymmetry by increasing the day-night asymmetry of the background field. The results are important for understanding the generation mechanism of chorus waves.

  7. Experimental observation of coherent cavity soliton frequency combs in silica microspheres

    NASA Astrophysics Data System (ADS)

    Webb, Karen E.; Erkintalo, Miro; Coen, Stéphane; Murdoch, Stuart G.

    2016-10-01

    We report on the experimental observation of coherent cavity soliton frequency combs in silica microspheres. Specifically, we demonstrate that careful alignment of the microsphere relative to the coupling fiber taper allows for the suppression of higher-order spatial modes, reducing mode interactions and enabling soliton formation. Our measurements show that the temporal cavity solitons have sub-100-fs durations, exhibit considerable Raman self-frequency shift, and generally come in groups of three or four, occasionally with equidistant spacing in the time domain. RF amplitude noise measurements and spectral interferometry confirm the high coherence of the observed soliton frequency combs, and numerical simulations show good agreement with experiments.

  8. On the contribution of sunspots to the observed frequency shifts of solar acoustic modes

    NASA Astrophysics Data System (ADS)

    Santos, A. R. G.; Cunha, M. S.; Avelino, P. P.; Chaplin, W. J.; Campante, T. L.

    2016-09-01

    Activity-related variations in the solar oscillation properties have been known for 30 years. However, the relative importance of the different contributions to the observed variations is not yet fully understood. Our goal is to estimate the relative contribution from sunspots to the observed activity-related variations in the frequencies of the acoustic modes. We use a variational principle to relate the phase differences induced by sunspots on the acoustic waves to the corresponding changes in the frequencies of the global acoustic oscillations. From the sunspot properties (area and latitude as a function of time), we are able to estimate the spot-induced frequency shifts. These are then combined with a smooth frequency shift component, associated with long-term solar-cycle variations, and the results compared with the frequency shifts derived from the Global Oscillation Network Group data. The result of this comparison is consistent with a sunspot contribution to the observed frequency shifts of roughly 30 per cent, with the remaining 70 per cent resulting mostly from a global, non-stochastic variation, possibly related to the changes in the overall magnetic field. Moreover, analysis of the residuals obtained after the subtraction of the model frequency shifts from the observations indicates the presence of a 1.5-yr periodicity in the data in phase with the quasi-biennial variations reported in the literature.

  9. 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.

  10. Effects of anisotropy on the frequency spectrum of gravity waves observed by MST radar

    NASA Technical Reports Server (NTRS)

    Liu, C. H.

    1986-01-01

    In the investigation of gravity waves using mesosphere-stratosphere-troposphere radar data, model gravity-wave spectra have been used. In these model spectra, one usually assumes azimuthal symmetry. The effect of spectral anisotropy on the observed spectrum is studied here. It is shown that for a general Garrett-Munk-type spectrum, the anisotropy does not affect the frequency spectrum observed by the vertically beamed radar. For the oblique beam, however, the observed frequency spectrum is changed. A general gravity wave spectrum including azimuthal anisotropy is considered.

  11. Observations of the frequency tuning effect in the 14 GHz CAPRICE ion source

    SciTech Connect

    Celona, L.; Ciavola, G.; Consoli, F.; Gammino, S.; Maimone, F.; Mascali, D.; Spaedtke, P.; Tinschert, K.; Lang, R.; Maeder, J.; Rossbach, J.; Barbarino, S.; Catalano, R. S.

    2008-02-15

    A set of measurements with the CAPRICE ion source at the GSI test bench has been carried out to investigate its behavior in terms of intensity and shape of the extracted beam when the microwaves generating the plasma sweep in a narrow range of frequency ({+-}40 MHz) around the klystron center frequency (14.5 GHz). Remarkable variations have been observed depending on the source and the beamline operating parameters, confirming that a frequency dependent electromagnetic distribution is preserved even in the presence of plasma inside the source. Moreover, these observations confirm that the frequency tuning is a powerful method to optimize the electron cyclotron resonance ion source performances. A description of the experimental setup and of the obtained results is given in the following.

  12. On the spectra of type-III solar radio bursts observed at low frequencies

    NASA Technical Reports Server (NTRS)

    Alvarez, H.

    1982-01-01

    The spectra of strong bursts observed at low frequencies by OGO-5 during 1968-1970 are presented. They usually exhibit an intense main peak between 100 kHz and 1 MHz, and sometimes a less intense secondary peak between 1 and 3.5 MHz. Main peaks of 10 to the -12th W per sq m per Hz or more were obtained in very strong events, but because of antenna calibration problems those could be one or two orders of magnitude too high. Recently published work supports the finding that type III bursts at low frequencies can be at least four orders of magnitude more intense than at ground-based frequencies of observation. It is found that the energy received at the earth increases with decreasing frequency approximately as f to the -n, where n is between 3 and 4.

  13. Genetic parameters and allele frequencies of five new European Standard Set STR loci (D10S1248, D22S1045, D2S441, D1S1656, D12S391) in the population of Romania

    PubMed Central

    Stanciu, Florin; Vladu, Simona; Cuţăr, Veronica; Cocioabă, Daniela; Iancu, Florentina; Cotolea, Adnana; Stoian, Ionel Marius

    2013-01-01

    Aim To establish allele frequencies and genetic parameters for 5 new European Standard Set short tandem repeat (STR) loci in the population of Romania and to compare them with those in other populations. Methods DNA was isolated using QIAamp 96 DNA Swab BioRobot Kit and Chelex 100 methods. Polymerase chain reaction amplification was done using Investigator ESSplexPlus Kit (D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D10S1248, D12S391, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, TH01, and vWA). For DNA typing, Applied Biosystems 3500/3500xL Genetic Analyzer was used. Statistical analysis was done using Powerstats, GDA, and Arlequin software. Results Power of discrimination and polymorphism information content was highest for two new ESS loci, D1S1656 and D12S391. Comparison of allele frequencies for 5 new ESS loci in Romanian population with previously published population data showed significant differences for all compared populations, with the exception of Hungary. Geographically more distant populations, such as Spain, Sweden, United Kingdom, Germany, and Portugal differed more than closer populations. Conclusion New ESS STR loci are very useful for the analysis of forensic samples (persons or traces) due to their characteristics (shortness and high polymorphism). In comparisons with other common STR markers, they have a higher power of discrimination and also higher polymorphism information content, and could be used in any national DNA database. PMID:23771753

  14. Short alleles revealed by PCR demonstrate no heterozygote deficiency at minisatellite loci D1S7, D7S21, and D12S11

    SciTech Connect

    Alonso, S.; Castro, A.; Fernandez-Fernandez, I.; Pancorbo, M.M. de

    1997-02-01

    Short VNTR alleles that go undetected after conventional Southern blot hybridization may constitute an alternative explanation for the heterozygosity deficiency observed at some minisatellite loci. To examine this hypothesis, we have employed a screening procedure based on PCR amplification of those individuals classified as homozygotes in our databases for the loci D1S7, D7S21, and D12S11. The results obtained indicate that the frequency of these short alleles is related to the heterozygosity deficiency observed. For the most polymorphic locus, D1S7, {approximately}60% of those individuals previously classified as homozygotes were in fact heterozygotes for a short allele. After the inclusion of these new alleles, the agreement between observed and expected heterozygosity, along with other statistical tests employed, provide additional evidence for lack of population substructuring. Comparisons of allele frequency distributions reveal greater differences between racial groups than between closely related populations. 45 refs., 3 figs., 6 tabs.

  15. Short alleles revealed by PCR demonstrate no heterozygote deficiency at minisatellite loci D1S7, D7S21, and D12S11.

    PubMed Central

    Alonso, S; Castro, A; Fernández-Fernández, I; de Pancorbo, M M

    1997-01-01

    Short VNTR alleles that go undetected after conventional Southern blot hybridization may constitute an alternative explanation for the heterozygosity deficiency observed at some minisatellite loci. To examine this hypothesis, we have employed a screening procedure based on PCR amplification of those individuals classified as homozygotes in our databases for the loci D1S7, D7S21, and D12S11. The results obtained indicate that the frequency of these short alleles is related to the heterozygosity deficiency observed. For the most polymorphic locus, D1S7, approximately 60% of those individuals previously classified as homozygotes were in fact heterozygotes for a short allele. After the inclusion of these new alleles, the agreement between observed and expected heterozygosity, along with other statistical tests employed, provide additional evidence for lack of population substructuring. Comparisons of allele frequency distributions reveal greater differences between racial groups than between closely related populations. Images Figure 2 Figure 3 PMID:9012415

  16. Improving Ambiguity Resolution for Medium Baselines Using Combined GPS and BDS Dual/Triple-Frequency Observations.

    PubMed

    Gao, Wang; Gao, Chengfa; Pan, Shuguo; Wang, Denghui; Deng, Jiadong

    2015-10-30

    The regional constellation of the BeiDou navigation satellite system (BDS) has been providing continuous positioning, navigation and timing services since 27 December 2012, covering China and the surrounding area. Real-time kinematic (RTK) positioning with combined BDS and GPS observations is feasible. Besides, all satellites of BDS can transmit triple-frequency signals. Using the advantages of multi-pseudorange and carrier observations from multi-systems and multi-frequencies is expected to be of much benefit for ambiguity resolution (AR). We propose an integrated AR strategy for medium baselines by using the combined GPS and BDS dual/triple-frequency observations. In the method, firstly the extra-wide-lane (EWL) ambiguities of triple-frequency system, i.e., BDS, are determined first. Then the dual-frequency WL ambiguities of BDS and GPS were resolved with the geometry-based model by using the BDS ambiguity-fixed EWL observations. After that, basic (i.e., L1/L2 or B1/B2) ambiguities of BDS and GPS are estimated together with the so-called ionosphere-constrained model, where the ambiguity-fixed WL observations are added to enhance the model strength. During both of the WL and basic AR, a partial ambiguity fixing (PAF) strategy is adopted to weaken the negative influence of new-rising or low-elevation satellites. Experiments were conducted and presented, in which the GPS/BDS dual/triple-frequency data were collected in Nanjing and Zhengzhou of China, with the baseline distance varying from about 28.6 to 51.9 km. The results indicate that, compared to the single triple-frequency BDS system, the combined system can significantly enhance the AR model strength, and thus improve AR performance for medium baselines with a 75.7% reduction of initialization time on average. Besides, more accurate and stable positioning results can also be derived by using the combined GPS/BDS system.

  17. Regular frequency patterns in the classical δ Scuti star HD 144277 observed by the MOST satellite

    NASA Astrophysics Data System (ADS)

    Zwintz, K.; Lenz, P.; Breger, M.; Pamyatnykh, A. A.; Zdravkov, T.; Kuschnig, R.; Matthews, J. M.; Guenther, D. B.; Moffat, A. F. J.; Rowe, J. F.; Rucinski, S. M.; Sasselov, D.; Weiss, W. W.

    2011-09-01

    Context. We present high-precision time-series photometry of the classical δ Scuti star HD 144277 obtained with the MOST (Microvariability and Oscillations of STars) satellite in two consecutive years. The observed regular frequency patterns are investigated asteroseismologically. Aims: HD 144277 is a hot A-type star that is located on the blue border of the classical instability strip. While we mostly observe low radial order modes in classical δ Scuti stars, HD 144277 presents a different case. Its high observed frequencies, i.e., between 59.9 d-1 (693.9 μHz) and 71.1 d-1 (822.8 μHz), suggest higher radial orders. We examine the progression of the regular frequency spacings from the low radial order to the asymptotic frequency region. Methods: Frequency analysis was performed using Period04 and SigSpec. The results from the MOST observing runs in 2009 and 2010 were compared to each other. The resulting frequencies were submitted to asteroseismic analysis. Results: HD 144277 was discovered to be a δ Scuti star using the time-series photometry observed by the MOST satellite. Twelve independent pulsation frequencies lying in four distinct groups were identified. Two additional frequencies were found to be combination frequencies. The typical spacing of 3.6 d-1 corresponds to the spacing between subsequent radial and dipole modes, therefore the spacing between radial modes is twice this value, 7.2 d-1. Based on the assumption of slow rotation, we find evidence that the two radial modes are the sixth and seventh overtones, and the frequency with the highest amplitude can be identified as a dipole mode. Conclusions: The models required to fit the observed instability range need slightly less metallicity and a moderate enhancement of the helium abundance compared to the standard chemical composition. Our asteroseismic models suggest that HD 144277 is a δ Scuti star close to the ZAMS with a mass of 1.66 M⊙. Based on data from the MOST satellite, a Canadian Space

  18. Cassini observations of low-frequency drifting radio bursts in Saturn's magnetosphere

    NASA Astrophysics Data System (ADS)

    Taubenschuss, U.; Leisner, J. S.; Fischer, G.; Gurnett, D. A.; Nemec, F.

    2010-12-01

    This study presents an analysis of a new type of Saturnian radio emission observed between 3 and 50 kHz by Cassini’s RPWS instrument. These emissions comprise radio bursts which last for several minutes and exhibit a characteristic drift in the time-frequency spectrograms. Spectral features (such as frequency range, bandwidth, and drift rate) and the spatial distribution of observations are subject to statistical analysis. Furthermore, this study uses the goniopolarimetric (“direction-finding”) mode to study the polarization. We discuss the obtained results in the context of possible source mechanisms and correlations between the radio bursts and the moons in Saturn’s inner magnetosphere.

  19. Frequency band enlargement of the penetrator seismometer and its application to moonquake observation

    NASA Astrophysics Data System (ADS)

    Yamada, Ryuhei; Nébut, Tanguy; Shiraishi, Hiroaki; Lognonné, Philippe; Kobayashi, Naoki; Tanaka, Satoshi

    2015-07-01

    Seismic data obtained over a broad frequency range are very useful in investigation of the internal structures of the Earth and other planetary bodies. However, planetary seismic data acquired through the NASA Apollo and Viking programs were obtained only over a very limited frequency range. To obtain effective seismic data over a broader frequency range on planetary surfaces, broadband seismometers suitable for planetary seismology must be developed. In this study, we have designed a new broadband seismometer based on a short-period seismometer whose resonant frequency is 1 Hz for future geophysical missions. The seismometer is of an electromagnetic type, light weight, small size and has good shock-durability, making it suitable for being loaded onto a penetrator, which is a small, hard-landing probe developed in the LUNAR-A Project, a previous canceled mission. We modified the short-period seismometer so as to have a flat frequency response above about 0.1 Hz and the detection limit could be lowered to cover frequencies below the frequency. This enlargement of the frequency band will allow us to investigate moonquakes for lower frequency components in which waveforms are less distorted because strong scattering due to fractured structures near the lunar surface is likely to be suppressed. The modification was achieved simply by connecting a feedback circuit to the seismometer, without making any mechanical changes to the short-period sensor. We have confirmed that the broadband seismometer exhibits the frequency response as designed and allows us to observe long-period components of small ground motions. Methods to improve the performance of the broadband seismometer from the current design are also discussed. These developments should promise to increase the opportunity for application of this small and tough seismometer in various planetary seismological missions.

  20. Observation of Low-Frequency Electromagnetic Radiation from Laser-Plasmas

    NASA Astrophysics Data System (ADS)

    Kando, Masaki; Kawase, Keigo; Daito, Izuru; Pirozhkov, Alexander S.; Esirkepov, Timur Zh.; Fukuda, Yuji; Kotaki, Hideyuki; Kameshima, Takashi; Faenov, Anatoly Ya.; Pikuz, Tatiana A.; Bulanov, Sergei V.

    2009-07-01

    When an intense short laser pulse interacts with plasmas, the nonlinear interaction causes various phenomena such as high energy particle generation, strong radiation in the x-ray to THz frequency range. Formation of solitons is one of these interesting topics and has been studied mainly from theoretical aspects. Solitons are formed in an underdense plasma in the process of the laser pulse frequency downshift. They store a portion of the EM wave energy with the polarization inherited from the laser pulse-driver and emit it at the plasma-vacuum interface in the form of low frequency EM bursts. Solitons were observed experimentally by proton-beam imaging and in the visible-near-infrared emissions from the plasma. A low frequency EM radiation emission has also been observed in our experiments. The interpretation invokes the relativistic electromagnetic solitons. We present the results of the polarization-resolved measurements of low frequency radiation from the plasma region irradiated by the intense laser pulse. A dominant component of the observed THz radiation has the same polarization as the driver laser pulse.

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

    PubMed Central

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

    2015-01-01

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

  2. 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.

  3. 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.

  4. HLA-A, HLA-B, HLA-DRB1 allele and haplotype frequencies in 6384 umbilical cord blood units and transplantation matching and engraftment statistics in the Zhejiang cord blood bank of China.

    PubMed

    Wang, F; He, J; Chen, S; Qin, F; Dai, B; Zhang, W; Zhu, F M; Lv, H J

    2014-02-01

    Umbilical cord blood (UCB) is a widely accepted source of progenitor cells, and now, many cord blood banks were established. Here, we analysed the HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies, HLA matching possibilities for searching potential donors and outcome of UCB transplantations in Zhejiang cord blood bank of China. A total of 6384 UCB units were characterized for 17 HLA-A, 30 HLA-B and 13 HLA-DRB1 alleles at the first field resolution level. Additionally, B*14, B*15 and B*40 were typed to the second field level. A total of 1372 distinct A-B-DRB1 haplotypes were identified. The frequencies of 7 haplotypes were more than 1%, and 439 haplotypes were <0.01%. A*02-B*46-DRB1*09, A*33-B*58-DRB1*03 and A*30-B*13-DRB1*07 were the most common haplotypes, with frequencies of 4.4%, 3.3%, and 2.9%, respectively. Linkage disequilibrium(LD) analysis showed that there were 83 A-B, 106 B-DRB1, 54 A-DRB1 haplotypes with positive LD, in which 51 A-B, 60 B-DRB1, 32 A-DRB1 haplotypes exhibited a significant LD (P < 0.05). In 682 search requests, 12.9%, 40.0% and 42.7% of patients were found to have 6 of 6, 5 of 6 and 4 of 6 HLA-A, HLA-B and HLA-DRB1 matching donors, respectively. A total of 30 UCB units were transplanted to 24 patients (3 patients not evaluated due to early death); 14 of 21 patients (66.7%) engrafted. This study reveals the HLA distribution and its transplantation application in the cord blood bank of Zhejiang province. These data can help to select potential UCB donors for transplantation and used to assess the scale of new cord blood banking endeavours.

  5. Observation of Modes at Frequencies Near the Second Alfvin Gap in TFTR

    SciTech Connect

    Fredrickson. E.; Van Dam, J.W.; Budny, R.V.; Darrow, D.; Fu, G.Y.; Hosea, J.; Phillips, C.K.; Wilson, J.R.

    1999-04-01

    Modes has been observed in the frequency range of the second Alfvenic gap in H-minority ICRF heated plasmas in TFTR. This observation is surprising in that the second gap is generally considered to be small in circular cross section plasmas. The mode is inferred to be a core mode, i.e., localized in some sense within the q=1 surface. This follows from the observation that the time dependence of the mode frequency is consistent with the changes in the central density, with the appearance of the mode in the latter part of the sawtooth period when the central fast ion beta has peaked up, and with the direction of propagation, the last of these being explained by a hollow first ion beta profile, which is only present in the core region. The modes are generally not observed during on-axis H-minority heating, but commonly observed during off-axis heating on the high field side (with the resonant layer outside the q=1 surface). A model has been proposed that the beta of the fast ions opens the second gap, allowing instability. For TFTR parameters, the model predicts a gap width of approximately 10 kHz, which is 2.5% of the second gap frequency. If the backwards mode propagation is due to a hollow fast ion profile (as indicated in the TRANSP calculations), then instability due to wave-particle resonance at the magnetic curvature precessional frequency can occur only if the precessional frequency is reversed--which can indeed be the case for off-axis heating on the high field side. Thus, trapped fast ion pressure effects seem to explain several of the observed features of these second gap fluctuations.

  6. Uncommon HLA alleles identified by hemizygous ultra-high Sanger sequencing: haplotype associations and reconsideration of their assignment in the Common and Well-Documented catalogue.

    PubMed

    Voorter, Christina E M; Groeneweg, Mathijs; Groeneveld, Lisette; Tilanus, Marcel G J

    2016-02-01

    Although the number of HLA alleles still increases, many of them have been reported being uncommon. This is partly due to lack of full length gene sequencing, especially for those alleles belonging to an allele ambiguity in which the first discovered allele has been assigned as the most frequent one. As members of the working group on Common and Well Documented (CWD) alleles and since we implemented full length group-specific sequencing as standard method routinely, we have investigated the presence of presumably rare alleles in our collection of HLA typing data. We identified 50 alleles, that were not previously encountered as Common or Well Documented. Sixteen of them should be added to the CWD catalogue, since we encountered them in 5 or more unrelated individuals. Another 11 could be added, based upon our results and the data present in the IMGT database and the rare allele section of the allele frequencies database. Furthermore, tight associations were observed between several different alleles even at the level of synonymous and non-coding sequences. In addition, in several cases the uncommon allele was found to be more frequent than its common counterpart.

  7. VERITAS observations of low- and intermediate-frequency peaked BL Lac objects

    NASA Astrophysics Data System (ADS)

    Nelson, T.; VERITAS Collaboration

    2012-12-01

    We present highlights of long-term monitoring of low- and intermediate-frequency peaked BL Lac objects with the VERITAS gamma-ray observatory carried out in 2010, 2011 and 2012. These include the key results obtained from observations of a bright VHE flare in BL Lacertae in June 2011, as well as preliminary results of monitoring observations of five northern blazars. Two IBLs-3C 66A and W Comae-are detected in low flux states for the first time.

  8. Multi-frequency solar observations at Metsähovi Radio Observatory and KAIRA

    NASA Astrophysics Data System (ADS)

    Kallunki, J.; Uunila, M.; McKay-Bukowski, D.

    2015-08-01

    We describe solar observations carried out for the first time jointly with Kilpisjärvi Atmospheric Imaging Receiver Array (KAIRA) and Aalto University Metsähovi Radio Observatory (MRO). KAIRA is new radio antenna array observing the decimeter and meter wavelength range. It is located near Kilpisjärvi, Finland, and operated by the Sodankylä Geophysical Observatory, University of Oulu. We investigate the feasibility of KAIRA for solar observations, and the additional benefits of carrying out multi-instrument solar observations with KAIRA and the MRO facilities, which are already used for regular solar observations. The data measured with three instruments at MRO, and with KAIRA during time period 2014 April-October were analyzed. One solar radio event, measured on 2014 April 18, was studied in detail. Seven solar flares were recorded with at least two of the three instruments at MRO, and with KAIRA during the chosen time period. KAIRA is a great versatile asset as a new Finnish instrument that can also be used for solar observations. Collaboration observations with MRO instruments and KAIRA enable detailed multi-frequency solar flare analysis. Flare pulsations, flare statistics and radio spectra of single flares can be investigated due to the broad frequency range observations. The Northern locations of both MRO and KAIRA make as long as 15-hour unique solar observations possible during summer time.

  9. Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression in Norway spruce (Picea abies).

    PubMed

    Chen, Jun; Källman, Thomas; Ma, Xiaofei; Gyllenstrand, Niclas; Zaina, Giusi; Morgante, Michele; Bousquet, Jean; Eckert, Andrew; Wegrzyn, Jill; Neale, David; Lagercrantz, Ulf; Lascoux, Martin

    2012-07-01

    Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (F(ST) = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to F(ST). The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.

  10. Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)

    PubMed Central

    Chen, Jun; Källman, Thomas; Ma, Xiaofei; Gyllenstrand, Niclas; Zaina, Giusi; Morgante, Michele; Bousquet, Jean; Eckert, Andrew; Wegrzyn, Jill; Neale, David; Lagercrantz, Ulf; Lascoux, Martin

    2012-01-01

    Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (FST = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to FST. The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants. PMID:22542968

  11. Observation of harmonically related solar radio zebra patterns in the 1-4 GHz frequency range

    NASA Astrophysics Data System (ADS)

    Sawant, H. S.; Karlický, M.; Fernandes, F. C. R.; Cecatto, J. R.

    2002-12-01

    A unique case of two zebra patterns related harmonically with ratio of ~ 1:2 was observed by distant radio telescopes at São José dos Campos and Ondřejov Observatories. Accompanied zebras show that the ratio of frequencies of the neighboring zebra lines is in the range of 1.009-1.037. There is a tendency of a decrease of this ratio with decreasing frequency within the specific zebra pattern. Both facts speak in favour of plasma emission models for the zebra pattern fine structure in radio burst continua.

  12. Impact of LISA's Low Frequency Sensitivity on Observations of Massive Black Hole Mergers

    NASA Technical Reports Server (NTRS)

    Baker, J.; Centrella, J.

    2005-01-01

    LISA will be able to detect gravitational waves from inspiralling massive black hole (MBH) binaries out to redshifts z > 10. If the binary masses and luminosity distances can be extracted from the Laser Interferometer Space Antenna (LISA) data stream, this information can be used to reveal the merger history of MBH binaries and their host galaxies in the evolving universe. Since this parameter extraction generally requires that LISA observe the inspiral for a significant fraction of its yearly orbit, carrying out this program requires adequate sensitivity at low frequencies, f < 10(exp -4) Hz. Using several candidate low frequency sensitivities, we examine LISA's potential for characterizing MBH binary coalescences at redshifts z > 1.

  13. Direct CW - NMR observation of forbidden transitions at double larmor frequency in hydrogen

    NASA Astrophysics Data System (ADS)

    Skrbek, L.; Sebek, J.; Safrata, R. S.

    1990-08-01

    By means of the classical transverse continuous wave nuclear magnetic resonance (NMR) the forbidden transitions at double Larmor frequency for hydrogen have been observed. The NMR spectra have been measured directly by scanning the external magnetic field up to 10 mT at temperatures about 30 mK. The intensity of the forbidden transition at double Larmor frequency I 2 is of the same order of magnitude as the intensity I 1 of the main Larmor line under these conditions. The intensity ratio I 1/I 2 depends on the external magnetic field in accordance with Cheng theory and NMR-SQUID measurements of Kohl and coworkers.

  14. Improving Ambiguity Resolution for Medium Baselines Using Combined GPS and BDS Dual/Triple-Frequency Observations.

    PubMed

    Gao, Wang; Gao, Chengfa; Pan, Shuguo; Wang, Denghui; Deng, Jiadong

    2015-01-01

    The regional constellation of the BeiDou navigation satellite system (BDS) has been providing continuous positioning, navigation and timing services since 27 December 2012, covering China and the surrounding area. Real-time kinematic (RTK) positioning with combined BDS and GPS observations is feasible. Besides, all satellites of BDS can transmit triple-frequency signals. Using the advantages of multi-pseudorange and carrier observations from multi-systems and multi-frequencies is expected to be of much benefit for ambiguity resolution (AR). We propose an integrated AR strategy for medium baselines by using the combined GPS and BDS dual/triple-frequency observations. In the method, firstly the extra-wide-lane (EWL) ambiguities of triple-frequency system, i.e., BDS, are determined first. Then the dual-frequency WL ambiguities of BDS and GPS were resolved with the geometry-based model by using the BDS ambiguity-fixed EWL observations. After that, basic (i.e., L1/L2 or B1/B2) ambiguities of BDS and GPS are estimated together with the so-called ionosphere-constrained model, where the ambiguity-fixed WL observations are added to enhance the model strength. During both of the WL and basic AR, a partial ambiguity fixing (PAF) strategy is adopted to weaken the negative influence of new-rising or low-elevation satellites. Experiments were conducted and presented, in which the GPS/BDS dual/triple-frequency data were collected in Nanjing and Zhengzhou of China, with the baseline distance varying from about 28.6 to 51.9 km. The results indicate that, compared to the single triple-frequency BDS system, the combined system can significantly enhance the AR model strength, and thus improve AR performance for medium baselines with a 75.7% reduction of initialization time on average. Besides, more accurate and stable positioning results can also be derived by using the combined GPS/BDS system. PMID:26528977

  15. Shallow Very-Low-Frequency Earthquakes off the Kii Peninsula Observed by Broadband Ocean Bottom Seismographs

    NASA Astrophysics Data System (ADS)

    Obana, K.; Ito, A.; Sugioka, H.; Ishihara, Y.; Nakamura, T.; Suetsugu, D.; Kodaira, S.; Kinoshita, M.; Araki, E.; Kaneda, Y.; Fukao, Y.; Okamoto, T.

    2010-12-01

    Anomalous very-low-frequency (VLF) earthquakes have been observed near the trough axis along the Nankai trough by land seismic networks (Ishihara, 2003, Obara and Ito, 2005). The focal mechanisms of the VLF earthquakes indicate an activity of thrust faults in the accretionary prism (Ito and Obara, 2006). After the 2004 Off Kii Peninsula earthquake (Mw=7.5), which occurred in the subducting Philippine Sea plate, many VLF earthquakes were observed in the aftershock area by the land seismic network (Obara and Ito, 2005). In addition to this, low-frequency tremors with dominant frequency range of 2-8Hz were observed by short-period ocean bottom seismographs (OBS) deployed off the Kii peninsula along the Nankai trough before the 2004 earthquake (Obana and Kodaira, 2009). We have conducted broadband ocean bottom seismographs (BBOBS) experiments off the Kii peninsula from July 2008 until October 2009. Aims of this BBOBS experiment are to obtain broadband records in source region and investigate source locations and focal mechanisms of VLF earthquakes. In March 2009, the VLF earthquake activity near the Nankai trough off the Kii peninsula was detected by land-based seismic network (NIED, 2009). Three BBOBSs observed these events in the source region and provided near-field broadband seismograms. The BBOBS records indicate that the VLF earthquakes contain the energy not only in the lower frequency range (~0.1 Hz) as observed by the land network but also in higher frequency range (1-10Hz). However, the VLF earthquakes do not contain the energy in the frequency range above 10 Hz. Source locations of the VLF earthquakes were estimated by using the seismograms in the higher frequency range. Onset times of the VLF signals were picked manually from the 1-8 Hz band-pass filtered seismograms. In addition to the onsets of the signals, relative arrival times were estimated from cross-correlation of the envelope seismograms. The VLF earthquakes were mainly located in the shallow

  16. Improving Ambiguity Resolution for Medium Baselines Using Combined GPS and BDS Dual/Triple-Frequency Observations

    PubMed Central

    Gao, Wang; Gao, Chengfa; Pan, Shuguo; Wang, Denghui; Deng, Jiadong

    2015-01-01

    The regional constellation of the BeiDou navigation satellite system (BDS) has been providing continuous positioning, navigation and timing services since 27 December 2012, covering China and the surrounding area. Real-time kinematic (RTK) positioning with combined BDS and GPS observations is feasible. Besides, all satellites of BDS can transmit triple-frequency signals. Using the advantages of multi-pseudorange and carrier observations from multi-systems and multi-frequencies is expected to be of much benefit for ambiguity resolution (AR). We propose an integrated AR strategy for medium baselines by using the combined GPS and BDS dual/triple-frequency observations. In the method, firstly the extra-wide-lane (EWL) ambiguities of triple-frequency system, i.e., BDS, are determined first. Then the dual-frequency WL ambiguities of BDS and GPS were resolved with the geometry-based model by using the BDS ambiguity-fixed EWL observations. After that, basic (i.e., L1/L2 or B1/B2) ambiguities of BDS and GPS are estimated together with the so-called ionosphere-constrained model, where the ambiguity-fixed WL observations are added to enhance the model strength. During both of the WL and basic AR, a partial ambiguity fixing (PAF) strategy is adopted to weaken the negative influence of new-rising or low-elevation satellites. Experiments were conducted and presented, in which the GPS/BDS dual/triple-frequency data were collected in Nanjing and Zhengzhou of China, with the baseline distance varying from about 28.6 to 51.9 km. The results indicate that, compared to the single triple-frequency BDS system, the combined system can significantly enhance the AR model strength, and thus improve AR performance for medium baselines with a 75.7% reduction of initialization time on average. Besides, more accurate and stable positioning results can also be derived by using the combined GPS/BDS system. PMID:26528977

  17. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar.

    PubMed

    Hodgson, Jason A; Pickrell, Joseph K; Pearson, Laurel N; Quillen, Ellen E; Prista, António; Rocha, Jorge; Soodyall, Himla; Shriver, Mark D; Perry, George H

    2014-08-22

    While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa. PMID:24990677

  18. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar.

    PubMed

    Hodgson, Jason A; Pickrell, Joseph K; Pearson, Laurel N; Quillen, Ellen E; Prista, António; Rocha, Jorge; Soodyall, Himla; Shriver, Mark D; Perry, George H

    2014-08-22

    While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa.

  19. Frequency driven inversion of tunnel magnetoimpedance and observation of positive tunnel magnetocapacitance in magnetic tunnel junctions

    NASA Astrophysics Data System (ADS)

    Parui, Subir; Ribeiro, Mário; Atxabal, Ainhoa; Bedoya-Pinto, Amilcar; Sun, Xiangnan; Llopis, Roger; Casanova, Fèlix; Hueso, Luis E.

    2016-08-01

    The relevance for modern computation of non-volatile high-frequency memories makes ac-transport measurements of magnetic tunnel junctions (MTJs) crucial for exploring this regime. Here, we demonstrate a frequency-mediated effect in which the tunnel magnetoimpedance reverses its sign in a classical Co/Al2O3/NiFe MTJ, whereas we only observe a gradual decrease in the tunnel magnetophase. Such effects are explained by the capacitive coupling of a parallel resistor and capacitor in the equivalent circuit model of the MTJ. Furthermore, we report a positive tunnel magnetocapacitance effect, suggesting the presence of a spin-capacitance at the two ferromagnet/tunnel-barrier interfaces. Our results are important for understanding spin transport phenomena at the high frequency regime in which the spin-polarized charge accumulation due to spin-dependent penetration depth at the two interfaces plays a crucial role.

  20. Experimental observation of standing wave effect in low-pressure very-high-frequency capacitive discharges

    SciTech Connect

    Liu, Yong-Xin; Gao, Fei; Liu, Jia; Wang, You-Nian

    2014-07-28

    Radial uniformity measurements of plasma density were carried out by using a floating double probe in a cylindrical (21 cm in electrode diameter) capacitive discharge reactor driven over a wide range of frequencies (27–220 MHz). At low rf power, a multiple-node structure of standing wave effect was observed at 130 MHz. The secondary density peak caused by the standing wave effect became pronounced and shifts toward the axis as the driving frequency further to increase, indicative of a much more shortened standing-wave wavelength. With increasing rf power, the secondary density peak shift toward the radial edge, namely, the standing-wave wavelength was increased, in good qualitative agreement with the previous theory and simulation results. At higher pressures and high frequencies, the rf power was primarily deposited at the periphery of the electrode, due to the fact that the waves were strongly damped as they propagated from the discharge edge into the center.

  1. Balloon observations of ultra-low-frequency waves in the electric field above the South Pole

    SciTech Connect

    Liao, B.; Benbrrook, J.R.; Bering E.A. III; Byrne, G.J.; Theall, J.R. )

    1988-01-01

    The physics of ultra-low-frequency waves in the magnetosphere, near the cusp and in the polar cap, is important because this region is one where ultra-low-frequency wave energy from the magnetopause can most easily enter the magnetosphere. During the 1985-1986 South Pole balloon campaign, eight stratospheric balloon payloads were launched from Amundsen-Scott Station, South Geographic Pole, Antarctica, to record data on ultra-low-frequency waves. The payloads were instrumented with three-axis double-probe electric field detectors and X-ray scintillation counters. This paper concentrates on the third flight of this series, which was launched at 2205 universal time on 21 December 1985. Good data were received from the payload until the transmitter failed at 0342 universal time on 22 December. During most of the four hours that the balloon was afloat, an intense ultra-low-frequency wave event was in progress. The electric-field data from this period have been examined in detail and compared with magnetic field data, obtained with ground-based fluxgate and induction magnetometers to determine the characteristics of the waves. After float was reached, the electric-field data in figure 1 show large-amplitude, quasi-periodic fluctuations suggesting the presence of intense ultra-low-frequency wave activity. In conclusion, the electric-field signature observed from flight 3 appears to have been essentially an electrostatic event or possibly a short-wavelength hydromagnetic wave with a varying and interesting polarization character. The authors are continuing the analysis of the data to determine the source of the observed ultra-low-frequency waves.

  2. Ground Radar Polarimetric Observations of High-Frequency Earth-Space Communication Links

    NASA Technical Reports Server (NTRS)

    Bolen, Steve; Chandrasekar, V.; Benjamin, Andrew

    2002-01-01

    Strategic roadmaps for NASA's Human Exploration and Development of Space (REDS) enterprise support near-term high-frequency communication systems that provide moderate to high data rates with dependable service. Near-earth and human planetary exploration will baseline Ka-Band, but may ultimately require the use of even higher frequencies. Increased commercial demand on low-frequency earth-space bands has also led to increased interest in the use of higher frequencies in regions like K u - and K,- band. Data is taken from the Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR), which operates at 13.8 GHz, and the true radar reflectivity profile is determined along the PR beam via low-frequency ground based polarimetric observations. The specific differential phase (Kdp) is measured along the beam and a theoretical model is used to determine the expected specific attenuation (k). This technique, called the k-Kdp method, uses a Fuzzy-Logic model to determine the hydrometeor type along the PR beam from which the appropriate k-Kdp relationship is used to determine k and, ultimately, the total path-integrated attenuation (PIA) on PR measurements. Measurements from PR and the NCAR S-POL radar were made during the TEFLUN-B experiment that took place near Melbourne, FL in 1998, and the TRMM-LBA campaign near Ji-Parana, Brazil in 1999.

  3. The Lockman Hole project: LOFAR observations and spectral index properties of low-frequency radio sources

    NASA Astrophysics Data System (ADS)

    Mahony, E. K.; Morganti, R.; Prandoni, I.; van Bemmel, I. M.; Shimwell, T. W.; Brienza, M.; Best, P. N.; Brüggen, M.; Rivera, G. Calistro; de Gasperin, F.; Hardcastle, M. J.; Harwood, J. J.; Heald, G.; Jarvis, M. J.; Mandal, S.; Miley, G. K.; Retana-Montenegro, E.; Röttgering, H. J. A.; Sabater, J.; Tasse, C.; van Velzen, S.; van Weeren, R. J.; Williams, W. L.; White, G. J.

    2016-09-01

    The Lockman Hole is a well-studied extragalactic field with extensive multi-band ancillary data covering a wide range in frequency, essential for characterising the physical and evolutionary properties of the various source populations detected in deep radio fields (mainly star-forming galaxies and AGNs). In this paper we present new 150-MHz observations carried out with the LOw Frequency ARray (LOFAR), allowing us to explore a new spectral window for the faint radio source population. This 150-MHz image covers an area of 34.7 square degrees with a resolution of 18.6×14.7 arcsec and reaches an rms of 160 μJy beam-1 at the centre of the field. As expected for a low-frequency selected sample, the vast majority of sources exhibit steep spectra, with a median spectral index of α _{150}^{1400}=-0.78± 0.015. The median spectral index becomes slightly flatter (increasing from α _{150}^{1400}=-0.84 to α _{150}^{1400}=-0.75) with decreasing flux density down to S150 ˜10 mJy before flattening out and remaining constant below this flux level. For a bright subset of the 150-MHz selected sample we can trace the spectral properties down to lower frequencies using 60-MHz LOFAR observations, finding tentative evidence for sources to become flatter in spectrum between 60 and 150 MHz. Using the deep, multi-frequency data available in the Lockman Hole, we identify a sample of 100 Ultra-steep spectrum (USS) sources and 13 peaked spectrum sources. We estimate that up to 21 per cent of these could have z > 4 and are candidate high-z radio galaxies, but further follow-up observations are required to confirm the physical nature of these objects.

  4. Low radio frequency observations and spectral modelling of the remnant of Supernova 1987A

    NASA Astrophysics Data System (ADS)

    Callingham, J. R.; Gaensler, B. M.; Zanardo, G.; Staveley-Smith, L.; Hancock, P. J.; Hurley-Walker, N.; Bell, M. E.; Dwarakanath, K. S.; Franzen, T. M. O.; Hindson, L.; Johnston-Hollitt, M.; Kapińska, A.; For, B.-Q.; Lenc, E.; McKinley, B.; Morgan, J.; Offringa, A. R.; Procopio, P.; Wayth, R. B.; Wu, C.; Zheng, Q.

    2016-10-01

    We present Murchison Widefield Array observations of the supernova remnant (SNR) 1987A between 72 and 230 MHz, representing the lowest frequency observations of the source to date. This large lever arm in frequency space constrains the properties of the circumstellar medium created by the progenitor of SNR 1987A when it was in its red supergiant phase. As of late 2013, the radio spectrum of SNR 1987A between 72 MHz and 8.64 GHz does not show any deviation from a non-thermal power law with a spectral index of -0.74 ± 0.02. This spectral index is consistent with that derived at higher frequencies, beneath 100 GHz, and with a shock in its adiabatic phase. A spectral turnover due to free-free absorption by the circumstellar medium has to occur below 72 MHz, which places upper limits on the optical depth of ≤0.1 at a reference frequency of 72 MHz, emission measure of ≲13 000 cm-6 pc, and an electron density of ≲110 cm-3. This upper limit on the electron density is consistent with the detection of prompt radio emission and models of the X-ray emission from the supernova. The electron density upper limit implies that some hydrodynamic simulations derived a red supergiant mass-loss rate that is too high, or a wind velocity that is too low. The mass-loss rate of ˜5 × 10-6 M⊙ yr-1 and wind velocity of 10 km s-1 obtained from optical observations are consistent with our upper limits, predicting a current turnover frequency due to free-free absorption between 5 and 60 MHz.

  5. Solution of the high-frequency variations of ERP from VLBI observations

    NASA Astrophysics Data System (ADS)

    Zhang, Bo; Li, Jin-ling; Wang, Guang-li; Zhao, Ming

    2005-07-01

    In the software CALC/SOLVE for the analysis of VLBI astrometric and geodetic data, the high-frequency variations of earth rotation parameters (ERP) are estimated by segmented linear fittings with additional constraints. That is, the rates of ERP between two epoch nodes are constrained to agree to within some preset value, and the ERP are required to be continuous at the nodes. Our analysis shows that when the data points are not very dense, the constraint and continuity requirement help to improve the stability of the solution, while at the same time they degrade the objectivity of the solution and make the solutions of ERP at different epoch nodes correlated. For this reason, based on the user partial entry of CALC/SOLVE, we have developed a module for the direct solution of the high-frequency variations of ERP, without the constraint on the ERP rate, nor the continuity requirement at the epoch nodes. It is shown by our reduction of real data that the direct solution mode is preferable. To derive the high-frequency variations of ERP from VLBI observations with a long time span, the error in the precession/nutation models (the celestial pole offset) should be taken into consideration and a corresponding module is developed. The global solutions of the high-frequency variations of ERP are successfully performed on the VLBI observations in the period from 1979 to 2003. It is demonstrated that when the errors in precession/nutation models are taken into consideration, the accuracy of the solution is noticeably improved. So, when seeking the high-frequency variations of ERP from VLBI observations, we recommend this direct solution mode, while taking the pole offset into consideration.

  6. Measurement of acoustic glitches in solar-type stars from oscillation frequencies observed by Kepler

    SciTech Connect

    Mazumdar, A.; Monteiro, M. J. P. F. G.; Cunha, M. S.; Ballot, J.; Antia, H. M.; Basu, S.; Houdek, G.; Silva Aguirre, V.; Christensen-Dalsgaard, J.; Metcalfe, T. S.; Mathur, S.; García, R. A.; Verner, G. A.; Chaplin, W. J.; Sanderfer, D. T.; Seader, S. E.; Smith, J. C.

    2014-02-10

    For the very best and brightest asteroseismic solar-type targets observed by Kepler, the frequency precision is sufficient to determine the acoustic depths of the surface convective layer and the helium ionization zone. Such sharp features inside the acoustic cavity of the star, which we call acoustic glitches, create small oscillatory deviations from the uniform spacing of frequencies in a sequence of oscillation modes with the same spherical harmonic degree. We use these oscillatory signals to determine the acoustic locations of such features in 19 solar-type stars observed by the Kepler mission. Four independent groups of researchers utilized the oscillation frequencies themselves, the second differences of the frequencies and the ratio of the small and large separation to locate the base of the convection zone and the second helium ionization zone. Despite the significantly different methods of analysis, good agreement was found between the results of these four groups, barring a few cases. These results also agree reasonably well with the locations of these layers in representative models of the stars. These results firmly establish the presence of the oscillatory signals in the asteroseismic data and the viability of several techniques to determine the location of acoustic glitches inside stars.

  7. 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.

  8. Combined Radiometer-Radar Microphysical Profile Estimations with Emphasis on High Frequency Brightness Temperature Observations

    NASA Technical Reports Server (NTRS)

    Jackson, Gail Skofronick; Wang, James R.; Heymsfield, Gerald M.; Hood, Robbie; Manning, Will; Meneghini, Robert; Weinman, James A.; Hildebrand, Peter (Technical Monitor)

    2001-01-01

    Information about the vertical microphysical cloud structure is useful in many modeling and predictive practices. Radiometers and radars are used to observe hydrometeor properties. This paper describes an iterative retrieval algorithm that combines the use of airborne active and wideband (10 to 340 GHz) passive observations to estimate the vertical content and particle size distributions of liquid and frozen hydrometeors. The physically-based retrieval algorithm relies on the high frequencies (greater than 89 GHz) to provide details on the frozen hydrometeors. Neglecting the high frequencies yielded acceptable estimates of the liquid profiles, but the ice profiles were poorly retrieved. Airborne radar and radiometer observations from the third Convection and Moisture EXperiment (CAMEX-3) were used in the retrieval algorithm as constraints. Nadir profiles were estimated for a minute each of flight time (approximately 12.5 km along track) from an anvil, convection, and quasi- stratiform rain. The complex structure of the frozen hydrometeors required the most iterations for convergence for the anvil cloud type. The wideband observations were found to more than double the estimated frozen hydrometeor content as compared to retrievals using only 90-GHz and below. The convective and quasi-stratiform quickly reached convergence (minimized difference between observations and calculations using the estimated profiles). A qualitative validation using coincident in situ CAMEX-3 observations shows that the retrieved particle size distributions are well corroborated with independent measurements.

  9. Low-frequency magnetic field fluctuations in comet P/Halley's magnetosheath - Giotto observations

    NASA Technical Reports Server (NTRS)

    Glassmeier, K. H.; Neubauer, F. M.; Acuna, M. H.; Mariani, F.

    1987-01-01

    The interaction region between comets and the solar wind is characterized by large amplitude, low frequency magnetic field fluctuations, both within the upstream region as well as in the magnetosheath. Magnetosheath observations of the magnetic field experiment onboard Giotto indicate values of delta B/B equal to about O(1). Power spectral peaks appear at frequencies of 10mHz with the spectrum exhibiting a power law dependence with an exponent of the order 2. Radial variation of the fluctuation level does not clearly increase with decreasing distance from the cometary nucleus as observed by the magnetometer onboard Vega-1 and as expected from quasi-linear theory. The entrance into the cometary bow shock is furthermore characterized by an order of magnitude increase of the fluctuation level, both on the in- and outbound pass of Giotto.

  10. Satellite observations of type 3 solar radio bursts at low frequencies

    NASA Technical Reports Server (NTRS)

    Fainberg, J.; Stone, R. G.

    1973-01-01

    Type III solar radio bursts were observed from 10 MHz to 10 KHz by satellite experiments above the terrestrial plasmasphere. Solar radio emission in this frequency range results from excitation of the interplanetary plasma by energetic particles propagating outward along open field lines over distances from 5 solar radii to at least 1 AU from the sun. This review summarizes the morphology, characteristics and analysis of individual as well as storms of bursts. Burst rise times are interpreted in terms of exciter length and dispersion while decay times refer to the radiation damping process. The combination of radio observations at the lower frequencies and in-situ measurements on nonrelativistic electrons at 1 AU provide data on the energy range and efficiency of the wave-particle interactions responsible for the radio emission.

  11. Estimating the Radius of the Convective Core of Main-sequence Stars from Observed Oscillation Frequencies

    NASA Astrophysics Data System (ADS)

    Yang, Wuming

    2016-10-01

    The determination of the size of the convective core of main-sequence stars is usually dependent on the construction of models of stars. Here we introduce a method to estimate the radius of the convective core of main-sequence stars with masses between about 1.1 and 1.5 M ⊙ from observed frequencies of low-degree p-modes. A formula is proposed to achieve the estimation. The values of the radius of the convective core of four known stars are successfully estimated by the formula. The radius of the convective core of KIC 9812850 estimated by the formula is 0.140 ± 0.028 R ⊙. In order to confirm this prediction, a grid of evolutionary models was computed. The value of the convective-core radius of the best-fit model of KIC 9812850 is 0.149 R ⊙, which is in good agreement with that estimated by the formula from observed frequencies. The formula aids in understanding the interior structure of stars directly from observed frequencies. The understanding is not dependent on the construction of models.

  12. Low-frequency waves within isolated magnetic clouds and complex structures: STEREO observations

    NASA Astrophysics Data System (ADS)

    Siu-Tapia, A.; Blanco-Cano, X.; Kajdic, P.; Aguilar-Rodriguez, E.; Russell, C. T.; Jian, L. K.; Luhmann, J. G.

    2015-04-01

    Complex Structures (CSs) formed by the interaction of magnetic cloud (MC)-like structures with other transients (e.g., another MC, a stream interaction region, or a fast stream of solar wind) were frequently observed in the interplanetary space by STEREO spacecraft during the solar minimum 23 and the rising phase of the solar cycle 24. Here we report the presence of low-frequency waves (LFWs) inside some isolated MCs (IMCs) and inside the CSs observed by STEREO during such period (2007-2011). It is important to study in detail the properties of waves in space plasmas since particle distribution functions can be modified by wave-particle interactions. We compare wave characteristics within IMCs with those waves observed inside CSs. Both left-handed (LH) and right-handed (RH), near-circularly polarized, transverse and almost parallel-propagating LFWs (around the proton cyclotron frequency) were sporadically observed inside both IMCs and CSs. In contrast, compressive mirror-mode waves (MMs) were observed only within CSs. We studied local plasma conditions inside the IMCs and CSs to gain insight about wave origin: most of the MMs within CSs were observed in regions with enhanced plasma beta (β>1) the majority of the LH waves were found in low beta plasmas (β<1), and the RH waves were predominantly observed at moderate betas (0.4<β≤2). These observations are in agreement with linear kinetic theory predictions for the growth of the mirror, the LH ion cyclotron, and the RH ion firehose instability, respectively. It is possible that the waves were generated locally inside the IMCs and CSs via temperature anisotropies. The plasma beta enhancements that were frequently observed inside the CSs may be the result of compressions and heating taking place inside the interacting structures.

  13. Geographic distributions of Idh-1 alleles in a cricket are linked to differential enzyme kinetic performance across thermal environments

    PubMed Central

    Huestis, Diana L; Oppert, Brenda; Marshall, Jeremy L

    2009-01-01

    Background Geographic clines within species are often interpreted as evidence of adaptation to varying environmental conditions. However, clines can also result from genetic drift, and these competing hypotheses must therefore be tested empirically. The striped ground cricket, Allonemobius socius, is widely-distributed in the eastern United States, and clines have been documented in both life-history traits and genetic alleles. One clinally-distributed locus, isocitrate dehydrogenase (Idh-1), has been shown previously to exhibit significant correlations between allele frequencies and environmental conditions (temperature and rainfall). Further, an empirical study revealed a significant genotype-by-environmental interaction (GxE) between Idh-1 genotype and temperature which affected fitness. Here, we use enzyme kinetics to further explore GxE between Idh-1 genotype and temperature, and test the predictions of kinetic activity expected under drift or selection. Results We found significant GxE between temperature and three enzyme kinetic parameters, providing further evidence that the natural distributions of Idh-1 allele frequencies in A. socius are maintained by natural selection. Differences in enzyme kinetic activity across temperatures also mirror many of the geographic patterns observed in allele frequencies. Conclusion This study further supports the hypothesis that the natural distribution of Idh-1 alleles in A. socius is driven by natural selection on differential enzymatic performance. This example is one of several which clearly document a functional basis for both the maintenance of common alleles and observed clines in allele frequencies, and provides further evidence for the non-neutrality of some allozyme alleles. PMID:19460149

  14. Oscillation mode frequencies of 61 main-sequence and subgiant stars observed by Kepler

    NASA Astrophysics Data System (ADS)

    Appourchaux, T.; Chaplin, W. J.; García, R. A.; Gruberbauer, M.; Verner, G. A.; Antia, H. M.; Benomar, O.; Campante, T. L.; Davies, G. R.; Deheuvels, S.; Handberg, R.; Hekker, S.; Howe, R.; Régulo, C.; Salabert, D.; Bedding, T. R.; White, T. R.; Ballot, J.; Mathur, S.; Silva Aguirre, V.; Elsworth, Y. P.; Basu, S.; Gilliland, R. L.; Christensen-Dalsgaard, J.; Kjeldsen, H.; Uddin, K.; Stumpe, M. C.; Barclay, T.

    2012-07-01

    Context. Solar-like oscillations have been observed by Kepler and CoRoT in several solar-type stars, thereby providing a way to probe the stars using asteroseismology Aims: We provide the mode frequencies of the oscillations of various stars required to perform a comparison with those obtained from stellar modelling. Methods: We used a time series of nine months of data for each star. The 61 stars observed were categorised in three groups: simple, F-like, and mixed-mode. The simple group includes stars for which the identification of the mode degree is obvious. The F-like group includes stars for which the identification of the degree is ambiguous. The mixed-mode group includes evolved stars for which the modes do not follow the asymptotic relation of low-degree frequencies. Following this categorisation, the power spectra of the 61 main-sequence and subgiant stars were analysed using both maximum likelihood estimators and Bayesian estimators, providing individual mode characteristics such as frequencies, linewidths, and mode heights. We developed and describe a methodology for extracting a single set of mode frequencies from multiple sets derived by different methods and individual scientists. We report on how one can assess the quality of the fitted parameters using the likelihood ratio test and the posterior probabilities. Results: We provide the mode frequencies of 61 stars (with their 1-σ error bars), as well as their associated échelle diagrams. Appendices are available in electronic form at http://www.aanda.org

  15. Common and Well-Documented HLA Alleles: 2012 Update to the CWD Catalogue

    PubMed Central

    Mack, Steven J.; Cano, Pedro; Hollenbach, Jill A.; He, Jun; Hurley, Carolyn Katovich; Middleton, Derek; Moraes, Maria Elisa; Pereira, Shalini E.; Kempenich, Jane H.; Reed, Elaine F.; Setterholm, Michelle; Smith, AnaJane G.; Tilanus, Marcel G.; Torres, Margareth; Varney, Michael D.; Voorter, Christien E. M.; Fischer, Gottfried F.; Fleischhauer, Katharina; Goodridge, Damian; Klitz, William; Little, Ann-Margaret; Maiers, Martin; Marsh, Steven G. E.; Müller, Carlheinz R.; Noreen, Harriet; Rozemuller, Erik H.; Sanchez-Mazas, Alicia; Senitzer, David; Trachtenberg, Elizabeth; Fernandez-Vina, Marcelo

    2013-01-01

    We have updated the catalogue of common and well-documented (CWD) HLA alleles to reflect current understanding of the prevalence of specific allele sequences. The original CWD catalogue designated 721 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, and –DPB1 loci in IMGT/HLA Database release 2.15.0 as being CWD. The updated CWD catalogue designates 1122 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1 and –DPB1 loci as being CWD, and represents 14.3% of the HLA alleles in IMGT/HLA Database release 3.9.0. In particular, we identified 415 of these alleles as being “common” (having known frequencies) and 707 as being “well-documented” on the basis of ~140,000 sequence-based typing observations and available HLA haplotype data. Using these allele prevalence data, we have also assigned CWD status to specific G and P designations. We identified 147/151 G groups and 290/415 P groups as being CWD. The CWD catalogue will be updated on a regular basis moving forward, and will incorporate changes to the IMGT/HLA Database as well as empirical data from the histocompatibility and immunogenetics community. This version 2.0.0 of the CWD catalogue is available online at cwd.immunogenomics.org, and will be integrated into the Allele Frequencies Net Database, the IMGT/HLA Database and National Marrow Donor Program’s bioinformatics web pages. PMID:23510415

  16. Common and well-documented HLA alleles: 2012 update to the CWD catalogue.

    PubMed

    Mack, S J; Cano, P; Hollenbach, J A; He, J; Hurley, C K; Middleton, D; Moraes, M E; Pereira, S E; Kempenich, J H; Reed, E F; Setterholm, M; Smith, A G; Tilanus, M G; Torres, M; Varney, M D; Voorter, C E M; Fischer, G F; Fleischhauer, K; Goodridge, D; Klitz, W; Little, A-M; Maiers, M; Marsh, S G E; Müller, C R; Noreen, H; Rozemuller, E H; Sanchez-Mazas, A; Senitzer, D; Trachtenberg, E; Fernandez-Vina, Marcelo

    2013-04-01

    We have updated the catalogue of common and well-documented (CWD) human leukocyte antigen (HLA) alleles to reflect current understanding of the prevalence of specific allele sequences. The original CWD catalogue designated 721 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, and -DPB1 loci in IMGT (IMmunoGeneTics)/HLA Database release 2.15.0 as being CWD. The updated CWD catalogue designates 1122 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1 and -DPB1 loci as being CWD, and represents 14.3% of the HLA alleles in IMGT/HLA Database release 3.9.0. In particular, we identified 415 of these alleles as being 'common' (having known frequencies) and 707 as being 'well-documented' on the basis of ~140,000 sequence-based typing observations and available HLA haplotype data. Using these allele prevalence data, we have also assigned CWD status to specific G and P designations. We identified 147/151 G groups and 290/415 P groups as being CWD. The CWD catalogue will be updated on a regular basis moving forward, and will incorporate changes to the IMGT/HLA Database as well as empirical data from the histocompatibility and immunogenetics community. This version 2.0.0 of the CWD catalogue is available online at cwd.immunogenomics.org, and will be integrated into the Allele Frequencies Net Database, the IMGT/HLA Database and National Marrow Donor Program's bioinformatics web pages. PMID:23510415

  17. Co-selection and replacement of resistance alleles to Lysinibacillus sphaericus in a Culex quinquefasciatus colony.

    PubMed

    Chalegre, Karlos Diogo de Melo; Tavares, Daniella A; Romão, Tatiany P; de Menezes, Heverly Suzany G; Nascimento, Nathaly A; de Oliveira, Cláudia Maria F; de-Melo-Neto, Osvaldo P; Silva-Filha, Maria Helena N L

    2015-09-01

    The Cqm1 α-glucosidase, expressed within the midgut of Culex quinquefasciatus mosquito larvae, is the receptor for the Binary toxin (Bin) from the entomopathogen Lysinibacillus sphaericus. Mutations of the Cqm1 α-glucosidase gene cause high resistance levels to this bacterium in both field and laboratory populations, and a previously described allele, cqm1REC, was found to be associated with a laboratory-resistant colony (R2362). This study described the identification of a novel resistance allele, cqm1REC-2, that was co-selected with cqm1REC within the R2362 colony. The two alleles display distinct mutations but both generate premature stop codons that prevent the expression of midgut-bound Cqm1 proteins. Using a PCR-based assay to monitor the frequency of each allele during long-term maintenance of the resistant colony, cqm1REC was found to predominate early on but later was replaced by cqm1REC-2 as the most abundant resistance allele. Homozygous larvae for each allele were then generated that displayed similar high-resistance phenotypes with equivalent low levels of transcript and lack of protein expression for both cqm1REC and cqm1REC-2. In progeny from a cross of homozygous individuals for each allele at a 1 : 1 ratio, analyzed for ten subsequent generations, cqm1REC showed a higher frequency than cqm1REC-2. The replacement of cqm1REC by cqm1REC -2 observed in the R2362 colony, kept for 210 generations, indicates changes in fitness related to traits that are unknown but linked to these two alleles, and constitutes a unique example of evolution of resistance within a controlled laboratory environment. PMID:26131741

  18. Low-frequency waves at comet 67P/Churyumov-Gerasimenko. Observations compared to numerical simulations

    NASA Astrophysics Data System (ADS)

    Koenders, C.; Perschke, C.; Goetz, C.; Richter, I.; Motschmann, U.; Glassmeier, K. H.

    2016-10-01

    Context. A new type of low-frequency wave was detected by the magnetometer of the Rosetta Plasma Consortium at the comet during the initial months after the arrival of the Rosetta spacecraft at comet 67P/Churyumov-Gerasimenko. This large-amplitude, nearly continuous wave activity is observed in the frequency range from 30 mHz to 80 mHz where 40 mHz to 50 mHz is the dominant frequency. This type of low frequency is not closely related to the gyrofrequency of newborn cometary ions, which differs from previous wave activity observed in the interaction region of comets with the solar wind. Aims: This work aims to reveal a global view on the wave activity region using simulations of the comet-solar wind interaction region. Parameters, such as wavelength, propagation direction, and propagation patterns, are within the focus of this study. While the Rosetta observations only provide local information, numerical simulations provide further information on the global wave properties. Methods: Standard hybrid simulations were applied to the comet-solar wind interaction scenario. In the model, the ions were described as particles, which allows us to describe kinetic processes of the ions. The electrons were described as a fluid. Results: The simulations exhibit a threefold wave structure of the interaction region. A Mach cone and a Whistler wing are observed downstream of the comet. The third kind of wave activity found are low-frequency waves at 97 mHz, which corresponds to the waves observed by Richter et al. (2015, Ann. Geophys., 33, 1031). These waves are caused by the initial pick-up of the cometary ions that are perpendicular to the solar wind flow and in the interplanetary magnetic field direction. The associated electric current becomes unstable. The simulations show that wave activity is only detectable in the + E hemisphere and that the Mach cone and whistler wings need to be distinguished from the newly found instability driven wave activity. The movie associated to

  19. Study of HLA-DQA1 alleles in celiac children.

    PubMed

    Nieto, A; Blanco Quirós, A; Arranz, E; Alonso Franch, M; Garrote, J A; Calvo, C

    1995-01-01

    The familial incidence of celiac disease (CD) confirms its genetic basis, although acquired factors are also involved. Many authors have reported a linkage between celiac disease and HLA antigens, but there are differences which depend on geographical areas, and nowadays the study must be done at the genetic level. Thirty-eight celiac children and 52 normal controls were included in this study. All individuals were chosen from the Castilla and Leon area. We used the reverse ¿dot block¿ technique, using sequence-specific oligonucleotide DNA probes (Cetus, USA) to determine the HLA-DQA1 alleles in DNA samples previously amplified by PCR (polymerase chain reaction). The different frequency of alleles in patients and controls was assessed by 3 statistical tests: chi square (chi(2)), relative risk (RR) and etiologic fraction (EF). A very high frequency of DQA1*0201 (chi(2):p <0.0001) and DQA1*0501 (chi(2): p <0.0001) alleles was observed in patients; all but one (97%) had the DQA1*0501 allele vs. 40% of controls (RR: 37.00; EF: 0.955). The DQA1*0201 allele also had a high prevalence in celiacs (58%)(RR: 1.375: EF:0.438). The DQA1*01 allele was only found in 10.5% of patients compared to 79% of controls (chi(2): p <0.0001) and the DQA1*03 allele was also decreased in celiacs. There was only one celiac girl without the DQA1*0501 allele. She had no other clinical or serological differences, as compared to the other patients. In the study of allele subtypes, among the DQA1*01 allele, 50% of patients were positive for DQA1*101 and the remaining 50% had DQA1*0102, but none of the individuals were positive for DQA1*0103. Among normal controls, 32 individuals (61.5%) expressed the DQA1*0102 subtype, 15 (28.9%) the DQA1*0101 subtype and 5 (9.6%) the DQA1*0103 subtype. All positive cases for DQA1-*05 belong to the DQA1* 0501 subtype, in both celiac and control groups. There were 10 possible combinations of HLA-DQA1 genes, but we found a very unequal distribution in both celiacs

  20. Significant reduction in arc frequency biased solar cells: Observations, diagnostics, and mitigation technique(s)

    NASA Technical Reports Server (NTRS)

    Upschulte, B. L.; Weyl, G. M.; Marinelli, W. J.; Aifer, E.; Hastings, D.; Snyder, D.

    1991-01-01

    A variety of experiments were performed which identify key factors contributing to the arcing of negatively biased high voltage solar cells. These efforts have led to reduction of greater than a factor of 100 in the arc frequency of a single cell following proper remediation procedures. Experiments naturally lead to and focussed on the adhesive/encapsulant that is used to bond the protective cover slip to the solar cell. An image-intensified charge coupled device (CCD) camera system recorded UV emission from arc events which occurred exclusively along the interfacial edge between the cover slip and the solar cell. Microscopic inspection of this interfacial region showed a bead of encapsulant along this entire edge. Elimination of this encapsulant bead reduced the arc frequency by two orders of magnitude. Water contamination was also identified as a key contributor which enhances arcing of the encapsulant bead along the solar cell edge. Spectrally resolved measurements of the observable UV light shows a feature assignable to OH(A-X) electronic emission, which is common for water contaminated discharges. Experiments in which the solar cell temperature was raised to 85 C showed a reduced arcing frequency, suggesting desorption of H2O. Exposing the solar cell to water vapor was shown to increase the arcing frequency. Clean dry gases such as O2, N2, and Ar show no enhancement of the arcing rate. Elimination of the exposed encapsulant eliminates any measurable sensitivity to H2O vapor.

  1. Airborne Remote Observations of L-Band Radio Frequency Interference and Implications for Satellite Missions

    NASA Technical Reports Server (NTRS)

    Laymon, Charles; Srinivasan, Karthik; Limaye, Ashutosh

    2011-01-01

    Passive remote sensing of the Earth s surface and atmosphere from space has significant importance in operational and research environmental studies, in particular for the scientific understanding, monitoring and prediction of climate change and its impacts. Passive remote sensing requires the measurement of naturally occurring radiations, usually of very low power levels, which contain essential information on the physical process under investigation. As such, these sensed radio frequency bands are a unique natural resource enabling space borne passive sensing of the atmosphere and the Earth s surface that deserves adequate allocation to the Earth Exploration Satellite Service and absolute protection from interference. Unfortunately, radio frequency interference (RFI) is an increasing problem for Earth remote sensing, particularly for passive observations of natural emissions. Because these natural signals tend to be very weak, even low levels of interference received by a passive sensor may degrade the fidelity of scientific data. The characteristics of RFI (low-level interference and radar-pulse noise) are not well known because there has been no systematic surveillance, spectrum inventory or mapping of RFI. While conducting a flight experiment over central Tennessee in May 2010, RFI, a concern for any instrument operating in the passive L band frequency, was observed across 16 subbands between 1402-1427 MHz. Such a survey provides rare characterization data from which to further develop mitigation technologies as well as to identify bandwidths to avoid in future sensor formulation.

  2. HIGH-RESOLUTION RADIO OBSERVATIONS OF THE REMNANT OF SN 1987A AT HIGH FREQUENCIES

    SciTech Connect

    Zanardo, Giovanna; Staveley-Smith, L.; Potter, T. M.; Ng, C.-Y.; Gaensler, B. M.; Manchester, R. N.; Tzioumis, A. K.

    2013-04-20

    We present new imaging observations of the remnant of Supernova (SN) 1987A at 44 GHz, performed in 2011 with the Australia Telescope Compact Array (ATCA). The 0.''35 Multiplication-Sign 0.''23 resolution of the diffraction-limited image is the highest achieved to date in high-dynamic range. We also present a new ATCA image at 18 GHz derived from 2011 observations, which is super-resolved to 0.''25. The flux density is 40 {+-} 2 mJy at 44 GHz and 81 {+-} 6 mJy at 18 GHz. At both frequencies, the remnant exhibits a ring-like emission with two prominent lobes, and an east-west brightness asymmetry that peaks on the eastern lobe. A central feature of fainter emission appears at 44 GHz. A comparison with previous ATCA observations at 18 and 36 GHz highlights higher expansion velocities of the remnant's eastern side. The 18-44 GHz spectral index is {alpha} = -0.80 (S{sub {nu}}{proportional_to}{nu}{sup {alpha}}). The spectral index map suggests slightly steeper values at the brightest sites on the eastern lobe, whereas flatter values are associated with the inner regions. The remnant morphology at 44 GHz generally matches the structure seen with contemporaneous X-ray and H{alpha} observations. Unlike the H{alpha} emission, both the radio and X-ray emission peaks on the eastern lobe. The regions of flatter spectral index align and partially overlap with the optically visible ejecta. Simple free-free absorption models suggest that emission from a pulsar wind nebula or a compact source inside the remnant may now be detectable at high frequencies or at low frequencies if there are holes in the ionized component of the ejecta.

  3. Experimental observation of further frequency upshift from dc to ac radiation converter with perpendicular dc magnetic field

    PubMed

    Higashiguchi; Yugami; Gao; Niiyama; Sasaki; Takahashi; Ito; Nishida

    2000-11-20

    A frequency upshift of a short microwave pulse is generated by the interaction between a relativistic underdense ionization front and a periodic electrostatic field with a perpendicular dc magnetic field. When the dc magnetic field is applied, further frequency upshift of 3 GHz is observed with respect to an unmagnetized case which has typically a GHz range. The radiation frequency depends on both the plasma density and the strength of the dc magnetic field, i.e., the plasma frequency and the cyclotron frequency. The frequency of the emitted radiation is in reasonable agreement with the theoretical values. PMID:11082591

  4. High-frequency observations of δ2H and δ18O in storm rainfall

    NASA Astrophysics Data System (ADS)

    Stoecker, F.; Klaus, J.; Pangle, L. A.; Garland, C.; McDonnell, J. J.

    2012-12-01

    Stable isotopes ratios of hydrogen (2H/1H) and oxygen (18O/16O) are indispensable tools for investigation of the hydrologic cycle. Recent technological advances with laser spectroscopy now enable high-frequency measurement of key water cycle components. While the controls on rainfall isotope composition have been known generally for some time, our understanding of the effect of inter- and intra-storm processes on fine scale rainfall isotope composition is poorly understood. Here we present a new approach to observe inter- and intra-storm isotope variability in precipitation in high-frequency. We investigate the temporal development of δ2H and δ18O within and between discrete rainstorm. δ2H and δ18O in precipitation was measured from November 2011 to February 2012 in Corvallis, OR using a flow-cell combined with a Liquid Water Isotope Analyzer (LWIA-24d, Los Gatos Research, Inc.). The average sample frequency was 15 samples per hour, resulting in more than 3100 samples during the observation period. 27 separate rainstorms were identified in the dataset based on minimum inter-event time, minimum precipitation depth, and minimum number of isotope measurements. Event meteoric water lines were developed for each event. We observed short-term isotopic patterns (e.g., V-shaped trends), high-rate changes (5.3‰/h) and large absolute changes in isotopic composition (20‰) on intra-event scale. V-shaped trends appeared to be related to individual storm fronts detected by air temperature, cloud heights (NEXRAD radar echo tops) and cloud trajectories (Hybrid Single Particle Lagrangian Integrated Trajectory Model (HYSPLIT)). Despite this, we could detect no linear correlation between event-based isotopic variables (slope, δ2H-intercept, δ2H, δ18O) and the event meteoric water line. Furthermore, the composite event meteoric water line (i.e. the local meteoric water line) showed a wider spread for heavy isotopes than for light isotopes, caused presumably by different

  5. Quasi-periodic frequency fluctuations observed during coronal radio sounding experiments 1991-2009

    NASA Astrophysics Data System (ADS)

    Efimov, Anatoli; Lukanina, L. A.; Samoznaev, Lev; Rudash, V. K.; Chashei, Igor; Bird, Michael; Paetzold, Martin

    Recent coronal radio sounding experiments with the ESA spacecraft Mars Express (MEX), Venus Express (VEX) and Rosetta (ROS) have provided a large volume of observational data supporting the presence of a quasi-periodic component (QPC) in frequency fluctuation spectra during solar conjunction. Further evidence for the QPC, first seen in data from the MEX conjunction in 2004, was found later in data from the MEX conjunctions in 2006 and 2008/09, as well as the VEX and ROS conjunctions in 2006. The QPC is detected with an occurrence frequency ≈ 18% (83.3 hours of the total 462.7 hours of data). In some cases the temporal spectra reveal two lines: the main QPC and its second harmonic. The average frequency of the spectral density maximum is νmax ≈ 5.5 mHz (corresponding QPC fluctuation period ≈ 3 min) at solar offset distances R < 8 Rs. The QPC spectral density maximum Gmax reaches an average factor of 2.88 above the background level G0 . The bandwidth of the spectral line ∆ν ≈ νmax . At larger solar distances (R > 8 Rs) the fluctuation frequency of the mean spectral density maximum is νmax ≈ 4.3 mHz (period ≈ 4 min). Both the fractional spectral line bandwidth ∆ν/νmax and the excess of spectral density Gmax above background are nearly unchanged from their values nearer the Sun. A reanalysis of earlier coronal sounding data obtained with the Ulysses (1991, 1995) and Galileo (1996/97) spacecraft has verified the existence of the QPC. Typical fluctuation periods lie between 4 and 5 min, but the QPC occurrence rate (12%) is smaller than that observed for MEX-VEX-ROS. This may be associated with the lower received signal level of Ulysses and Galileo compared to the ESA spacecraft. The Ulysses coronal sounding experiments in 1995 provided an interesting possibility to observe the QPC at high solar latitudes. Preliminary results show that the QPC frequency can reach νmax = 6-7 mHz at heliolatitudes 60° -80° .

  6. Allelic associations of two polymorphic microsatellites in intron 40 of the human von Willebrand factor gene

    SciTech Connect

    Pena, S.D.J.; De Souza, K.T. ); De Andrade, M.; Chakraborty, R. )

    1994-01-18

    At intron 40 of the von Willebrand factor (vWF) gene, two GATA-repeat polymorphic sites exist that are physically separated by 212 bp. At the first site (vWF1 locus), seven segregating repeat alleles were observed in a Brazilian Caucasian population, and at the second (vWF2 locus) there were eight alleles, detected through PCR amplifications of this DNA region. Haplotype analysis of individuals revealed 36 different haplotypes in a sample of 338 chromosomes examined. Allele frequencies between generations and gender at each locus were not significantly different, and the genotype frequencies were consistent with their Hardy-Weinberg expectations. Linkage disequilibrium between loci is highly significant with positive allele size association; that is, large alleles at the loci tend to occur together, and so do the same alleles. Variability at each locus appeared to have arisen in a stepwise fashion, suggesting replication slippage as a possible mechanism of production of new alleles. However, the authors observed an increased number of haplotypes, in contrast with the predictions of a stepwise production of variation in the entire region, suggesting some form of cooperative changes between loci that could be due to either gene conversion, or a common control mechanism of production of new variation at these repeat polymorphism sites. The high degree of polymorphism (gene diversity values of 72% and 78% at vWF1 and vWF2, respectively, and of 93% at the haplotype level) makes these markers informative for paternity testing, genetic counseling, and individual-identification purposes.

  7. Association of the apolipoprotein E {epsilon}4 allele with clinical subtypes of autopsy-confirmed Alzheimer`s Disease

    SciTech Connect

    Zubenko, G.S.; Stiffler, S.; Kopp, U.

    1994-09-15

    Consistent with previous reports, we observed a significant association of the APOE {epsilon}4 allele with Alzheimer`s Disease (AD) in a series of 91 autopsy-confirmed cases. The {epsilon}4 allele frequency was higher in cases with a family history of AD-like dementia (0.54 {+-} 0.07), although the {epsilon}4 allele frequency in the AD cases with a negative family history (0.38 {+-} 0.05) remained significantly greater than that for the non-AD control group (0.13 {+-} 0.03). A similar increase in {epsilon}4 allele frequency (0.54 {+-} 0.07) was observed in the AD cases with amyloid angiopathy, compared to those who did not have amyloid angiopathy (0.35 {+-} 0.04). Contrary to previous reports, no effect of the dosage of the {epsilon}4 allele was found on the age of onset of dementia among the AD cases and, contrary to reports suggesting an association of {epsilon}4 and atherosclerosis, the {epsilon}4 allele frequency was similar in cases with or without concurrent brain infarcts. Modest but consistent correlations were observed between the dosage of {epsilon}4 alleles and the cortical density of senile plaques, but not neurofibrillary tangles. The last finding suggests that the pathogenic events mediated by the {epsilon}4 allele may be more directly involved in the formation of senile plaques, the identifying lesions in AD, than neurofibrillary tangles. A robust association of both the presence of an {epsilon}4 allele and a family history of AD-like dementia with concurrent amyloid angiopathy occurred within our sample of AD cases. This association arose from an interaction of the {epsilon}4 allele with a separate familial factor for which a family history of dementia served as a surrogate. These results suggest that amyloid angiopathy may be a common or central feature of a form of familial AD that is associated with the transmission of the APOE {epsilon}4 allele. 22 refs., 2 figs., 5 tabs.

  8. Vibration Mode Observation of Piezoelectric Disk-type Resonator by High Frequency Laser Doppler Vibrometer

    NASA Astrophysics Data System (ADS)

    Matsumura, Takeshi; Esashi, Masayoshi; Harada, Hiroshi; Tanaka, Shuji

    For future mobile phones based on cognitive radio technology, a compact multi-band RF front-end architecture is strongly required and an integrated multi-band RF filter bank is a key component in it. Contour-mode resonators are receiving increased attention for a multi-band filter solution, because its resonant frequency is mainly determined by its size and shape, which are defined by lithography. However, spurious responses including flexural vibration are also excited due to its thin structure. To improve resonator performance and suppress spurious modes, visual observation with a laser probe system is very effective. In this paper, we have prototyped a mechanically-coupled disk-array filter, which consists of a Si disk and 2 disk-type resonators of higher-order wine-glass mode, and observed its vibration modes using a high-frequency laser-Doppler vibrometer (UHF-120, Polytec, Inc.). As a result, it was confirmed that higher order wine-glass mode vibration included a compound displacement, and that its out-of-plane vibration amplitude was much smaller than other flexural spurious modes. The observed vibration modes were compared with FEM (Finite Element Method) simulation results. In addition, it was also confirmed that the fabrication error, e.g. miss-alignment, induced asymmetric vibration.

  9. Satellite observations of type III solar radio bursts at low frequencies

    NASA Technical Reports Server (NTRS)

    Fainberg, J.; Stone, R. G.

    1974-01-01

    Type III solar radio bursts have been observed from 10 MHz to 10 kHz by satellite experiments above the terrestrial plasmasphere. Solar radio emission in this frequency range results from excitation of the interplanetary plasma by energetic particles propagating outward along open field lines over distances from 5 earth radii to at least 1 AU from the sun. This review summarizes the morphology, characteristics, and analysis of individual as well as storms of bursts. Substantial evidence is available to show that the radio emission is observed at the second harmonic instead of the fundamental of the plasma frequency. This brings the density scale derived by radio observations into better agreement with direct solar wind density measurements at 1 AU and relaxes the requirement for type III propagation along large density-enhanced regions. This density scale with the measured direction of arrival of the radio burst allows the trajectory of the exciter path to be determined from 10 earth radii to 1 AU.

  10. 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...

  11. IS THE OBSERVED HIGH-FREQUENCY RADIO LUMINOSITY DISTRIBUTION OF QSOs BIMODAL?

    SciTech Connect

    Mahony, Elizabeth K.; Sadler, Elaine M.; Croom, Scott M.; Murphy, Tara; Ekers, Ronald D.; Feain, Ilana J.

    2012-07-20

    The distribution of QSO radio luminosities has long been debated in the literature. Some argue that it is a bimodal distribution, implying that there are two separate QSO populations (normally referred to as 'radio-loud' and 'radio-quiet'), while others claim it forms a more continuous distribution characteristic of a single population. We use deep observations at 20 GHz to investigate whether the distribution is bimodal at high radio frequencies. Carrying out this study at high radio frequencies has an advantage over previous studies as the radio emission comes predominantly from the core of the active galactic nucleus, and hence probes the most recent activity. Studies carried out at lower frequencies are dominated by the large-scale lobes where the emission is built up over longer timescales (10{sup 7}-10{sup 8} yr), thereby confusing the sample. Our sample comprises 874 X-ray-selected QSOs that were observed as part of the 6dF Galaxy Survey. Of these, 40% were detected down to a 3{sigma} detection limit of 0.2-0.5 mJy. No evidence of bimodality is seen in either the 20 GHz luminosity distribution or in the distribution of the R{sub 20} parameter: the ratio of the radio to optical luminosities traditionally used to classify objects as being either radio-loud or radio-quiet. Previous results have claimed that at low radio luminosities, star formation processes can dominate the radio emission observed in QSOs. We attempt to investigate these claims by stacking the undetected sources at 20 GHz and discuss the limitations in carrying out this analysis. However, if the radio emission was solely due to star formation processes, we calculate that this corresponds to star formation rates ranging from {approx}10 M{sub Sun} yr{sup -1} to {approx}2300 M{sub Sun} yr{sup -1}.

  12. Polymorphisms in the cytochrome P450 CYP1A2 gene (CYP1A2) in colorectal cancer patients and controls: allele frequencies, linkage disequilibrium and influence on caffeine metabolism

    PubMed Central

    Sachse, Christoph; Bhambra, Upinder; Smith, Gillian; Lightfoot, Tracy J; Barrett, Jennifer H; Scollay, Jenna; Garner, R Colin; Boobis, Alan R; Wolf, C Roland; Gooderham, Nigel J

    2003-01-01

    Aim Several single nucleotide polymorphisms (SNPs) of the cytochrome P450 enzyme 1A2 gene (CYP1A2) have been reported. Here, frequencies, linkage disequilibrium and phenotypic consequences of six SNPs are described. Methods From genomic DNA, 114 British Caucasians (49 colorectal cancer cases and 65 controls) were genotyped for the CYP1A2 polymorphisms −3858G→A (allele CYP1A2*1C), −2464T→delT (CYP1A2*1D), −740T→G (CYP1A2*1E and *1G), −164A→C (CYP1A2*1F), 63C→G (CYP1A2*2), and 1545T→C (alleles CYP1A2*1B, *1G, *1H and *3), using polymerase chain reaction–restriction fragment length polymorphism assays. All patients and controls were phenotyped for CYP1A2 by h.p.l.c. analysis of urinary caffeine metabolites. Results In 114 samples, the most frequent CYP1A2 SNPs were 1545T→C (38.2% of tested chromosomes), −164A→C (CYP1A2*1F, 33.3%) and −2464T→delT (CYP1A2*1D, 4.82%). The SNPs were in linkage disequilibrium: the most frequent constellations were found to be −3858G/−2464T/−740T/−164A/63C/1545T (61.8%), −3858G/−2464T/−740T/−164C/63C/1545C (33.3%), and −3858G/−2464delT/−740T/−164A/63C/1545C (3.51%), with no significant frequency differences between cases and controls. In the phenotype analysis, lower caffeine metabolic ratios were detected in cases than in controls. This was significant in smokers (n = 14, P = 0.020), and in a subgroup of 15 matched case-control pairs (P = 0.007), but it was not significant in nonsmokers (n = 100, P = 0.39). There was no detectable association between CYP1A2 genotype and caffeine phenotype. Conclusions (i) CYP1A2 polymorphisms are in linkage disequilibrium. Therefore, only −164A→C (CYP1A2*1F) and −2464T→delT (CYP1A2*1D) need to be analysed in the routine assessment of CYP1A2 genotype; (ii) in vivo CYP1A2 activity is lower in colorectal cancer patients than in controls, and (iii) CYP1A2 genotype had no effect on phenotype (based on the caffeine metabolite ratio). However, this

  13. Selective observation of starch in a water plant using optical sum-frequency microscopy.

    PubMed

    Miyauchi, Yoshihiro; Sano, Haruyuki; Mirzutani, Goro

    2006-07-01

    The photosynthesis, transfer, and storage of starch are the most important biogenic processes occurring in plants. In order to observe the colorless and transparent starch granules in a plant, a chemical pretreatment such as staining of the starch is currently required, which seriously damages the tissue cells in the plant. We demonstrate that nondestructive chemical analysis of starch granules in a plant can be performed by using optical second-harmonic and sum-frequency microscopy. These techniques for in vivo analysis will provide extremely useful information about saccharides in a plant and can be extended to the analysis of many other materials, from living tissue to semiconductors.

  14. Comparison between Modern Violin Bridge and Baroque Violin Bridge by Photoelastic Observation and Frequency Analysis

    NASA Astrophysics Data System (ADS)

    Matsutani, Akihiro

    2004-05-01

    A comparison between the modern bridge and the baroque bridge of the violin by photoelastic observation was carried out. The relationship between the stress part and the hole is symmetric in the modern and baroque bridges. The measured spectral envelopes of baroque bridges are similar to those of modern bridges in D- or G-strings, and have peaks at a frequency higher than those of modern bridges in E-string. The visualization method as used in this study may provide hints for the design of violin bridges.

  15. Experimental Observation and Computational Analysis of Striations in Electronegative Capacitively Coupled Radio-Frequency Plasmas

    NASA Astrophysics Data System (ADS)

    Liu, Yong-Xin; Schüngel, Edmund; Korolov, Ihor; Donkó, Zoltán; Wang, You-Nian; Schulze, Julian

    2016-06-01

    Self-organized spatial structures in the light emission from the ion-ion capacitive rf plasma of a strongly electronegative gas (CF4 ) are observed experimentally for the first time. Their formation is analyzed and understood based on particle-based kinetic simulations. These "striations" are found to be generated by the resonance between the driving radio frequency and the eigenfrequency of the ion-ion plasma (derived from an analytical model) that establishes a modulation of the electric field, the ion densities, as well as the energy gain and loss processes of electrons in the plasma. The growth of the instability is followed by the numerical simulations.

  16. Experimental Observation and Computational Analysis of Striations in Electronegative Capacitively Coupled Radio-Frequency Plasmas.

    PubMed

    Liu, Yong-Xin; Schüngel, Edmund; Korolov, Ihor; Donkó, Zoltán; Wang, You-Nian; Schulze, Julian

    2016-06-24

    Self-organized spatial structures in the light emission from the ion-ion capacitive rf plasma of a strongly electronegative gas (CF_{4}) are observed experimentally for the first time. Their formation is analyzed and understood based on particle-based kinetic simulations. These "striations" are found to be generated by the resonance between the driving radio frequency and the eigenfrequency of the ion-ion plasma (derived from an analytical model) that establishes a modulation of the electric field, the ion densities, as well as the energy gain and loss processes of electrons in the plasma. The growth of the instability is followed by the numerical simulations. PMID:27391730

  17. Direct observation of photonic jets and corresponding backscattering enhancement at microwave frequencies

    NASA Astrophysics Data System (ADS)

    Zhao, L.; Ong, C. K.

    2009-06-01

    We report the direct observation of photonic nanojets that emerged from the shadow side of a dielectric cylinder illuminated by plane waves in the microwave frequencies (8-13 GHz). Using our recently developed two-dimensional spatial field mapping system, we carried out a point-by-point measurement of both the phase and intensity of spatial electric field distribution inside and around scattering dielectric cylinders. The direct electric field maps confirm the subwavelength waist of the photonic jet. In addition, we also confirmed the superbackscattering enhancement induced by the presence of a particle much smaller than the initial focusing cylinder within the photonic jet.

  18. Veritas Observations of Relativistic Outflows in - and Intermediate-Frequency BL Lac Objects

    NASA Astrophysics Data System (ADS)

    Prokoph, Heike

    2014-03-01

    The majority of blazars detected at very high energies (VHE; E > 100 GeV) are high-frequency-peaked BL Lac objects (HBLs). Low- and intermediate-frequency-peaked BL Lacs (LBLs/IBLs with synchrotron-peak frequencies in the infrared and optical regime) are generally more powerful, more luminous, and have a richer jet environment than HBLs. However, only a handful of these IBL and LBLs have been detected by ground-based gamma-ray telescopes, typically during high-flux states. The VERITAS array has been monitoring five known VHE LBLs/IBLs since 2009: 3C 66A, W Comae, PKS 1424+240, S5 0716+714 and BL Lacertae, with typical exposures of 5-10 hours per year. The results of these long-term observations are presented, including a bright, subhour-scale VHE flare of BL Lacertae in June 2011, the first low-state detections of 3C 66A and W Comae, and the detection and characterization of the IBL B2 1215+30.

  19. Observed frequency-independent torque in flagellar bacterial motors optimizes space exploration.

    PubMed

    Di Salvo, Mario E; Condat, C A

    2012-12-01

    A surprising feature of many bacterial motors is the apparently conserved form of their torque-frequency relation. Experiments indicate that the torque provided by the bacterial rotary motor is approximately constant over a large range of angular speeds. This is observed in both monotrichous and peritrichous bacteria, independently of whether they are propelled by a proton flux or by a Na(+) ion flux. If the relation between angular speed ω and swimming speed is linear, a ω-independent torque implies that the power spent in active motion is proportional to the instantaneous bacterial speed. Using realistic values of the relevant parameters, we show that a constant torque maximizes the volume of the region explored by a bacterium in a resource-depleted medium. Given that nutrients in the ocean are often concentrated in separate, ephemeral patches, we propose that the observed constancy of the torque may be a trait evolved to maximize bacterial survival in the ocean.

  20. Comparison of flood frequency estimates from synthetic and observed data on small drainage areas in Mississippi

    USGS Publications Warehouse

    Colson, B.E.

    1986-01-01

    In 1964 the U.S. Geological Survey in Mississippi expanded the small stream gaging network for collection of rainfall and runoff data to 92 stations. To expedite availability of flood frequency information a rainfall-runoff model using available long-term rainfall data was calibrated to synthesize flood peaks. Results obtained from observed annual peak flow data for 51 sites having 16 yr to 30 yr of annual peaks are compared with the synthetic results. Graphical comparison of the 2, 5, 10, 25, 50, and 100-year flood discharges indicate good agreement. The root mean square error ranges from 27% to 38% and the synthetic record bias from -9% to -18% in comparison with the observed record. The reduced variance in the synthetic results is attributed to use of only four long-term rainfall records and model limitations. The root mean square error and bias is within the accuracy considered to be satisfactory. (Author 's abstract)

  1. Low-frequency Observations of Transient Quasi-periodic Radio Emission from the Solar Atmosphere

    NASA Astrophysics Data System (ADS)

    Sasikumar Raja, K.; Ramesh, R.

    2013-09-01

    We report low-frequency observations of quasi-periodic, circularly polarized, harmonic type III radio bursts whose associated sunspot active regions were located close to the solar limb. The measured periodicity of the bursts at 80 MHz was ≈5.2 s, and their average degree of circular polarization (dcp) was ≈0.12. We calculated the associated magnetic field B (1) using the empirical relationship between the dcp and B for the harmonic type III emission, and (2) from the observed quasi-periodicity of the bursts. Both the methods result in B ≈ 4.2 G at the location of the 80 MHz plasma level (radial distance r ≈ 1.3 R ⊙) in the active region corona.

  2. LOW-FREQUENCY OBSERVATIONS OF TRANSIENT QUASI-PERIODIC RADIO EMISSION FROM THE SOLAR ATMOSPHERE

    SciTech Connect

    Sasikumar Raja, K.; Ramesh, R.

    2013-09-20

    We report low-frequency observations of quasi-periodic, circularly polarized, harmonic type III radio bursts whose associated sunspot active regions were located close to the solar limb. The measured periodicity of the bursts at 80 MHz was ≈5.2 s, and their average degree of circular polarization (dcp) was ≈0.12. We calculated the associated magnetic field B (1) using the empirical relationship between the dcp and B for the harmonic type III emission, and (2) from the observed quasi-periodicity of the bursts. Both the methods result in B ≈ 4.2 G at the location of the 80 MHz plasma level (radial distance r ≈ 1.3 R{sub ☉}) in the active region corona.

  3. LOW-FREQUENCY RADIO OBSERVATIONS OF PICOFLARE CATEGORY ENERGY RELEASES IN THE SOLAR ATMOSPHERE

    SciTech Connect

    Ramesh, R.; Sasikumar Raja, K.; Kathiravan, C.; Satya Narayanan, A.

    2013-01-10

    We report low-frequency (80 MHz) radio observations of circularly polarized non-thermal type I radio bursts ({sup n}oise storms{sup )} in the solar corona whose estimated energy is {approx}10{sup 21} erg. These are the weakest energy release events reported to date in the solar atmosphere. The plot of the distribution of the number of bursts (dN) versus their corresponding peak flux density in the range S to S+dS shows a power-law behavior, i.e., dN {proportional_to} S {sup {gamma}} dS. The power-law index {gamma} is in the range -2.2 to -2.7 for the events reported in the present work. The present results provide independent observational evidence for the existence of picoflare category energy releases in the solar atmosphere which are yet to be explored.

  4. Extended radar observations with the frequency radar domain interferometric imaging (FII) technique

    NASA Astrophysics Data System (ADS)

    Luce, H.; Yamamoto, M.; Fukao, S.; Crochet, M.

    2001-07-01

    In this paper, we present high-resolution observations obtained with the Middle and Upper Atmosphere (MU) radar (Shigaraki, Japan, /34.85°N, /136.10°E) using the frequency radar domain interferometric imaging (FII) technique. This technique has recently been introduced for improving the range resolution capabilities of the mesosphere-stratosphere-troposphere (MST) radars which are limited by their minimum pulse length. The Fourier-based imaging, the Capon method have been performed with 5 equally spaced frequencies between 46.25 and 46.75MHz and with an initial range resolution of 300m. These results have been compared firstly to results obtained using the frequency domain interferometry (FDI) technique with Δf=0.5MHz and, secondly, to results from a classical Doppler beam swinging (DBS) mode applied with a range resolution of 150m. Thin echoing structures could be tracked owing to the improved radar range resolution and some complex structures possibly related to Kelvin Helmholtz instabilities have been detected. Indeed, these structures appeared within the core of a wind shear and were associated with intense vertical wind fluctuations. Moreover, a well-defined thin echo layer was found in an altitude range located below the height of the wind shear. The radar observations have not been fully interpreted yet because the radar configuration was not adapted for this kind of study and because of the lack of complementary information provided by other techniques when the interesting echoing phenomena occurred. However, the results confirm the high potentialities of the FII technique for the study of atmospheric dynamics at small scales.

  5. Observing the Moon at Microwave Frequencies Using a Large-Diameter Deep Space Network Antenna

    NASA Astrophysics Data System (ADS)

    Morabito, David D.; Imbriale, William; Keihm, Stephen

    2008-03-01

    The Moon radiates energy at infrared and microwave wavelengths, in addition to reflecting sunlight at optical wavelengths. As a result, an antenna pointed at or near the Moon will result in an increase in system operating noise temperature, which needs to be accounted for in RF telecommunications, radio science or radiometric link calculations. The NASA Deep Space Network (DSN) may use its large-diameter antennas in future lunar robotic or human missions, and thus it is important to understand the nature of this temperature incre ase as a function of observing frequency, lunar phase, and angular position of the antenna beam on the lunar disk. This paper reports on a comprehensive lunar noise temperature measurement campaign and associated theoretical treatment for a 34-m diameter Deep Space Network antenna observing an extended source such as the Moon. A set of measurements over a wide range of lunar phase angles was acquired at DSS-13, a 34-m diameter beam waveguide antenna (BWG) located at Goldstone, California at 2.3 GHz (S-band), 8.4 GHz (X-band) and 32 GHz (Ka-band). For validation purposes, independent predictions of noise temperature increase were derived using a physical optics characterization of the 34-m diameter antenna gain patterns and Apollo model-based brightness temperature maps of the Moon as input. The model-based predictions of noise temperature increase were compared with the measurements at all three frequencies. In addition, a methodology is presented that relates noise temperature increase due to the Moon to disk-centered or disk-averaged brightness temperature of the Moon at the microwave frequencies of interest. Comparisons were made between the measurements and models in the domain of lunar disk-centered and disk-averaged brightness temperatures. It is anticipated that the measurements and associated theoretical development will be useful in developing telecommunications strategies for future high-rate Ka-band communications where large

  6. A hypervariable STR polymorphism in the CFI gene: southern origin of East Asian-specific group H alleles.

    PubMed

    Yuasa, Isao; Jin, Feng; Harihara, Shinji; Matsusue, Aya; Fujihara, Junko; Takeshita, Haruo; Akane, Atsushi; Umetsu, Kazuo; Saitou, Naruya; Chattopadhyay, Prasanta K

    2013-09-01

    Previous studies of four populations revealed that a hypervariable short tandem repeat (iSTR) in intron 7 of the human complement factor I (CFI) gene on chromosome 4q was unique, with 17 possible East Asian-specific group H alleles observed at relatively high frequencies. To develop a deeper anthropological and forensic understanding of iSTR, 1161 additional individuals from 11 Asian populations were investigated. Group H alleles of iSTR and c.1217A allele of a SNP in exon 11 of the CFI gene were associated with each other and were almost entirely confined to East Asian populations. Han Chinese in Changsha, southern China, showed the highest frequency for East Asian-specific group H alleles (0.201) among 15 populations. Group H alleles were observed to decrease gradually from south to north in 11 East Asian populations. This expansion of group H alleles provides evidence that southern China and Southeast Asia are a hotspot of Asian diversity and a genetic reservoir of Asians after they entered East Asia. The expected heterozygosity values of iSTR ranged from 0.927 in Thais to 0.874 in Oroqens, higher than those of an STR in the fibrinogen alpha chain (FGA) gene on chromosome 4q. Thus, iSTR is a useful marker for anthropological and forensic genetics.

  7. Observations of λ /4 structure in a low-loss radio-frequency-dressed optical lattice

    NASA Astrophysics Data System (ADS)

    Lundblad, N.; Ansari, S.; Guo, Y.; Moan, E.

    2014-11-01

    We load a Bose-Einstein condensate into a one-dimensional (1D) optical lattice altered through the use of radio-frequency (rf) dressing. The rf resonantly couples the three levels of the 87Rb F =1 manifold and combines with a spin-dependent "bare" optical lattice to result in adiabatic potentials of variable shape, depth, and spatial frequency content. We choose dressing parameters such that the altered lattice is stable over lifetimes exceeding tens of ms at higher depths than in previous work. We observe significant differences between the BEC momentum distributions of the dressed lattice as compared to the bare lattice, and find general agreement with a 1D band-structure calculation informed by the dressing parameters. Previous work using such lattices was limited by very shallow dressed lattices and strong Landau-Zener tunneling loss between adiabatic potentials, equivalent to failure of the adiabatic criterion. In this work we operate with significantly stronger rf coupling (increasing the avoided-crossing gap between adiabatic potentials), observing dressed lifetimes of interest for optical lattice-based analog solid-state physics.

  8. High spatial resolution radar observations of ultralow frequency waves in the southern polar cap

    NASA Astrophysics Data System (ADS)

    Bland, Emma C.; McDonald, Andrew J.

    2016-05-01

    We present an analysis of ultralow frequency (ULF) waves detected in the southern polar cap using the Super Dual Auroral Radar Network (SuperDARN). These waves manifest as quasi-sinusoidal oscillations in the Doppler velocity, which arise due to the oscillating ULF wave electric field in the F region ionosphere. The event reported in this study occurred during the southern polar winter under quiet geomagnetic conditions. The 1.1-1.3 mHz oscillations were observed throughout the polar cap by the McMurdo, Dome C East, and South Pole Station SuperDARN radars and also by the Dome Concordia and Scott Base magnetometers at corrected geomagnetic latitudes of ˜89°S and ˜80°S, respectively. In contrast to large-scale toroidal field line resonances observed at auroral latitudes, we find that the magnetic perturbation vector of the polar cap oscillations did not undergo a 90° rotation upon transmission from the ionosphere to the ground and was instead rotated by about 30°. The polar cap oscillations were also accompanied by simultaneous field line resonance (FLR) activity in the dayside auroral zone, in the field of view of the Zhongshan SuperDARN radar. This FLR occurred at the same frequency and exhibited a similar azimuthal phase velocity to the polar cap oscillations, indicating that they may have been driven by the same source mechanism.

  9. Comparison of Model Predictions and Laboratory Observations of Transgene Frequencies in Continuously-Breeding Mosquito Populations.

    PubMed

    Valerio, Laura; North, Ace; Collins, C Matilda; Mumford, John D; Facchinelli, Luca; Spaccapelo, Roberta; Benedict, Mark Q

    2016-01-01

    The persistence of transgenes in the environment is a consideration in risk assessments of transgenic organisms. Combining mathematical models that predict the frequency of transgenes and experimental demonstrations can validate the model predictions, or can detect significant biological deviations that were neither apparent nor included as model parameters. In order to assess the correlation between predictions and observations, models were constructed to estimate the frequency of a transgene causing male sexual sterility in simulated populations of a malaria mosquito Anopheles gambiae that were seeded with transgenic females at various proportions. Concurrently, overlapping-generation laboratory populations similar to those being modeled were initialized with various starting transgene proportions, and the subsequent proportions of transgenic individuals in populations were determined weekly until the transgene disappeared. The specific transgene being tested contained a homing endonuclease gene expressed in testes, I-PpoI, that cleaves the ribosomal DNA and results in complete male sexual sterility with no effect on female fertility. The transgene was observed to disappear more rapidly than the model predicted in all cases. The period before ovipositions that contained no transgenic progeny ranged from as little as three weeks after cage initiation to as long as 11 weeks. PMID:27669312

  10. Field observation of low-to-mid-frequency acoustic propagation characteristics of an estuarine salt wedge.

    PubMed

    Reeder, D Benjamin

    2016-01-01

    The estuarine environment often hosts a salt wedge, the stratification of which is a function of the tide's range and speed of advance, river discharge volumetric flow rate, and river mouth morphology. Competing effects of temperature and salinity on sound speed in this stratified environment control the degree of acoustic refraction occurring along an acoustic path. A field experiment was carried out in the Columbia River Estuary to test the hypothesis: the estuarine salt wedge is acoustically observable in terms of low-to-mid-frequency acoustic propagation. Linear frequency-modulated acoustic signals in the 500-2000 Hz band were transmitted during the advance and retreat of the salt wedge during May 27-29, 2013. Results demonstrate that the salt wedge front is the dominant physical mechanism controlling acoustic propagation in this environment: received signal energy is relatively stable before and after the passage of the salt wedge front when the acoustic path consists of a single medium (either entirely fresh water or entirely salt water), and suffers a 10-15 dB loss and increased variability during salt wedge front passage. Physical parameters and acoustic propagation modeling corroborate and inform the acoustic observations. PMID:26827001

  11. Comparison of Model Predictions and Laboratory Observations of Transgene Frequencies in Continuously-Breeding Mosquito Populations.

    PubMed

    Valerio, Laura; North, Ace; Collins, C Matilda; Mumford, John D; Facchinelli, Luca; Spaccapelo, Roberta; Benedict, Mark Q

    2016-01-01

    The persistence of transgenes in the environment is a consideration in risk assessments of transgenic organisms. Combining mathematical models that predict the frequency of transgenes and experimental demonstrations can validate the model predictions, or can detect significant biological deviations that were neither apparent nor included as model parameters. In order to assess the correlation between predictions and observations, models were constructed to estimate the frequency of a transgene causing male sexual sterility in simulated populations of a malaria mosquito Anopheles gambiae that were seeded with transgenic females at various proportions. Concurrently, overlapping-generation laboratory populations similar to those being modeled were initialized with various starting transgene proportions, and the subsequent proportions of transgenic individuals in populations were determined weekly until the transgene disappeared. The specific transgene being tested contained a homing endonuclease gene expressed in testes, I-PpoI, that cleaves the ribosomal DNA and results in complete male sexual sterility with no effect on female fertility. The transgene was observed to disappear more rapidly than the model predicted in all cases. The period before ovipositions that contained no transgenic progeny ranged from as little as three weeks after cage initiation to as long as 11 weeks.

  12. Allelic distribution of CCR5 and CCR2 genes in an Italian population sample.

    PubMed

    Romano-Spica, V; Ianni, A; Arzani, D; Cattarini, L; Majore, S; Dean, M

    2000-01-20

    Genetic polymorphisms of CCR5 and CCR2 human chemokine receptors have been associated with resistance during HIV-1 infection and disease progression. The protective effect of mutant alleles at these loci has important implications in AIDS pathogenesis. Chemokine receptors have a role in viral entry into target cells as well as in immune response modulation. In the present report, we studied the frequency of CCR5delta32 and CCR264I allelic variants among a representative sample of the Italian population. Observed allelic frequencies were 0.0454 and 0.0655, respectively. In both cases, genotype distribution was in equilibrium as predicted by the Hardy-Weinberg equation. Taken as a whole, about 21% of the population sample was found to be heterozygous for one or another of those two mutated alleles. Distribution of CCR5delta32 and CCR264I allelic variants within a population can be considered as a measure of genetic susceptibility to HIV infection and disease progression. PMID:10659048

  13. Analysis and Design of Robust H∞ Fault Estimation Observer With Finite-Frequency Specifications for Discrete-Time Fuzzy Systems.

    PubMed

    Zhang, Ke; Jiang, Bin; Shi, Peng; Xu, Jinfa

    2015-07-01

    This paper addresses the problem of fault estimation observer design with finite-frequency specifications for discrete-time Takagi-Sugeno (T-S) fuzzy systems. First, for such T-S fuzzy models, an H∞ fault estimation observer with pole-placement constraint is proposed to achieve fault estimation. Based on the generalized Kalman-Yakubovich-Popov lemma, the given finite-frequency observer possesses less conservatism compared with the design of the entire-frequency domain. Furthermore, the performance of the presented fault estimation observer is further enhanced by adding the degree of freedom. Finally, two examples are presented to illustrate the effectiveness of the proposed strategy.

  14. Two prevalent h alleles in para-Bombay haplotypes among 250,000 Taiwanese.

    PubMed

    Chen, Ding-Ping; Tseng, Ching-Ping; Wang, Wei-Ting; Peng, Chien-Ting; Tsao, Kuo-Chien; Wu, Tsu-Lan; Lin, Kuan-Tsou; Sun, Chien-Feng

    2004-01-01

    Alpha(1,2)-fucosyltransferase catalyzes the transfer of fucose to the C-2 position of galactose on type II precursor substrate Gal beta1-4GlcNAc beta1-R. It plays an important biological role in the formation of H antigen, a precursor oligosaccharide for both A and B antigens on red blood cells. Aberration of alpha(1,2)-fucosyltransferase activity by gene mutations results in decreased synthesis of H antigen, leading to the para-Bombay phenotype. In this study, we collected about 250,000 blood samples in Taiwan during 5 yr and identified the subjects with para-Bombay phenotype. Then we analyzed the sequence of the alpha(1,2)-fucosyltransferase gene by direct sequencing and gene cloning methods, using the blood samples of 30 para-Bombay individuals and 30 control subjects who were randomly selected. The goals of this study were to search for new h alleles, to determine the h allele frequencies, and to test whether the sporadic theory is applicable in Taiwan. Six different h alleles (ha, 547-548 AG-del; hb, 880-881 TT-del; hc, R220C; hd, R220H; he, F174L; and hf, N327T) were observed. Two h alleles, he and hf, were newly discovered in Taiwan. The he allele has a nucleotide 522C>A point mutation, predicting the amino acid 174 substitution of Phe to Leu; the hf allele has missense mutation of nucleotide 980A>C, predicting the amino acid 327 substitution of Asn to Thr. Frequencies of the 6 alleles are ha 46.67%, hb 38.33%, hc 5.00%, hd 1.67%, he 3.33%, and hf 5.00%, respectively. These findings in the Taiwanese population confirm previous observations in other populations that the Bombay and para-Bombay phenotypes are due to diverse, sporadic, nonfunctional alleles, predominantly ha and hb, leading to H deficiency of red blood cells. In contrast to previous reports of non-prevalent associations of h alleles with para-Bombay phenotype, our results suggest a regional allele preference associated with para-Bombay individuals in Taiwan.

  15. Sea level measurements using multi-frequency GPS and GLONASS observations

    NASA Astrophysics Data System (ADS)

    Löfgren, Johan S.; Haas, Rüdiger

    2014-12-01

    Global Positioning System (GPS) tide gauges have been realized in different configurations, e.g., with one zenith-looking antenna, using the multipath interference pattern for signal-to-noise ratio (SNR) analysis, or with one zenith- and one nadir-looking antenna, analyzing the difference in phase delay, to estimate the sea level height. In this study, for the first time, we use a true Global Navigation Satellite System (GNSS) tide gauge, installed at the Onsala Space Observatory. This GNSS tide gauge is recording both GPS and Globalnaya Navigatsionnaya Sputnikovaya Sistema (GLONASS) signals and makes it possible to use both the one- and two-antenna analysis approach. Both the SNR analysis and the phase delay analysis were evaluated using dual-frequency GPS and GLONASS signals, i.e., frequencies in the L-band, during a 1-month-long campaign. The GNSS-derived sea level results were compared to independent sea level observations from a co-located pressure tide gauge and show a high correlation for both systems and frequency bands, with correlation coefficients of 0.86 to 0.97. The phase delay results show a better agreement with the tide gauge sea level than the SNR results, with root-mean-square differences of 3.5 cm (GPS L1 and L2) and 3.3/3.2 cm (GLONASS L1/L2 bands) compared to 4.0/9.0 cm (GPS L1/L2) and 4.7/8.9 cm (GLONASS L1/L2 bands). GPS and GLONASS show similar performance in the comparison, and the results prove that for the phase delay analysis, it is possible to use both frequencies, whereas for the SNR analysis, the L2 band should be avoided if other signals are available. Note that standard geodetic receivers using code-based tracking, i.e., tracking the un-encrypted C/A-code on L1 and using the manufacturers' proprietary tracking method for L2, were used. Signals with the new C/A-code on L2, the so-called L2 C , were not tracked. Using wind speed as an indicator for sea surface roughness, we find that the SNR analysis performs better in rough sea

  16. Near-field Observations of Very-low-frequency Earthquakes on the San Andreas Fault

    NASA Astrophysics Data System (ADS)

    Peña-Castro, A. F.; Harrington, R. M.; Cochran, E. S.

    2015-12-01

    Fault rupture at varying time scales has been detected in multiple subduction zones, e.g., in slow-slip events (SSEs), very-low-frequency earthquakes (VLFEs), and low-frequency earthquakes (LFEs) or tectonic tremor. However, only LFEs or tremor have been identified and studied in detail along strike-slip faults, like the San Andreas Fault (SAF). Here, we present evidence for VLFEs on the SAF near Parkfield, California. Using data from permanent broadband stations and a temporary deployment of 13 broadband stations installed in 2010-2011 near Cholame, California, we detect 5 VLFEs, with 1 VLFE occurring unambiguosly when there is visible tremor activity. We check that the signals we detect are local by confirming that they appear only on stations within a 70 km radius, and removing time periods when teleseismic events occur, as identified in the global Centroid Moment Tensor (CMT) and the Northern California Seismic Network (NCSN) catalogs. VLFEs have to-date been observed to only occur simultaneously in time and space with tremor activity, but our detections suggests that VLFEs can occur independent of tremor along strike-slip faults. This may indicate that the slipping patches that produce slow earthquakes in transform faults have different mechanical properties than the patches in subducting plates, althought it does not rule out that VLFEs are only observed with tremor in subduction zones simply due to detection methods. An approximate estimation of the apparent velocity, based on a grid-search location using variance reduction, suggests that the observed phase velocity of the VLFEs is ~ 3km/s, corresponding to surface waves. We perform a focal mechanism inversion with a grid search to find a more precise location, depth and orientation of the VLFEs. These results provide new insight into the behavior of the SAF and more generally contribute to an improved understanding of transform fault systems.

  17. Allelic Diversity of MSP1 Gene in Plasmodium falciparum from Rural and Urban Areas of Gabon.

    PubMed

    Mawili-Mboumba, Denise Patricia; Mbondoukwe, Noé; Adande, Elvire; Bouyou-Akotet, Marielle Karine

    2015-08-01

    The present study determined and compared the genetic diversity of Plasmodium falciparum strains infecting children living in 2 areas from Gabon with different malaria endemicity. Blood samples were collected from febrile children from 2008 to 2009 in 2 health centres from rural (Oyem) and urban (Owendo) areas. Genetic diversity was determined in P. falciparum isolates by analyzing the merozoite surface protein-1 (msp1) gene polymorphism using nested-PCR. Overall, 168 children with mild falciparum malaria were included. K1, Ro33, and Mad20 alleles were found in 110 (65.5%), 94 (55.9%), and 35 (20.8%) isolates, respectively, without difference according to the site (P>0.05). Allelic families' frequencies were comparable between children less than 5 years old from the 2 sites; while among the older children the proportions of Ro33 and Mad20 alleles were 1.7 to 2.0 fold higher at Oyem. Thirty-three different alleles were detected, 16 (48.5%) were common to both sites, and 10 out of the 17 specific alleles were found at Oyem. Furthermore, multiple infection carriers were frequent at Oyem (57.7% vs 42.2% at Owendo; P=0.04) where the complexity of infection was of 1.88 (±0.95) higher compared to that found at Owendo (1.55±0.75). Extended genetic diversity of P. falciparum strains infecting Gabonese symptomatic children and high multiplicity of infections were observed in rural area. Alleles common to the 2 sites were frequent; the site-specific alleles predominated in the rural area. Such distribution of the alleles should be taken into accounts when designing MSP1 or MSP2 malaria vaccine.

  18. Phenotypic instability of Arabidopsis alleles affecting a disease Resistance gene cluster

    PubMed Central

    Yi, Hankuil; Richards, Eric J

    2008-01-01

    Background Three mutations in Arabidopsis thaliana strain Columbia – cpr1, snc1, and bal – map to the RPP5 locus, which contains a cluster of disease Resistance genes. The similar phenotypes, gene expression patterns, and genetic interactions observed in these mutants are related to constitutive activation of pathogen defense signaling. However, these mutant alleles respond differently to various conditions. Exposure to mutagens, such as ethyl methanesulfonate (EMS) and γ-irradiation, induce high frequency phenotypic instability of the bal allele. In addition, a fraction of the bal and cpr1 alleles segregated from bal × cpr1 F1 hybrids also show signs of phenotypic instability. To gain more insight into the mechanism of phenotypic instability of the bal and cpr1 mutations, we systematically compared the behavior of these unusual alleles with that of the missense gain-of-function snc1 allele in response to DNA damage or passage through F1 hybrids. Results We found that the cpr1 allele is similar to the bal allele in its unstable behavior after EMS mutagenesis. For both the bal and cpr1 mutants, destabilization of phenotypes was observed in more than 10% of EMS-treated plants in the M1 generation. In addition, exceptions to simple Mendelian inheritance were identified in the M2 generation. Like cpr1 × bal F1 hybrids, cpr1 × snc1 F1 hybrids and bal × snc1 F1 hybrids exhibited dwarf morphology. While only dwarf F2 plants were produced from bal × snc1 F1 hybrids, about 10% wild-type F2 progeny were produced from cpr1 × snc1 F1 hybrids, as well as from cpr1 × bal hybrids. Segregation analysis suggested that the cpr1 allele in cpr1 × snc1 crosses was destabilized during the late F1 generation to early F2 generation. Conclusion With exposure to EMS or different F1 hybrid contexts, phenotypic instability is induced for the bal and cpr1 alleles, but not for the snc1 allele. Our results suggest that the RPP5 locus can adopt different metastable genetic or

  19. First Frequency-Domain Interferometry Observations of Large-Scale Vertical Motion in the Atmosphere.

    NASA Astrophysics Data System (ADS)

    Muschinski, Andreas; Chilson, Phillip B.; Kern, Stefan; Nielinger, Jost; Schmidt, Gerhard; Prenosil, Thomas

    1999-05-01

    The spatiotemporal distribution of the vertical velocity at synoptic and subsynoptic scales is key to the patterns of weather and climate on earth. On these scales, the vertical velocity is on the order of one to a few centimeters per second, typically about three orders of magnitude smaller than typical horizontal wind velocities. Because of the smallness of large-scale vertical velocities relative to typical horizontal velocities, a direct observation of the large-scale vertical air velocity is extremely difficult.In a case study on observational material obtained during a 68-h experiment using the SOUSY very high frequency (VHF) radar in the Harz Mountains in Germany, the authors present the first intercomparison between three different sources of physical information that can provide large-scale vertical wind velocities: (i) the Doppler shifts observed with a vertically pointing VHF radar; (ii) the rates of change of the altitudes of refractive-index discontinuities as identified with frequency-domain interferometry (FDI), which is still a relatively unexplored technique in meteorology; and (iii) the output of a regional numerical weather prediction model (NWPM), which has been set up to model the meteorological situation during the observational period.There are several phenomena that have been known to possibly cause significant biases in mean vertical velocities retrieved from the Doppler shifts measured with vertically pointing clear-air VHF radars: (i) stationary or nonstationary gravity waves with vertical-velocity amplitudes up to the order of 1 m s1; (ii) stationary or horizontally advected tilted refractive-index discontinuities that are aspect sensitive in the VHF regime; and (iii) a correlation between the radar-reflectivity fluctuations and the vertical-velocity fluctuations within a vertically propagating gravity wave.On the basis of an intercomparison between the vertical velocities retrieved from (i) `standard Doppler' VHF radar observations, (ii

  20. Influence of HLA DRB1 alleles in the susceptibility of rheumatoid arthritis and the regulation of antibodies against citrullinated proteins and rheumatoid factor

    PubMed Central

    2010-01-01

    Introduction The purpose of this study was to investigate the association between HLA-DRB1 alleles with susceptibility to rheumatoid arthritis (RA) and production of antibodies against citrullinated proteins (ACPA) and rheumatoid factor (RF). Methods We studied 408 patients (235 with RA, 173 non-RA) and 269 controls. ACPA, RF and HLA-DR typing were determined. Results We found an increased frequency of HLA DRB1 alleles with the shared epitope (SE) in ACPA-positive RA. Inversely, HLA DRB1 alleles encoding DERAA sequences were more frequent in controls than in ACPA-positive RA, and a similar trend was found for HLA DR3. However, these results could not be confirmed after stratification for the presence of the SE, probably due to the relatively low number of patients. These data may suggest that the presence of these alleles may confer a protective role for ACPA-positive RA. In RA patients we observed association between SE alleles and ACPA titers in a dose-dependent effect. The presence of HLA DR3 or DERAA-encoding alleles was associated with markedly reduced ACPA levels. No association between RF titers and HLA DR3 or DERAA-encoding alleles was found. Conclusions HLA DRB1 alleles with the SE are associated with production of ACPA. DERAA-encoding HLA-DR alleles and HLA DR3 may be protective for ACPA-positive RA. PMID:20370905

  1. Paternal-specific S-allele transmission in sweet cherry (Prunus avium L.): the potential for sexual selection.

    PubMed

    Hedhly, A; Wünsch, A; Kartal, Ö; Herrero, M; Hormaza, J I

    2016-03-01

    Homomorphic self-incompatibility is a well-studied example of a physiological process that is thought to increase population diversity and reduce the expression of inbreeding depression. Whereas theoretical models predict the presence of a large number of S-haplotypes with equal frequencies at equilibrium, unequal allele frequencies have been repeatedly reported and attributed to sampling effects, population structure, demographic perturbation, sheltered deleterious mutations or selection pressure on linked genes. However, it is unclear to what extent unequal segregations are the results of gametophytic or sexual selection. Although these two forces are difficult to disentangle, testing S-alleles in the offspring of controlled crosses provides an opportunity to separate these two phenomena. In this work, segregation and transmission of S-alleles have been characterized in progenies of mixed donors and fully compatible pollinations under field conditions in Prunus avium. Seed set patterns and pollen performance have also been characterized. The results reveal paternal-specific distorted transmission of S-alleles in most of the crosses. Interestingly, S-allele segregation within any given paternal or maternal S-locus was random. Observations on pollen germination, pollen tube growth rate, pollen tube cohort size, seed set dynamics and transmission patterns strongly suggest post-pollination, prezygotic sexual selection, with male-male competition as the most likely mechanism. According to these results, post-pollination sexual selection takes precedence over frequency-dependent selection in explaining unequal S-haplotype frequencies.

  2. Evidence of low frequency waves penetration in the ionosphere observed by Chibis-M satellite

    NASA Astrophysics Data System (ADS)

    Pronenko, Vira; Dudkin, Fedir; Korepanov, Valery

    2016-07-01

    Chibis-M microsatellite (MS) was launched using ISS infrastructure to the 500 km circular orbit with inclination 52° and successfully operated during the years 2012-2014. One of the main tasks of this experiment was the study of how powerful natural and technogenic processes are reflected in the ionosphere. For this study, the magnetic wave complex (MWC) was used which measured one electrical component and three components of the magnetic vector in the frequency range 0.1 Hz-40 kHz. Due to the proximity of the magnetic sensors and the satellite control system, their high sensitivity (up to 0.02 pT/sqrt(Hz)) was not used in full because the level of magnetic noise was about 10 pT/sqrt(Hz) in the low-frequency range. Nevertheless, owing to the symmetric fixation of the electric probes relative to the satellite body, the electrical sensor provided high accuracy measurements (about 0.8-0.04 (µV/m)/sqrt(Hz)) in the frequency range of 0.1-40 000 Hz, despite the very small measurement base of 0.42 m. This allowed us to collect valuable information which revealed a number of interesting physical effects, especially in ultralow frequency (ULF) range. In ULF range the ionospheric emissions with a central frequency of 50 (60) Hz - power line emissions (PLE) and the Schumann resonance harmonics (SR) were detected, though, according to the present model of the ionosphere, they have not penetrate there. A detailed study of the obtained data revealed the features of PLE and SR. The spatial distribution of PLE and their connection with the power lines location on the ground were analyzed. It was found that the intensity of PLE depends on the load characteristics of the power line and usually has a minimum in the morning. The cases of an extra long distance of PLE propagation in the Earth's ionosphere over oceans in the equatorial region have been also observed. Further, it was detected that PLE has been recorded both in the shaded and sunlit parts of the orbits and their

  3. Observations on the Reliability of Rubidium Frequency Standards on Block 2/2A GPS Satellites

    NASA Technical Reports Server (NTRS)

    Dieter, Gary L.

    1996-01-01

    Currently, the block 2/2A Global Positioning System (GPS) satellites are equipped with two rubidium frequency standards. These frequency standards were originally intended to serve as the back-ups to two cesium frequency standards. As the constellation ages, the master Control Station is forced to initialize and increasing number or rubidium frequency standards. Unfortunately the operational use of these frequency standards has not lived up to initial expectations. Although the performance of these rubidium frequency standards has met and even exceeded GPS requirements, their reliability has not. The number of unscheduled outage times and the short operational lifetimes of the rubidium frequency standards compare poorly to the track record of the cesium frequency standards. Only a small number of rubidium frequency standards have actually been made operational. Of these, a large percentage have exhibited poor reliability. If this trend continues, it is unlikely that the rubidium frequency standards will help contribute to the navigation payload meeting program specification.

  4. MESSENGER Magnetic Field Observations of Upstream Ultra-Low Frequency Waves at Mercury

    NASA Technical Reports Server (NTRS)

    Le, G.; Chi, P. J.; Boardsen, S.; Blanco-Cano, X.; Anderosn, B. J.; Korth, H.

    2012-01-01

    The region upstream from a planetary bow shock is a natural plasma laboratory containing a variety of wave particle phenomena. The study of foreshocks other than the Earth's is important for extending our understanding of collisionless shocks and foreshock physics since the bow shock strength varies with heliocentric distance from the Sun, and the sizes of the bow shocks are different at different planets. The Mercury's bow shock is unique in our solar system as it is produced by low Mach number solar wind blowing over a small magnetized body with a predominately radial interplanetary magnetic field. Previous observations of Mercury upstream ultra-low frequency (ULF) waves came exclusively from two Mercury flybys of Mariner 10. The MESSENGER orbiter data enable us to study of upstream waves in the Mercury's foreshock in depth. This paper reports an overview of upstream ULF waves in the Mercury's foreshock using high-time resolution magnetic field data, 20 samples per second, from the MESSENGER spacecraft. The most common foreshock waves have frequencies near 2 Hz, with properties similar to the I-Hz waves in the Earth's foreshock. They are present in both the flyby data and in every orbit of the orbital data we have surveyed. The most common wave phenomenon in the Earth's foreshock is the large-amplitude 30-s waves, but similar waves at Mercury have frequencies at near 0.1 Hz and occur only sporadically with short durations (a few wave cycles). Superposed on the "30-s" waves, there are spectral peaks at near 0.6 Hz, not reported previously in Mariner 10 data. We will discuss wave properties and their occurrence characteristics in this paper.

  5. Developments of frequency comb microwave reflectometer for the interchange mode observations in LHD plasma

    NASA Astrophysics Data System (ADS)

    Soga, R.; Tokuzawa, T.; Watanabe, K. Y.; Tanaka, K.; Yamada, I.; Inagaki, S.; Kasuya, N.

    2016-02-01

    We have upgraded the multi-channel microwave reflectometer system which uses a frequency comb as a source and measure the distribution of the density fluctuation caused by magneto-hydro dynamics instability. The previous multi-channel system was composed of the Ka-band, and the U-band system has been developed. Currently, the U-band system has eight frequency channels, which are 43.0, 45.0, 47.0, 49.0, 51.0, 53.0, 55.0, and 57.0 GHz, in U-band. Before the installation to the Large Helical Device (LHD), several tests for understanding the system characteristics, which are the phase responsibility, the linearity of output signal, and others, have been carried out. The in situ calibration in LHD has been done for the cross reference. In the neutral beam injected plasma experiments, we can observe the density fluctuation of the interchange mode and obtain the radial distribution of fluctuation amplitude.

  6. Electromagnetic waves with frequencies near the local proton gyrofrequency: ISEE-3 1 AU observations

    NASA Technical Reports Server (NTRS)

    Tsurutani, Bruce T.; Arballo, John K.; Mok, John; Smith, Edward J.; Mason, Glenn M.; Tan, Lun C.

    1994-01-01

    Low Frequency (LF) electromagnetic waves with periods near the local proton gyrofrequency have been detected in interplanetary space by the magnetometer onboard International-Sun-Earth-Explorer-3 (ISEE-3). Transverse peak-to-peak amplitudes as large as delta vector B/absolute value of B approximately 0.4 have been noted with compressional components (Delta absolute value of B/absolute value of B) typically less than or = 0.1. Generally, the waves have even smaller amplitudes, or are not detectable within the solar wind turbulence. The waves are elliptically/linearly polarized and are often, but not always, found to propagate nearly along vector B(sub zero). Both right- and left-hand polarizations in the spacecraft-frame have been detected. The waves are observed during all orientations of the interplanetary magnetic field, with the Parker spiral orientation being the most common case. Because the waves are detected at and near the local proton cyclotron frequency, the generation mechanism must almost certainly be solar wind pickup of freshly created hydrogen ions. Possible sources for the hydrogen are the Earth's atmosphere, coronal mass ejections from the Sun, comets and interstellar neutral atoms. At this time it is not obvious which potential source is the correct one. Statistical tests employing over one year of ISEE-3 data will be done in the near future to eliminate/confirm some of these possibilities.

  7. Spectral analysis of temperature and Brunt-Vaisala frequency fluctuations observed by radiosondes

    NASA Technical Reports Server (NTRS)

    Tsuda, T.; Vanzandt, T. E.; Kato, S.; Fukao, S.; Sato, T.

    1989-01-01

    Recent studies have revealed that vertical wave number spectra of wind velocity and temperture fluctuations in the troposphere and the lower stratosphere are fairly well explained by a saturated gravity wave spectrum. But N(2) (N:Brunt-Vaisala (BV) frequency) spectra seem to be better for testing the scaling of the vertical wave number spectra in layers with different stratifications, beause its energy density is proportional only to the background value of N(2), while that for temperature depends on both the BV frequency and the potential temperature. From temperature profiles observed in June to August 1987 over the MU Observatory, Japan, by using a radiosonde with 30 m height resolution, N(2) spectra are determined in the 2 to 8.5 km (troposphere) and 18.5 to 25 km (lower stratosphere) ranges. Although individual spectra show fairly large day-by-day variability, the slope of the median of 34 spectra agrees reasonably with the theoretical value of -1 in the wave number range of 6 x 10(-4) similar to 3 x 10(-3) (c/m). The ratio of the spectral energy between these two height regions is about equal to the ratio of N(2), consistent with the prediction of saturated gravity wave theory.

  8. Observations of coronal mass ejections (CMEs) at low frequency radio region on 15th April 2012

    NASA Astrophysics Data System (ADS)

    Hamidi, Z. S.; Abidin, Z. Z.; Ibrahim, Z. A.; Shariff, N. N. M.; Monstein, C.

    2013-05-01

    We have carried out a case study on Coronal Mass Ejections (CMEs) as a massive burst of solar wind and magnetic fields rising above the solar corona. During 15th April 2012, solar filament eruption was accompanied by intense CMEs. This explosion of CMEs observed by the Solar Dynamics Observatory with sunspot AR1458 is crackling with C-class solar flares. Solar flare type B3 and C2 were observed beginning 2241 UT and 0142 UT in the active region AR1458. In the present work, we focus in the range of the low frequency region from 150 MHz to 400 MHz. At preliminary stage, starting from 12.00 UT till 1.00 UT there is a strong signal which indicates a formation of burst. Type II burst originated from solar corona can be observed in the range of 150 MHz to 230 MHz. Instead of type II, a moving type IV and continuum type III burst can be detected at 150 MHz and lasting for 1 hours. This event is considered as second largest CMEs been detected since five (5) years. We can then conclude that currently, the Sun is in the phase of gradually increase to reach maximum 24th solar cycle.

  9. Multiyear high-frequency physical and environmental observations at the Guadiana Estuary

    NASA Astrophysics Data System (ADS)

    Garel, E.; Ferreira, Ó.

    2015-07-01

    High-frequency data collected continuously over a multiyear time frame are required for investigating the various agents that drive ecological and hydrodynamic processes in estuaries. Here, we present water quality and current in-situ observations from a fixed monitoring station operating from 2008 to 2014 in the lower Guadiana Estuary, southern Portugal (37°11.30' N, 7°24.67' W). The data were recorded by: a multi-parametric probe providing hourly records of temperature, chlorophyll, dissolved oxygen, turbidity, and pH at a water depth of ~ 1 m; and, a bottom-mounted acoustic Doppler current profiler measuring the pressure, near-bottom temperature, and flow velocity through the water column every 15 min. The time-series, in particular the probe one, present substantial data gaps arising from equipment failure and maintenance, which are ineluctable with this type of observations in harsh environments. However, prolonged (months-long) periods of observations during contrasted external forcing conditions are available. The raw data are reported together with quality flags indicating the status (valid/non-valid) of each record. Hourly river discharge data from two hydrographic stations located near the estuary head are also provided to support data analysis and interpretation. The dataset is publicly available at PANGAEA (doi:10.1594/PANGAEA.845750) in machine-readable format.

  10. Multi-year high-frequency physical and environmental observations at the Guadiana Estuary

    NASA Astrophysics Data System (ADS)

    Garel, E.; Ferreira, Ó.

    2015-11-01

    High-frequency data collected continuously over a multi-year time frame are required for investigating the various agents that drive ecological and hydrodynamic processes in estuaries. Here, we present water quality and current in situ observations from a fixed monitoring station operating from 2008 to 2014 in the lower Guadiana Estuary, southern Portugal (37°11.30' N, 7°24.67' W). The data were recorded by a multi-parametric probe providing hourly records (temperature, salinity, chlorophyll, dissolved oxygen, turbidity, and pH) at a water depth of ~ 1 m, and by a bottom-mounted acoustic Doppler current profiler measuring the pressure, near-bottom temperature, and flow velocity through the water column every 15 min. The time series data, in particular the probe ones, present substantial gaps arising from equipment failure and maintenance, which are ineluctable with this type of observation in harsh environments. However, prolonged (months-long) periods of multi-parametric observations during contrasted external forcing conditions are available. The raw data are reported together with flags indicating the quality status of each record. River discharge data from two hydrographic stations located near the estuary head are also provided to support data analysis and interpretation. The data set is publicly available in machine-readable format at PANGAEA (doi:10.1594/PANGAEA.845750).

  11. MAVEN observation of an obliquely propagating low-frequency wave upstream of Mars

    NASA Astrophysics Data System (ADS)

    Ruhunusiri, Suranga; Halekas, J. S.; Connerney, J. E. P.; Espley, J. R.; McFadden, J. P.; Mazelle, C.; Brain, D.; Collinson, G.; Harada, Y.; Larson, D. E.; Mitchell, D. L.; Livi, R.; Jakosky, B. M.

    2016-03-01

    We report Mars Atmosphere and Volatile EvolutioN mission observations of a large amplitude low-frequency plasma wave that propagated oblique to the ambient magnetic field upstream of Mars along with a non-solar-wind plasma component that had a flow velocity perpendicular to the magnetic field. We consider nine possibilities for this wave that include various combinations of its propagation direction, polarization in the solar wind frame, and ion source responsible for its generation. Using the observed wave parameters and the measured plasma parameters as constraints, we uniquely identify the wave by systematically discarding these possibilities. We determine that the wave is a right-hand polarized wave that propagated upstream in the solar wind frame. We find two possibilities for the ion source that can be responsible for this wave generation. They are either newly born pickup protons or reflected solar wind protons from the bow shock. We determine that the observed non-solar-wind component is not responsible for the wave generation, and it is likely that the non-solar-wind component was merely perturbed by the passage of the wave.

  12. Core damage frequency observations and insights of LWRs based on the IPEs

    SciTech Connect

    Dingman, S.E.; Camp, A.L.; Drouin, M.T.

    1995-04-01

    Seventy-eight plants are expected to submit Individual Plant Examinations (IPEs) for severe accident vulnerabilities to the US Nuclear Regulatory Commission (NRC). The majority of the plants have elected to perform full Level 1 probabilistic risk assessments (PRAs) to meet the intent of the IPEs. Because of this, it is possible to compare the results from the IPE submittals to determine general observations and {open_quotes}lessons learned{close_quotes} from the IPEs. The IPE Insights Program is performing this evaluation, and preliminary results are presented in this paper. The core damage frequency and core damage sequences are identified and compared for pressurized water reactors and boiling water reactors. Examination of the results indicates that variations among plant results are due to a combination of actual plant design/operational features and analysis approaches. The findings are consistent with previous NRC studies, such as WASH-1400 and NUREG-1150.

  13. Direct observation of frequency modulated transcription in single cells using light activation

    PubMed Central

    Larson, Daniel R; Fritzsch, Christoph; Sun, Liang; Meng, Xiuhau; Lawrence, David S; Singer, Robert H

    2013-01-01

    Single-cell analysis has revealed that transcription is dynamic and stochastic, but tools are lacking that can determine the mechanism operating at a single gene. Here we utilize single-molecule observations of RNA in fixed and living cells to develop a single-cell model of steroid-receptor mediated gene activation. We determine that steroids drive mRNA synthesis by frequency modulation of transcription. This digital behavior in single cells gives rise to the well-known analog dose response across the population. To test this model, we developed a light-activation technology to turn on a single steroid-responsive gene and follow dynamic synthesis of RNA from the activated locus. DOI: http://dx.doi.org/10.7554/eLife.00750.001 PMID:24069527

  14. Observation of ICRF (ion cyclotron range of frequencies) wave-packet propagation in a tokamak plasma

    SciTech Connect

    Greene, G.J.; Gould, R.W.

    1987-11-01

    Experimental observation of ICRF wave-packet propagation in a tokamak plasma is reported. Studies were carried out in the Caltech Research Tokamak in a pure hydrogen plasma and in a regime where fast-wave damping was sufficiently small to permit multiple toroidal transits of the wave-packet. Waves were launched by exciting a small loop antenna with a short burst of rf current and were detected with shielded magnetic probes. Probe scans revealed a large increase in wave-packet amplitude at smaller minor radii, and the packet velocity was found to be independent of radial position. Measurement of the packet transit time yielded direct information about the wave group velocity. Packet velocity was investigated as a function of the fundamental excitation frequency, plasma density, and toroidal magnetic field. Results are compared with the predictions of a cold plasma model which includes a vacuum layer at the edge. 24 refs., 8 figs.

  15. Observation of the Mating Behavior of Honey Bee (Apis mellifera L.) Queens Using Radio-Frequency Identification (RFID): Factors Influencing the Duration and Frequency of Nuptial Flights.

    PubMed

    Heidinger, Ina Monika Margret; Meixner, Marina Doris; Berg, Stefan; Büchler, Ralph

    2014-07-01

    We used radio-frequency identification (RFID) to record the duration and frequency of nuptial flights of honey bee queens (Apis mellifera carnica) at two mainland mating apiaries. We investigated the effect of a number of factors on flight duration and frequency: mating apiary, number of drone colonies, queen's age and temperature. We found significant differences between the two locations concerning the number of flights on the first three days. We also observed an effect of the ambient temperature, with queens flying less often but longer at high temperatures compared to lower temperatures. Increasing the number of drone colonies from 33 to 80 colonies had no effect on the duration or on the frequency of nuptial flights. Since our results agree well with the results of previous studies, we suggest RFID as an appropriate tool to investigate the mating behavior of honey bee queens.

  16. Observation of the Mating Behavior of Honey Bee (Apis mellifera L.) Queens Using Radio-Frequency Identification (RFID): Factors Influencing the Duration and Frequency of Nuptial Flights.

    PubMed

    Heidinger, Ina Monika Margret; Meixner, Marina Doris; Berg, Stefan; Büchler, Ralph

    2014-01-01

    We used radio-frequency identification (RFID) to record the duration and frequency of nuptial flights of honey bee queens (Apis mellifera carnica) at two mainland mating apiaries. We investigated the effect of a number of factors on flight duration and frequency: mating apiary, number of drone colonies, queen's age and temperature. We found significant differences between the two locations concerning the number of flights on the first three days. We also observed an effect of the ambient temperature, with queens flying less often but longer at high temperatures compared to lower temperatures. Increasing the number of drone colonies from 33 to 80 colonies had no effect on the duration or on the frequency of nuptial flights. Since our results agree well with the results of previous studies, we suggest RFID as an appropriate tool to investigate the mating behavior of honey bee queens. PMID:26462822

  17. Observation of the Mating Behavior of Honey Bee (Apis mellifera L.) Queens Using Radio-Frequency Identification (RFID): Factors Influencing the Duration and Frequency of Nuptial Flights

    PubMed Central

    Heidinger, Ina Monika Margret; Meixner, Marina Doris; Berg, Stefan; Büchler, Ralph

    2014-01-01

    We used radio-frequency identification (RFID) to record the duration and frequency of nuptial flights of honey bee queens (Apis mellifera carnica) at two mainland mating apiaries. We investigated the effect of a number of factors on flight duration and frequency: mating apiary, number of drone colonies, queen’s age and temperature. We found significant differences between the two locations concerning the number of flights on the first three days. We also observed an effect of the ambient temperature, with queens flying less often but longer at high temperatures compared to lower temperatures. Increasing the number of drone colonies from 33 to 80 colonies had no effect on the duration or on the frequency of nuptial flights. Since our results agree well with the results of previous studies, we suggest RFID as an appropriate tool to investigate the mating behavior of honey bee queens. PMID:26462822

  18. CCN frequency distributions and aerosol chemical composition from long-term observations at European ACTRIS supersites

    NASA Astrophysics Data System (ADS)

    Decesari, Stefano; Rinaldi, Matteo; Schmale, Julia Yvonne; Gysel, Martin; Fröhlich, Roman; Poulain, Laurent; Henning, Silvia; Stratmann, Frank; Facchini, Maria Cristina

    2016-04-01

    Cloud droplet number concentration is regulated by the availability of aerosol acting as cloud condensation nuclei (CCN). Predicting the air concentrations of CCN involves knowledge of all physical and chemical processes that contribute to shape the particle size distribution and determine aerosol hygroscopicity. The relevance of specific atmospheric processes (e.g., nucleation, coagulation, condensation of secondary organic and inorganic aerosol, etc.) is time- and site-dependent, therefore the availability of long-term, time-resolved aerosol observations at locations representative of diverse environments is strategic for the validation of state-of-the-art chemical transport models suited to predict CCN concentrations. We focused on long-term (year-long) datasets of CCN and of aerosol composition data including black carbon, and inorganic as well as organic compounds from the Aerosol Chemical Speciation Monitor (ACSM) at selected ACTRIS supersites (http://www.actris.eu/). We discuss here the joint frequency distribution of CCN levels and of aerosol chemical components concentrations for two stations: an alpine site (Jungfraujoch, CH) and a central European rural site (Melpitz, DE). The CCN frequency distributions at Jungfraujoch are broad and generally correlated with the distributions of the concentrations of aerosol chemical components (e.g., high CCN concentrations are most frequently found for high organic matter or black carbon concentrations, and vice versa), which can be explained as an effect of the strong seasonality in the aerosol characteristics at the mountain site. The CCN frequency distributions in Melpitz show a much weaker overlap with the distributions of BC concentrations or other chemical compounds. However, especially at high CCN concentration levels, a statistical correlation with organic matter (OM) concentration can be observed. For instance, the number of CCN (with particle diameter between 20 and 250 nm) at a supersaturation of 0.7% is

  19. Dynamics of Adaptive Alleles in Divergently Selected Body Weight Lines of Chickens

    PubMed Central

    Pettersson, Mats E.; Johansson, Anna M.; Siegel, Paul B.; Carlborg, Örjan

    2013-01-01

    By studying genomic changes over time in populations subjected to strong artificial directional selection, we can gain insights to the dynamics of beneficial alleles originating from the founder population or emerging as novel mutations undergoing ongoing selection. The Virginia lines are a chicken resource population generated by long-term bi-directional, single-trait selection for juvenile body weight. We studied genome-wide allele frequency changes from generation 40 to 53 using genome-wide genotypes from directional and relaxed selection lines. Overall, there were small changes in allele frequencies at individual loci over the studied time period; but, on average, the changes were greater in lines with larger phenotypic changes. This is consistent with previous findings that much of the response to selection over the first 40 years of selection was attributable to utilization of standing genetic variation at many loci in the genome, indicating a mostly polygenic architecture for body weight. Over the course of the selection experiment, the largest phenotypic response to selection was observed in the high-weight selected line, and in this line we detected a single locus where the allele frequency changed rapidly during a late stage of the experiment. This locus likely contains a novel, beneficial mutation that appeared between generations 40 and 45 and was driven to fixation in 5 to 10 generations. This result illustrates the dependence of continued long-term selection response on standing genetic variation at many loci as well as strong, novel, beneficial mutations. PMID:24170737

  20. Global Survey and Statistics of Radio-Frequency Interference in AMSR-E Land Observations

    NASA Technical Reports Server (NTRS)

    Njoku, Eni G.; Ashcroft, Peter; Chan, Tsz K.; Li, Li

    2005-01-01

    Radio-frequency interference (RFI) is an increasingly serious problem for passive and active microwave sensing of the Earth. To satisfy their measurement objectives, many spaceborne passive sensors must operate in unprotected bands, and future sensors may also need to operate in unprotected bands. Data from these sensors are likely to be increasingly contaminated by RFI as the spectrum becomes more crowded. In a previous paper we reported on a preliminary investigation of RFI observed over the United States in the 6.9-GHz channels of the Advanced Microwave Scanning Radiometer (AMSR-E) on the Earth Observing System Aqua satellite. Here, we extend the analysis to an investigation of RFI in the 6.9- and 10.7-GHz AMSR-E channels over the global land domain and for a one-year observation period. The spatial and temporal characteristics of the RFI are examined by the use of spectral indices. The observed RFI at 6.9 GHz is most densely concentrated in the United States, Japan, and the Middle East, and is sparser in Europe, while at 10.7 GHz the RFI is concentrated mostly in England, Italy, and Japan. Classification of RFI using means and standard deviations of the spectral indices is effective in identifying strong RFI. In many cases, however, it is difficult, using these indices, to distinguish weak RFI from natural geophysical variability. Geophysical retrievals using RFI-filtered data may therefore contain residual errors due to weak RFI. More robust radiometer designs and continued efforts to protect spectrum allocations will be needed in future to ensure the viability of spaceborne passive microwave sensing.

  1. Runoff-generated debris flows: observations and modeling of surge initiation, magnitude, and frequency

    USGS Publications Warehouse

    Kean, Jason W.; McCoy, Scott W.; Tucker, Gregory E.; Staley, Dennis M.; Coe, Jeffrey A.

    2013-01-01

    Runoff during intense rainstorms plays a major role in generating debris flows in many alpine areas and burned steeplands. Yet compared to debris flow initiation from shallow landslides, the mechanics by which runoff generates a debris flow are less understood. To better understand debris flow initiation by surface water runoff, we monitored flow stage and rainfall associated with debris flows in the headwaters of two small catchments: a bedrock-dominated alpine basin in central Colorado (0.06 km2) and a recently burned area in southern California (0.01 km2). We also obtained video footage of debris flow initiation and flow dynamics from three cameras at the Colorado site. Stage observations at both sites display distinct patterns in debris flow surge characteristics relative to rainfall intensity (I). We observe small, quasiperiodic surges at low I; large, quasiperiodic surges at intermediate I; and a single large surge followed by small-amplitude fluctuations about a more steady high flow at high I. Video observations of surge formation lead us to the hypothesis that these flow patterns are controlled by upstream variations in channel slope, in which low-gradient sections act as “sediment capacitors,” temporarily storing incoming bed load transported by water flow and periodically releasing the accumulated sediment as a debris flow surge. To explore this hypothesis, we develop a simple one-dimensional morphodynamic model of a sediment capacitor that consists of a system of coupled equations for water flow, bed load transport, slope stability, and mass flow. This model reproduces the essential patterns in surge magnitude and frequency with rainfall intensity observed at the two field sites and provides a new framework for predicting the runoff threshold for debris flow initiation in a burned or alpine setting.

  2. Solar Observations at THz Frequencies on Board of a Trans-Antartic Stratospheric Balloon Flight

    NASA Astrophysics Data System (ADS)

    Kaufmann, Pierre; Abrantes, André; Bortolucci, Emilio; Caspi, Amir; Fernandes, Luis Olavo T.; Kropotov, Grigory; Kudaka, Amauri; Laurent, Glenn Thomas; Machado, Nelson; Marcon, Rogério; Marun, Adolfo; Nicolaev, Valery; Hidalgo Ramirez, Ray Fernando; Raulin, Jean-Pierre; Saint-Hilaire, Pascal; Shih, Albert; Silva, Claudemir; Timofeevsky, Alexander

    2016-05-01

    Sub-THz and 30 THz solar burst observations revealed a new spectral component, with fluxes increasing towards THz frequencies, simultaneously with the well known component peaking at microwaves, bringing challenging constraints for interpretation. The THz flare spectra can be completed with measurements made from space. A new system of two photometers was built to observe the Sun at 3 and 7 THz named SOLAR-T. An innovative optical setup allows observations of the full solar disk and detect small burst with sub-second time resolution. The photometers use two Golay cell detectors at the foci of 7.6 cm Cassegrain telescopes. The incoming radiation undergoes low-pass filters made of rough surface primary mirrors and membranes, 3 and 7 THz band-pass filters, and choppers. The system has been integrated to redundant data acquisition system and Iridium short-burst data services telemetry for monitoring during the flight. SOLAR-T has been flown coupled to U.C. Berkeley solar hard X-ray and gamma-ray imaging spectro-polarimeter GRIPS experiment launched on a NASA CSBF stratospheric balloon from U.S. McMurdo base on January 19, 2016, on a trans-Antarctic flight. The mission ended on January 30. The SOLAR-T on-board computers were recovered from the payload that landed in the Argentina Mountain Range, nearly 2100 km from McMurdo. The SOLAR-T performance was successfully attained, with full space qualification instrumentation. Preliminary results provide the solar disk THz brightness temperatures and indicate a 7 THz burst enhancement time coincident to a sub-THz burst observed by SST during the 28 January GOES C9.6 class soft X-ray burst, the largest occurred during the flight.

  3. Runoff-generated debris flows: Observations and modeling of surge initiation, magnitude, and frequency

    NASA Astrophysics Data System (ADS)

    Kean, Jason W.; McCoy, Scott W.; Tucker, Gregory E.; Staley, Dennis M.; Coe, Jeffrey A.

    2013-12-01

    during intense rainstorms plays a major role in generating debris flows in many alpine areas and burned steeplands. Yet compared to debris flow initiation from shallow landslides, the mechanics by which runoff generates a debris flow are less understood. To better understand debris flow initiation by surface water runoff, we monitored flow stage and rainfall associated with debris flows in the headwaters of two small catchments: a bedrock-dominated alpine basin in central Colorado (0.06 km2) and a recently burned area in southern California (0.01 km2). We also obtained video footage of debris flow initiation and flow dynamics from three cameras at the Colorado site. Stage observations at both sites display distinct patterns in debris flow surge characteristics relative to rainfall intensity (I). We observe small, quasiperiodic surges at low I; large, quasiperiodic surges at intermediate I; and a single large surge followed by small-amplitude fluctuations about a more steady high flow at high I. Video observations of surge formation lead us to the hypothesis that these flow patterns are controlled by upstream variations in channel slope, in which low-gradient sections act as "sediment capacitors," temporarily storing incoming bed load transported by water flow and periodically releasing the accumulated sediment as a debris flow surge. To explore this hypothesis, we develop a simple one-dimensional morphodynamic model of a sediment capacitor that consists of a system of coupled equations for water flow, bed load transport, slope stability, and mass flow. This model reproduces the essential patterns in surge magnitude and frequency with rainfall intensity observed at the two field sites and provides a new framework for predicting the runoff threshold for debris flow initiation in a burned or alpine setting.

  4. Mesospheric potassium layer observation by a frequency-tunable resonance scattering lidar system

    NASA Astrophysics Data System (ADS)

    Ejiri, Mitsumu K.; Nakamura, Takuji; Kawahara, Takuya D.; Abo, Makoto; Nishiyama, Takanori; Tsuda, Takuo T.

    J/pulse at approximately 25 Hz (i.e., ~3-4 W) and the backscattered signal is received with a 83 cm (or 35 cm) diameter telescope. Three-frequency wind/temperature measurement method [She and Yu, 1994] is applied to measurement of K density and temperature profiles and the wavelengths of laser pulse are calibrated by an assumption that 1-hour mean of measured vertical wind speed is zero m/s. In this talk, current status of the system developments and the observation results of K density and temperature in the mid-latitude will be presented.

  5. High frequency water quality and flow observations of a hypereutrophic Coastal Plain millpond

    NASA Astrophysics Data System (ADS)

    Andres, S.; Ullman, W. J.; Voynova, Y. G.

    2014-12-01

    Eutrophication due to runoff of N and P occurs in many impoundments in agricultural areas around the world with deleterious impacts on fisheries, drinking water, and recreational resources. Coursey Pond, a hypereutrophic, shallow, Coastal Plain mill pond located on the Murderkill River in central Delaware has seasonal algal blooms between May and October. High frequency automated water quality, meteorlogical, and flow observations initiated in June 2014 as part of the NEWRNet project provide insights into the relationships between hydrologic events, changes in water quality, and primary productivity. During blooms the pond becomes stratified, allowing for dissolved oxygen (DO) levels at the surface to exceed 150% saturation, while DO within 2 m of the surface to falls below 50% saturation. During fair weather turbidity and dissolved organic carbon (DOC) also gradually rise. Turbidity, DOC, and DO quickly decrease in response to storms and increased flow, indicating that storms are important regulators of water column stratification. Decreases in primary productivity due to decreased sunlight, dilution by addition of rain and runoff, and mixing in response to storm winds and flows abruptly end blooms, although they often return within a few days of storm events. Analysis of hourly meterological data will help determine the importance of solar insolation, winds, and rainfall intensity to the timing, rate, and magnitude of these water quality changes. Groundwater is the primary source of water to the streams that feed the pond and delivers nitrogen as nitrate. Historical grab sample nitrate concentration data from summer months (<1 mg/L) in comparison to winter months (4-8 mg/L) indicate that primary productivity consumes nearly all available nitrate during algal blooms, and perhaps improving water quality in downstream areas. There is no clear relationship between storms, flow and nitrate in the short period of high frequency observations, when nitrate concentrations

  6. HLA-A, HLA-B, and HLA-DRB1 allele distribution in a large Armenian population sample.

    PubMed

    Matevosyan, L; Chattopadhyay, S; Madelian, V; Avagyan, S; Nazaretyan, M; Hyussian, A; Vardapetyan, E; Arutunyan, R; Jordan, F

    2011-07-01

    Human leukocyte antigen (HLA)-A, HLA-B, and HLA-DRB1 gene frequencies were investigated in 4279 unrelated Armenian bone marrow donors. HLA alleles were defined by using PCR amplification with sequence specific primers (PCR-SSP) high- and low-resolution kits. The aim of this study was to examine the HLA diversity at the high-resolution level in a large Armenian population sample, and to compare HLA allele group distribution in Armenian subpopulations. The most frequently observed alleles in the HLA class I were HLA-A*0201, A*0101, A*2402, A*0301, HLA-B*5101, HLA-B*3501, and B*4901. Among DRB1 alleles, high frequencies of DRB1*1104 and DRB1*1501 were observed, followed by DRB1*1101 and DRB1*1401. The most common three-locus haplotype found in the Armenian population was A*33-B*14-DRB1*01, followed by A*03-B*35-DRB1*01. Our results show a similar distribution of alleles in Armenian subpopulations from different countries, and from different regions of the Republics of Armenia and Karabagh. The low level of genetic distances between subpopulations indicates a high level of population homogeneity, and the genetic distances between Armenians and other populations show Armenians as a distinct ethnic group relative to others, reflecting the fact that Armenians have been an 'isolated population' throughout centuries. This study is the first comprehensive investigation of HLA-allele group distribution in a subset of Armenian populations, and the first to provide HLA-allele and haplotype frequencies at a high-resolution level. It is a valuable reference for organ transplantation and for future studies of HLA-associated diseases in Armenian populations.

  7. Identification of new primer binding site mutations at TH01 and D13S317 loci and determination of their corresponding STR alleles by allele-specific PCR.

    PubMed

    Li, Fengrui; Xuan, Jinfeng; Xing, Jiaxin; Ding, Mei; Wang, Baojie; Pang, Hao

    2014-01-01

    Several commercial multiplex PCR kits for the amplification of short tandem repeat (STR) loci have been extensively applied in forensic genetics. Consequently, large numbers of samples have been genotyped, and the number of discordant genotypes observed has also increased. We observed allele dropout with two novel alleles at the STR loci TH01 and D13S317 during paternity testing using the AmpFℓSTR Identifiler PCR Amplification Kit. The lost alleles reappeared when alternative PCR primer pairs were used. A sequence analysis revealed a G-to-A substitution 82 bases downstream of the last TCAT motif of the repeat region at the TH01 locus (GenBank accession: D00269) and a G-to-T substitution 90 bases upstream of the first TATC motif of the repeat region at the D13S317 locus (GenBank accession: G09017). The frequencies of these two point mutations were subsequently investigated in the Chinese population using sequence-specific primer PCR (SSP-PCR), but neither of these mutations was detected in any of the samples tested. In addition, the DNA samples in which the mutations were identified were amplified to type the point mutations by SSP-PCR to determine the corresponding STR alleles at the two loci. Subsequently, the amplified PCR products with different point mutations and STR repeat numbers were directly sequenced because this strategy overcomes the appearance overlapping peaks generated by different STR alleles and accurately characterizes genotypes. Thus, our findings not only provide useful information for DNA databases and forensic identification but also establish an effective strategy for typing STR alleles with primer binding site mutations.

  8. Gamma Ray and Very Low Frequency Radio Observations from a Balloon-Borne Platform

    NASA Astrophysics Data System (ADS)

    Quinn, C.; Sheldon, A.; Cully, C. M.; Davalos, A.; Osakwe, C.; Galts, D.; Delfin, J.; Duffin, C.; Mansell, J.; Russel, M.; Bootsma, M.; Williams, R.; Patrick, M.; Mazzino, M. L.; Knudsen, D. J.

    2015-12-01

    The University of Calgary's Student Organization for Aerospace Research (SOAR) built an instrument to participate in the High Altitude Student Platform (HASP) initiative organized by Louisiana State University and supported by the NASA Balloon Program Office (BPO) and the Louisiana Space Consortium (LaSPACE). The HASP platform will be launched in early September 2015 from Fort Sumner, New Mexico and will reach heights of 36 kilometers with a flight duration of 15 to 20 hours. The instrument, Atmospheric Phenomenon Observer Gamma/VLF Emissions Experiment (APOGEE), measures Terrestrial Gamma-Ray Flashes (TGF) and sferics from lightning strikes with the use of Geiger tubes and a VLF detector. TGFs, which are quick bursts of high energy radiation that can occur alongside lightning, are believed to be the result of Relativistic Runaway Electron Avalanche (RREA). RREA occurs when a large number of relativistic electrons overcome atmospheric frictional forces and accelerate to relativistic velocities which excite secondary electrons that collide with the atmosphere causing bremsstrahlung radiation. Lightning strikes also produce sferics within the Extremely Low Frequency (ELF) and Very Low Frequency (VLF) bands which can be detected and used to locate the strikes. The goal of APOGEE is to further investigate the link between TGFs and RREA. These phenomena are very difficult to measure together as Bremsstrahlung radiation is easily detected from space but ionospheric reflection facilitates surface detection of sferics. A high altitude balloon provides a unique opportunity to study both phenomena using one instrument because both phenomena can easily be detected from its altitude. APOGEE has been designed and built by undergraduate students at the University of Calgary with faculty assistance and funding, and is equipped with three devices for data collection: a camera to have visual conformation of events, a series of Geiger Tubes to obtain directional gamma readings, and

  9. High frequency variations of Earth Rotation Parameters from GPS and GLONASS observations.

    PubMed

    Wei, Erhu; Jin, Shuanggen; Wan, Lihua; Liu, Wenjie; Yang, Yali; Hu, Zhenghong

    2015-01-28

    The Earth's rotation undergoes changes with the influence of geophysical factors, such as Earth's surface fluid mass redistribution of the atmosphere, ocean and hydrology. However, variations of Earth Rotation Parameters (ERP) are still not well understood, particularly the short-period variations (e.g., diurnal and semi-diurnal variations) and their causes. In this paper, the hourly time series of Earth Rotation Parameters are estimated using Global Positioning System (GPS), Global Navigation Satellite System (GLONASS), and combining GPS and GLONASS data collected from nearly 80 sites from 1 November 2012 to 10 April 2014. These new observations with combining different satellite systems can help to decorrelate orbit biases and ERP, which improve estimation of ERP. The high frequency variations of ERP are analyzed using a de-trending method. The maximum of total diurnal and semidiurnal variations are within one milli-arcseconds (mas) in Polar Motion (PM) and 0.5 milli-seconds (ms) in UT1-UTC. The semidiurnal and diurnal variations are mainly related to the ocean tides. Furthermore, the impacts of satellite orbit and time interval used to determinate ERP on the amplitudes of tidal terms are analyzed. We obtain some small terms that are not described in the ocean tide model of the IERS Conventions 2010, which may be caused by the strategies and models we used or the signal noises as well as artifacts. In addition, there are also small differences on the amplitudes between our results and IERS convention. This might be a result of other geophysical excitations, such as the high-frequency variations in atmospheric angular momentum (AAM) and hydrological angular momentum (HAM), which needs more detailed analysis with more geophysical data in the future.

  10. High frequency variations of Earth Rotation Parameters from GPS and GLONASS observations.

    PubMed

    Wei, Erhu; Jin, Shuanggen; Wan, Lihua; Liu, Wenjie; Yang, Yali; Hu, Zhenghong

    2015-01-01

    The Earth's rotation undergoes changes with the influence of geophysical factors, such as Earth's surface fluid mass redistribution of the atmosphere, ocean and hydrology. However, variations of Earth Rotation Parameters (ERP) are still not well understood, particularly the short-period variations (e.g., diurnal and semi-diurnal variations) and their causes. In this paper, the hourly time series of Earth Rotation Parameters are estimated using Global Positioning System (GPS), Global Navigation Satellite System (GLONASS), and combining GPS and GLONASS data collected from nearly 80 sites from 1 November 2012 to 10 April 2014. These new observations with combining different satellite systems can help to decorrelate orbit biases and ERP, which improve estimation of ERP. The high frequency variations of ERP are analyzed using a de-trending method. The maximum of total diurnal and semidiurnal variations are within one milli-arcseconds (mas) in Polar Motion (PM) and 0.5 milli-seconds (ms) in UT1-UTC. The semidiurnal and diurnal variations are mainly related to the ocean tides. Furthermore, the impacts of satellite orbit and time interval used to determinate ERP on the amplitudes of tidal terms are analyzed. We obtain some small terms that are not described in the ocean tide model of the IERS Conventions 2010, which may be caused by the strategies and models we used or the signal noises as well as artifacts. In addition, there are also small differences on the amplitudes between our results and IERS convention. This might be a result of other geophysical excitations, such as the high-frequency variations in atmospheric angular momentum (AAM) and hydrological angular momentum (HAM), which needs more detailed analysis with more geophysical data in the future. PMID:25635416

  11. High Frequency Variations of Earth Rotation Parameters from GPS and GLONASS Observations

    PubMed Central

    Wei, Erhu; Jin, Shuanggen; Wan, Lihua; Liu, Wenjie; Yang, Yali; Hu, Zhenghong

    2015-01-01

    The Earth's rotation undergoes changes with the influence of geophysical factors, such as Earth's surface fluid mass redistribution of the atmosphere, ocean and hydrology. However, variations of Earth Rotation Parameters (ERP) are still not well understood, particularly the short-period variations (e.g., diurnal and semi-diurnal variations) and their causes. In this paper, the hourly time series of Earth Rotation Parameters are estimated using Global Positioning System (GPS), Global Navigation Satellite System (GLONASS), and combining GPS and GLONASS data collected from nearly 80 sites from 1 November 2012 to 10 April 2014. These new observations with combining different satellite systems can help to decorrelate orbit biases and ERP, which improve estimation of ERP. The high frequency variations of ERP are analyzed using a de-trending method. The maximum of total diurnal and semidiurnal variations are within one milli-arcseconds (mas) in Polar Motion (PM) and 0.5 milli-seconds (ms) in UT1-UTC. The semidiurnal and diurnal variations are mainly related to the ocean tides. Furthermore, the impacts of satellite orbit and time interval used to determinate ERP on the amplitudes of tidal terms are analyzed. We obtain some small terms that are not described in the ocean tide model of the IERS Conventions 2010, which may be caused by the strategies and models we used or the signal noises as well as artifacts. In addition, there are also small differences on the amplitudes between our results and IERS convention. This might be a result of other geophysical excitations, such as the high-frequency variations in atmospheric angular momentum (AAM) and hydrological angular momentum (HAM), which needs more detailed analysis with more geophysical data in the future. PMID:25635416

  12. Associations of HLA-A, HLA-B and HLA-C Alleles Frequency with Prevalence of Herpes Simplex Virus Infections and Diseases Across Global Populations: Implication for the Development of an Universal CD8+ T-Cell Epitope-Based Vaccine

    PubMed Central

    Samandary, Sarah; Kridane-Miledi, Hédia; Sandoval, Jacqueline S.; Choudhury, Zareen; Langa-Vives, Francina; Spencer, Doran; Chentoufi, Aziz A.; Lemonnier, François A.; BenMohamed, Lbachir

    2014-01-01

    A significant portion of the world’s population is infected with herpes simplex virus type 1 and/or type 2 (HSV-1 and/or HSV-2), that cause a wide range of diseases including genital herpes, oro-facial herpes, and the potentially blinding ocular herpes. While the global prevalence and distribution of HSV-1 and HSV-2 infections cannot be exactly established, the general trends indicate that: (i) HSV-1 infections are much more prevalent globally than HSV-2; (ii) Over half billion people worldwide are infected with HSV-2; (iii) the sub-Saharan African populations account for a disproportionate burden of genital herpes infections and diseases; (iv) the dramatic differences in the prevalence of herpes infections between regions of the world appear to be associated with differences in the frequencies of human leukocyte antigen (HLA) alleles. The present report: (i) analyzes the prevalence of HSV-1 and HSV-2 infections across various regions of the world; (ii) analyzes potential associations of common HLA-A, HLA-B and HLA-C alleles with the prevalence of HSV-1 and HSV-2 infections in the Caucasoid, Oriental, Hispanic and Black major populations; and (iii) discusses how our recently developed HLA-A, HLA-B, and HLA-C transgenic/H-2 class I null mice will help validate HLA/herpes prevalence associations. Overall, high prevalence of herpes infection and disease appears to be associated with high frequency of HLA-A*24, HLA-B*27, HLA-B*53 and HLA-B*58 alleles. In contrast, low prevalence of herpes infection and disease appears to be associated with high frequency of HLA-B*44 allele. The finding will aid in developing a T-cell epitope-based universal herpes vaccine and immunotherapy. PMID:24798939

  13. Associations of HLA-A, HLA-B and HLA-C alleles frequency with prevalence of herpes simplex virus infections and diseases across global populations: implication for the development of an universal CD8+ T-cell epitope-based vaccine.

    PubMed

    Samandary, Sarah; Kridane-Miledi, Hédia; Sandoval, Jacqueline S; Choudhury, Zareen; Langa-Vives, Francina; Spencer, Doran; Chentoufi, Aziz A; Lemonnier, François A; BenMohamed, Lbachir

    2014-08-01

    A significant portion of the world's population is infected with herpes simplex virus type 1 and/or type 2 (HSV-1 and/or HSV-2), that cause a wide range of diseases including genital herpes, oro-facial herpes, and the potentially blinding ocular herpes. While the global prevalence and distribution of HSV-1 and HSV-2 infections cannot be exactly established, the general trends indicate that: (i) HSV-1 infections are much more prevalent globally than HSV-2; (ii) over a half billion people worldwide are infected with HSV-2; (iii) the sub-Saharan African populations account for a disproportionate burden of genital herpes infections and diseases; (iv) the dramatic differences in the prevalence of herpes infections between regions of the world appear to be associated with differences in the frequencies of human leukocyte antigen (HLA) alleles. The present report: (i) analyzes the prevalence of HSV-1 and HSV-2 infections across various regions of the world; (ii) analyzes potential associations of common HLA-A, HLA-B and HLA-C alleles with the prevalence of HSV-1 and HSV-2 infections in the Caucasoid, Oriental, Hispanic and Black major populations; and (iii) discusses how our recently developed HLA-A, HLA-B, and HLA-C transgenic/H-2 class I null mice will help validate HLA/herpes prevalence associations. Overall, high prevalence of herpes infection and disease appears to be associated with high frequency of HLA-A(∗)24, HLA-B(∗)27, HLA-B(∗)53 and HLA-B(∗)58 alleles. In contrast, low prevalence of herpes infection and disease appears to be associated with high frequency of HLA-B(∗)44 allele. The finding will aid in developing a T-cell epitope-based universal herpes vaccine and immunotherapy. PMID:24798939

  14. Associations of HLA-A, HLA-B and HLA-C alleles frequency with prevalence of herpes simplex virus infections and diseases across global populations: implication for the development of an universal CD8+ T-cell epitope-based vaccine.

    PubMed

    Samandary, Sarah; Kridane-Miledi, Hédia; Sandoval, Jacqueline S; Choudhury, Zareen; Langa-Vives, Francina; Spencer, Doran; Chentoufi, Aziz A; Lemonnier, François A; BenMohamed, Lbachir

    2014-08-01

    A significant portion of the world's population is infected with herpes simplex virus type 1 and/or type 2 (HSV-1 and/or HSV-2), that cause a wide range of diseases including genital herpes, oro-facial herpes, and the potentially blinding ocular herpes. While the global prevalence and distribution of HSV-1 and HSV-2 infections cannot be exactly established, the general trends indicate that: (i) HSV-1 infections are much more prevalent globally than HSV-2; (ii) over a half billion people worldwide are infected with HSV-2; (iii) the sub-Saharan African populations account for a disproportionate burden of genital herpes infections and diseases; (iv) the dramatic differences in the prevalence of herpes infections between regions of the world appear to be associated with differences in the frequencies of human leukocyte antigen (HLA) alleles. The present report: (i) analyzes the prevalence of HSV-1 and HSV-2 infections across various regions of the world; (ii) analyzes potential associations of common HLA-A, HLA-B and HLA-C alleles with the prevalence of HSV-1 and HSV-2 infections in the Caucasoid, Oriental, Hispanic and Black major populations; and (iii) discusses how our recently developed HLA-A, HLA-B, and HLA-C transgenic/H-2 class I null mice will help validate HLA/herpes prevalence associations. Overall, high prevalence of herpes infection and disease appears to be associated with high frequency of HLA-A(∗)24, HLA-B(∗)27, HLA-B(∗)53 and HLA-B(∗)58 alleles. In contrast, low prevalence of herpes infection and disease appears to be associated with high frequency of HLA-B(∗)44 allele. The finding will aid in developing a T-cell epitope-based universal herpes vaccine and immunotherapy.

  15. Preliminary Analysis of Observations on the Ultra-Low Frequency Electric Field in the Beijing Region

    NASA Astrophysics Data System (ADS)

    Zhuang, Jiancang; Vere-Jones, David; Guan, Huaping; Ogata, Yosihiko; Ma, Li

    2005-06-01

    This paper presents a preliminary analysis of observations on ultra-low frequency ground electric signals from stations operated by the China Seismological Bureau over the last 20 years. A brief description of the instrumentation, operating procedures and data processing procedures is given. The data analyzed consists of estimates of the total strengths (cumulated amplitudes) of the electric signals during 24-hour periods. The thresholds are set low enough so that on most days a zero observation is returned. Non-zero observations are related to electric and magnetic storms, occasional man-made electrical effects, and, apparently, some pre-, co-, or postseismic signals. The main purpose of the analysis is to investigate the extent that the electric signals can be considered as preseismic in character. For this purpose the electric signals from each of five stations are jointly analyzed with the catalogue of local earthquakes within circular regions around the selected stations. A version of Ogata’s Lin-Lin algorithm is used to estimate and test the existence of a pre-seismic signal. This model allows the effect of the electric signals to be tested, even after allowing for the effects of earthquake clustering. It is found that, although the largest single effect influencing earthquake occurrence is the clustering tendency, there remains a significant preseismic component from the electrical signals. Additional tests show that the apparent effect is not postseismic in character, and persists even under variations of the model and the time periods used in the analysis. Samples of the data are presented and the full data sets have been made available on local websites.

  16. Observation of - mixing and measurement of mixing frequencies using semileptonic B decays

    NASA Astrophysics Data System (ADS)

    Aaij, R.; Adeva, B.; Adinolfi, M.; Adrover, C.; Affolder, A.; Ajaltouni, Z.; Albrecht, J.; Alessio, F.; Alexander, M.; Ali, S.; Alkhazov, G.; Alvarez Cartelle, P.; Alves, A. A.; Amato, S.; Amerio, S.; Amhis, Y.; Anderlini, L.; Anderson, J.; Andreassen, R.; Andrews, J. E.; Andrianala, F.; Appleby, R. B.; Aquines Gutierrez, O.; Archilli, F.; Artamonov, A.; Artuso, M.; Aslanides, E.; Auriemma, G.; Baalouch, M.; Bachmann, S.; Back, J. J.; Baesso, C.; Balagura, V.; Baldini, W.; Barlow, R. J.; Barschel, C.; Barsuk, S.; Barter, W.; Bauer, Th.; Bay, A.; Beddow, J.; Bedeschi, F.; Bediaga, I.; Belogurov, S.; Belous, K.; Belyaev, I.; Ben-Haim, E.; Bencivenni, G.; Benson, S.; Benton, J.; Berezhnoy, A.; Bernet, R.; Bettler, M.-O.; van Beuzekom, M.; Bien, A.; Bifani, S.; Bird, T.; Bizzeti, A.; Bjørnstad, P. M.; Blake, T.; Blanc, F.; Blouw, J.; Blusk, S.; Bocci, V.; Bondar, A.; Bondar, N.; Bonivento, W.; Borghi, S.; Borgia, A.; Bowcock, T. J. V.; Bowen, E.; Bozzi, C.; Brambach, T.; van den Brand, J.; Bressieux, J.; Brett, D.; Britsch, M.; Britton, T.; Brook, N. H.; Brown, H.; Burducea, I.; Bursche, A.; Busetto, G.; Buytaert, J.; Cadeddu, S.; Callot, O.; Calvi, M.; Calvo Gomez, M.; Camboni, A.; Campana, P.; Campora Perez, D.; Carbone, A.; Carboni, G.; Cardinale, R.; Cardini, A.; Carranza-Mejia, H.; Carson, L.; Carvalho Akiba, K.; Casse, G.; Castillo Garcia, L.; Cattaneo, M.; Cauet, Ch.; Cenci, R.; Charles, M.; Charpentier, Ph.; Chen, P.; Chiapolini, N.; Chrzaszcz, M.; Ciba, K.; Cid Vidal, X.; Ciezarek, G.; Clarke, P. E. L.; Clemencic, M.; Cliff, H. V.; Closier, J.; Coca, C.; Coco, V.; Cogan, J.; Cogneras, E.; Collins, P.; Comerma-Montells, A.; Contu, A.; Cook, A.; Coombes, M.; Coquereau, S.; Corti, G.; Couturier, B.; Cowan, G. A.; Craik, D. C.; Cunliffe, S.; Currie, R.; D'Ambrosio, C.; David, P.; David, P. N. Y.; Davis, A.; De Bonis, I.; De Bruyn, K.; De Capua, S.; De Cian, M.; De Miranda, J. M.; De Paula, L.; De Silva, W.; De Simone, P.; Decamp, D.; Deckenhoff, M.; Del Buono, L.; Déléage, N.; Derkach, D.; Deschamps, O.; Dettori, F.; Di Canto, A.; Dijkstra, H.; Dogaru, M.; Donleavy, S.; Dordei, F.; Dosil Suárez, A.; Dossett, D.; Dovbnya, A.; Dupertuis, F.; Durante, P.; Dzhelyadin, R.; Dziurda, A.; Dzyuba, A.; Easo, S.; Egede, U.; Egorychev, V.; Eidelman, S.; van Eijk, D.; Eisenhardt, S.; Eitschberger, U.; Ekelhof, R.; Eklund, L.; El Rifai, I.; Elsasser, Ch.; Falabella, A.; Färber, C.; Fardell, G.; Farinelli, C.; Farry, S.; Ferguson, D.; Fernandez Albor, V.; Ferreira Rodrigues, F.; Ferro-Luzzi, M.; Filippov, S.; Fiore, M.; Fitzpatrick, C.; Fontana, M.; Fontanelli, F.; Forty, R.; Francisco, O.; Frank, M.; Frei, C.; Frosini, M.; Furcas, S.; Furfaro, E.; Gallas Torreira, A.; Galli, D.; Gandelman, M.; Gandini, P.; Gao, Y.; Garofoli, J.; Garosi, P.; Garra Tico, J.; Garrido, L.; Gaspar, C.; Gauld, R.; Gersabeck, E.; Gersabeck, M.; Gershon, T.; Ghez, Ph.; Gibson, V.; Giubega, L.; Gligorov, V. V.; Göbel, C.; Golubkov, D.; Golutvin, A.; Gomes, A.; Gorbounov, P.; Gordon, H.; Gotti, C.; Grabalosa Gándara, M.; Graciani Diaz, R.; Granado Cardoso, L. A.; Graugés, E.; Graziani, G.; Grecu, A.; Greening, E.; Gregson, S.; Griffith, P.; Grünberg, O.; Gui, B.; Gushchin, E.; Guz, Yu.; Gys, T.; Hadjivasiliou, C.; Haefeli, G.; Haen, C.; Haines, S. C.; Hall, S.; Hamilton, B.; Hampson, T.; Hansmann-Menzemer, S.; Harnew, N.; Harnew, S. T.; Harrison, J.; Hartmann, T.; He, J.; Head, T.; Heijne, V.; Hennessy, K.; Henrard, P.; Hernando Morata, J. A.; van Herwijnen, E.; Hess, M.; Hicheur, A.; Hicks, E.; Hill, D.; Hoballah, M.; Hombach, C.; Hopchev, P.; Hulsbergen, W.; Hunt, P.; Huse, T.; Hussain, N.; Hutchcroft, D.; Hynds, D.; Iakovenko, V.; Idzik, M.; Ilten, P.; Jacobsson, R.; Jaeger, A.; Jans, E.; Jaton, P.; Jawahery, A.; Jing, F.; John, M.; Johnson, D.; Jones, C. R.; Joram, C.; Jost, B.; Kaballo, M.; Kandybei, S.; Kanso, W.; Karacson, M.; Karbach, T. M.; Kenyon, I. R.; Ketel, T.; Keune, A.; Khanji, B.; Kochebina, O.; Komarov, I.; Koopman, R. F.; Koppenburg, P.; Korolev, M.; Kozlinskiy, A.; Kravchuk, L.; Kreplin, K.; Kreps, M.; Krocker, G.; Krokovny, P.; Kruse, F.; Kucharczyk, M.; Kudryavtsev, V.; Kurek, K.; Kvaratskheliya, T.; La Thi, V. N.; Lacarrere, D.; Lafferty, G.; Lai, A.; Lambert, D.; Lambert, R. W.; Lanciotti, E.; Lanfranchi, G.; Langenbruch, C.; Latham, T.; Lazzeroni, C.; Le Gac, R.; van Leerdam, J.; Lees, J.-P.; Lefèvre, R.; Leflat, A.; Lefrançois, J.; Leo, S.; Leroy, O.; Lesiak, T.; Leverington, B.; Li, Y.; Li Gioi, L.; Liles, M.; Lindner, R.; Linn, C.; Liu, B.; Liu, G.; Lohn, S.; Longstaff, I.; Lopes, J. H.; Lopez-March, N.; Lu, H.; Lucchesi, D.; Luisier, J.; Luo, H.; Machefert, F.; Machikhiliyan, I. V.; Maciuc, F.; Maev, O.; Malde, S.; Manca, G.; Mancinelli, G.; Maratas, J.; Marconi, U.; Marino, P.; Märki, R.; Marks, J.; Martellotti, G.; Martens, A.; Martín Sánchez, A.; Martinelli, M.; Martinez Santos, D.; Martins Tostes, D.; Martynov, A.; Massafferri, A.; Matev, R.; Mathe, Z.; Matteuzzi, C.; Maurice, E.; Mazurov, A.; McCarthy, J.; McNab, A.; McNulty, R.; McSkelly, B.; Meadows, B.; Meier, F.; Meissner, M.; Merk, M.; Milanes, D. A.; Minard, M.-N.; Molina Rodriguez, J.; Monteil, S.; Moran, D.; Morawski, P.; Mordà, A.; Morello, M. J.; Mountain, R.; Mous, I.; Muheim, F.; Müller, K.; Muresan, R.; Muryn, B.; Muster, B.; Naik, P.; Nakada, T.; Nandakumar, R.; Nasteva, I.; Needham, M.; Neubert, S.; Neufeld, N.; Nguyen, A. D.; Nguyen, T. D.; Nguyen-Mau, C.; Nicol, M.; Niess, V.; Niet, R.; Nikitin, N.; Nikodem, T.; Nomerotski, A.; Novoselov, A.; Oblakowska-Mucha, A.; Obraztsov, V.; Oggero, S.; Ogilvy, S.; Okhrimenko, O.; Oldeman, R.; Orlandea, M.; Otalora Goicochea, J. M.; Owen, P.; Oyanguren, A.; Pal, B. K.; Palano, A.; Palczewski, T.; Palutan, M.; Panman, J.; Papanestis, A.; Pappagallo, M.; Parkes, C.; Parkinson, C. J.; Passaleva, G.; Patel, G. D.; Patel, M.; Patrick, G. N.; Patrignani, C.; Pavel-Nicorescu, C.; Pazos Alvarez, A.; Pellegrino, A.; Penso, G.; Pepe Altarelli, M.; Perazzini, S.; Perez Trigo, E.; Pérez-Calero Yzquierdo, A.; Perret, P.; Perrin-Terrin, M.; Pescatore, L.; Pesen, E.; Petridis, K.; Petrolini, A.; Phan, A.; Picatoste Olloqui, E.; Pietrzyk, B.; Pilař, T.; Pinci, D.; Playfer, S.; Plo Casasus, M.; Polci, F.; Polok, G.; Poluektov, A.; Polycarpo, E.; Popov, A.; Popov, D.; Popovici, B.; Potterat, C.; Powell, A.; Prisciandaro, J.; Pritchard, A.; Prouve, C.; Pugatch, V.; Puig Navarro, A.; Punzi, G.; Qian, W.; Rademacker, J. H.; Rakotomiaramanana, B.; Rangel, M. S.; Raniuk, I.; Rauschmayr, N.; Raven, G.; Redford, S.; Reid, M. M.; dos Reis, A. C.; Ricciardi, S.; Richards, A.; Rinnert, K.; Rives Molina, V.; Roa Romero, D. A.; Robbe, P.; Roberts, D. A.; Rodrigues, E.; Rodriguez Perez, P.; Roiser, S.; Romanovsky, V.; Romero Vidal, A.; Rouvinet, J.; Ruf, T.; Ruffini, F.; Ruiz, H.; Ruiz Valls, P.; Sabatino, G.; Saborido Silva, J. J.; Sagidova, N.; Sail, P.; Saitta, B.; Salustino Guimaraes, V.; Sanmartin Sedes, B.; Sannino, M.; Santacesaria, R.; Santamarina Rios, C.; Santovetti, E.; Sapunov, M.; Sarti, A.; Satriano, C.; Satta, A.; Savrie, M.; Savrina, D.; Schaack, P.; Schiller, M.; Schindler, H.; Schlupp, M.; Schmelling, M.; Schmidt, B.; Schneider, O.; Schopper, A.; Schune, M.-H.; Schwemmer, R.; Sciascia, B.; Sciubba, A.; Seco, M.; Semennikov, A.; Senderowska, K.; Sepp, I.; Serra, N.; Serrano, J.; Seyfert, P.; Shapkin, M.; Shapoval, I.; Shatalov, P.; Shcheglov, Y.; Shears, T.; Shekhtman, L.; Shevchenko, O.; Shevchenko, V.; Shires, A.; Silva Coutinho, R.; Sirendi, M.; Skwarnicki, T.; Smith, N. A.; Smith, E.; Smith, J.; Smith, M.; Sokoloff, M. D.; Soler, F. J. P.; Soomro, F.; Souza, D.; Souza De Paula, B.; Spaan, B.; Sparkes, A.; Spradlin, P.; Stagni, F.; Stahl, S.; Steinkamp, O.; Stevenson, S.; Stoica, S.; Stone, S.; Storaci, B.; Straticiuc, M.; Straumann, U.; Subbiah, V. K.; Sun, L.; Swientek, S.; Syropoulos, V.; Szczekowski, M.; Szczypka, P.; Szumlak, T.; T'Jampens, S.; Teklishyn, M.; Teodorescu, E.; Teubert, F.; Thomas, C.; Thomas, E.; van Tilburg, J.; Tisserand, V.; Tobin, M.; Tolk, S.; Tonelli, D.; Topp-Joergensen, S.; Torr, N.; Tournefier, E.; Tourneur, S.; Tran, M. T.; Tresch, M.; Tsaregorodtsev, A.; Tsopelas, P.; Tuning, N.; Ubeda Garcia, M.; Ukleja, A.; Urner, D.; Ustyuzhanin, A.; Uwer, U.; Vagnoni, V.; Valenti, G.; Vallier, A.; Van Dijk, M.; Vazquez Gomez, R.; Vazquez Regueiro, P.; Vázquez Sierra, C.; Vecchi, S.; Velthuis, J. J.; Veltri, M.; Veneziano, G.; Vervink, K.; Vesterinen, M.; Viaud, B.; Vieira, D.; Vilasis-Cardona, X.; Vollhardt, A.; Volyanskyy, D.; Voong, D.; Vorobyev, A.; Vorobyev, V.; Voß, C.; Voss, H.; Waldi, R.; Wallace, C.; Wallace, R.; Wandernoth, S.; Wang, J.; Ward, D. R.; Watson, N. K.; Webber, A. D.; Websdale, D.; Whitehead, M.; Wicht, J.; Wiechczynski, J.; Wiedner, D.; Wiggers, L.; Wilkinson, G.; Williams, M. P.; Williams, M.; Wilson, F. F.; Wimberley, J.; Wishahi, J.; Wislicki, W.; Witek, M.; Wotton, S. A.; Wright, S.; Wu, S.; Wyllie, K.; Xie, Y.; Xing, Z.; Yang, Z.; Young, R.; Yuan, X.; Yushchenko, O.; Zangoli, M.; Zavertyaev, M.; Zhang, F.; Zhang, L.; Zhang, W. C.; Zhang, Y.; Zhelezov, A.; Zhokhov, A.; Zhong, L.; Zvyagin, A.

    2013-12-01

    The and B 0 mixing frequencies, Δ m s and Δ m d , are measured using a data sample corresponding to an integrated luminosity of 1.0 fb-1 collected by the LHCb experiment in pp collisions at a centre of mass energy of 7 TeV during 2011. Around 1.8×106 candidate events are selected of the type (+ anything), where about half are from peaking and combinatorial backgrounds. To determine the B decay times, a correction is required for the momentum carried by missing particles, which is performed using a simulation-based statistical method. Associated production of muons or mesons allows us to tag the initial-state flavour and so to resolve oscillations due to mixing. We obtain The hypothesis of no oscillations is rejected by the equivalent of 5.8 standard deviations for and 13.0 standard deviations for B 0. This is the first observation of mixing to be made using only semileptonic decays.

  17. The widest frequency radio relic spectra: observations from 150 MHz to 30 GHz

    NASA Astrophysics Data System (ADS)

    Stroe, Andra; Shimwell, Timothy; Rumsey, Clare; van Weeren, Reinout; Kierdorf, Maja; Donnert, Julius; Jones, Thomas W.; Röttgering, Huub J. A.; Hoeft, Matthias; Rodríguez-Gonzálvez, Carmen; Harwood, Jeremy J.; Saunders, Richard D. E.

    2016-01-01

    Radio relics are patches of diffuse synchrotron radio emission that trace shock waves. Relics are thought to form when intracluster medium electrons are accelerated by cluster merger-induced shock waves through the diffusive shock acceleration mechanism. In this paper, we present observations spanning 150 MHz to 30 GHz of the `Sausage' and `Toothbrush' relics from the Giant Metrewave and Westerbork telescopes, the Karl G. Jansky Very Large Array, the Effelsberg telescope, the Arcminute Microkelvin Imager and Combined Array for Research in Millimeter-wave Astronomy. We detect both relics at 30 GHz, where the previous highest frequency detection was at 16 GHz. The integrated radio spectra of both sources clearly steepen above 2 GHz, at the ≳6σ significance level, supporting the spectral steepening previously found in the `Sausage' and the Abell 2256 relic. Our results challenge the widely adopted simple formation mechanism of radio relics and suggest more complicated models have to be developed that, for example, involve re-acceleration of aged seed electrons.

  18. DENSITY OF WARM IONIZED GAS NEAR THE GALACTIC CENTER: LOW RADIO FREQUENCY OBSERVATIONS

    SciTech Connect

    Roy, Subhashis

    2013-08-10

    We have observed the Galactic center (GC) region at 0.154 and 0.255 GHz with the Giant Metrewave Radio Telescope. A total of 62 compact likely extragalactic (EG) sources are detected. Their scattering sizes decrease linearly with increasing angular distance from the GC up to about 1 Degree-Sign . The apparent scattering sizes of the sources are more than an order of magnitude less than predicted earlier by the NE2001 model of Galactic electron distribution within 359. Degree-Sign 5 < l < 0. Degree-Sign 5 and -0. Degree-Sign 5 < b < 0. Degree-Sign 5 (Hyperstrong Scattering Region) of the Galaxy. High free-free optical depths ({tau}) are observed toward most of the extended non-thermal sources within 0. Degree-Sign 6 from the GC. Significant variation of {tau} indicates that the absorbing medium is patchy at an angular scale of {approx}10' and n{sub e} is {approx}10 cm{sup -3}, which matches the NE2001 model. This model predicts the EG sources to be resolved out from 1.4 GHz interferometric surveys. However, out of 10 EG sources expected in the region, 8 likely EG are present in the 1.4 GHz catalog. Ionized interfaces of dense molecular clouds to the ambient medium are most likely responsible for strong scattering and low radio frequency absorption. However, dense GC clouds traced by CS J = 1-0 emission are found to have a narrow distribution of {approx}0. Degree-Sign 2 across the Galactic plane. Angular distribution of most EG sources seen through the so-called Hyperstrong Scattering Region are random in b, and typically {approx}7 out of 10 sources will not be seen through the dense molecular clouds, which explains why most of them are not scatter broadened at 1.4 GHz.

  19. Influence of HLA-DRB alleles on haemorrhagic fever with renal syndrome in a Chinese Han population in Hubei Province, China.

    PubMed

    Zhu, N; Luo, F; Chen, Q; Li, N; Xiong, H; Feng, Y; Yang, Z; Hou, W

    2015-01-01

    Specific human leucocyte antigen (HLA) alleles are considered a genetic risk factor for the progression of haemorrhagic fever with renal syndrome (HFRS) caused by hantaviruses. The aim of this study was to establish whether HLA-DRB alleles are associated with the severity of HFRS caused by different types of hantaviruses in a Chinese Han population from Hubei Province of central China. Twenty-two specific HLA-DRB alleles were analysed by sequence-specific primer-polymerase chain reaction (SSP-PCR) in 100 HFRS patients and 213 healthy volunteers. Associations of HLA-DRB alleles with the severity and clinical parameters of HFRS caused by Hantaan virus (HTNV) or Seoul virus (SEOV) infection were evaluated. Six alleles (HLA-DRB1*0401-0411, HLA-DRB1*1001, HLA-DRB1*1101-1105, HLA-DRB1*1201-1202, HLA-DRB1*1305 and DRB5*0101-0201) demonstrated strong associations with HFRS caused by HTNV and SEOV infections. Further comparison of these HLA-DRB1 allele frequencies between HFRS patients with differing severities and healthy controls demonstrated that the HLA-DRB1*0401-0411, HLA-DRB1*1001 and DRB1*1305 alleles were more frequent in the moderate course of HTNV-infected HFRS. Meanwhile, the DRB1*1101-1105 allele was more frequently observed in the severe course of HTNV-infected HFRS. We also found that the HLA-DRB1*1201-1202 allele frequency was higher in the moderate course of SEOV-infected HFRS, whereas the DRB5*0101-0201 allele may play a protective role in moderate HFRS caused by both HTNV and SEOV infections. These results provide evidence of the influence of HLA-DRB on the severity of HFRS and confirm the effect of HLA-DRB on HFRS during different types of hantavirus infection in a Chinese Han population in Hubei Province, China.

  20. Experimental observation of short-pulse upshifted frequency microwaves from a laser-created overdense plasma.

    PubMed

    Yugami, Noboru; Niiyama, Toshihiko; Higashiguchi, Takeshi; Gao, Hong; Sasaki, Shigeo; Ito, Hiroaki; Nishida, Yasushi

    2002-03-01

    A short and frequency upshifted from a source microwave pulse is experimentally generated by the overdense plasma that is rapidly created by a laser. The source wave, whose frequency is 9 GHz, is propagating in the waveguide filled with tetrakis-dimethyl-amino-ethylene gas, which is to be converted to the overdense plasma by the laser. The detected frequency of the pulse is over 31.4 GHz and its duration is 10 ns. This technique has the potential for the generation of a tunable frequency source.

  1. Very low frequency radio events with a reduced intensity observed by the low-altitude DEMETER spacecraft

    NASA Astrophysics Data System (ADS)

    Záhlava, J.; Němec, F.; Santolík, O.; Kolmašová, I.; Parrot, M.; Rodger, C. J.

    2015-11-01

    We present results of a systematic study of unusual very low frequency (VLF) radio events with a reduced intensity observed in the frequency-time spectrograms measured by the low-orbiting Detection of Electro-Magnetic Emissions Transmitted from Earthquake Regions (DEMETER) spacecraft. They occur exclusively on the nightside. During these events, the intensity of fractional hop whistlers at specific frequencies is significantly reduced. These frequencies are usually above about 3.4 kHz (second Earth-ionosphere waveguide cutoff frequency), but about 20% of events extend down to about 1.7 kHz (first Earth-ionosphere waveguide cutoff frequency). The frequencies of a reduced intensity vary smoothly with time. We have inspected 6.5 years of DEMETER data, and we identified in total 1601 such events. We present a simple model of the event formation based on the wave propagation in the Earth-ionosphere waveguide. We apply the model to two selected events, and we demonstrate that the model is able to reproduce both the minimum frequencies of the events and their approximate frequency-time shapes. The overall geographic distribution of the events is shifted by about 3000 km westward and slightly southward with respect to the areas with high long-term average lightning activity. We demonstrate that this shift is related to the specific DEMETER orbit, and we suggest its qualitative explanation by the east-west asymmetry of the wave propagation in the Earth-ionosphere waveguide.

  2. Scintillation Arcs in Low-frequency Observations of the Timing-array Millisecond Pulsar PSR J0437-4715

    NASA Astrophysics Data System (ADS)

    Bhat, N. D. R.; Ord, S. M.; Tremblay, S. E.; McSweeney, S. J.; Tingay, S. J.

    2016-02-01

    Low-frequency observations of pulsars provide a powerful means for probing the microstructure in the turbulent interstellar medium (ISM). Here we report on high-resolution dynamic spectral analysis of our observations of the timing-array millisecond pulsar PSR J0437-4715 with the Murchison Widefield Array (MWA), enabled by our recently commissioned tied-array beam processing pipeline for voltage data recorded from the high time resolution mode of the MWA. A secondary spectral analysis reveals faint parabolic arcs akin to those seen in high-frequency observations of pulsars with the Green Bank and Arecibo telescopes. Data from Parkes observations at a higher frequency of 732 MHz reveal a similar parabolic feature with a curvature that scales approximately as the square of the observing wavelength (λ2) to the MWA's frequency of 192 MHz. Our analysis suggests that scattering toward PSR J0437-4715 predominantly arises from a compact region about 115 pc from the Earth, which matches well with the expected location of the edge of the Local Bubble that envelopes the local Solar neighborhood. As well as demonstrating new and improved pulsar science capabilities of the MWA, our analysis underscores the potential of low-frequency pulsar observations for gaining valuable insights into the local ISM and for characterizing the ISM toward timing-array pulsars.

  3. Multiple-Station Observation of Frequency Dependence and Polarization Characteristics of ELF/VLF waves generated via Ionospheric Modification

    NASA Astrophysics Data System (ADS)

    Maxworth, A. S.; Golkowski, M.; Cohen, M.; Moore, R. C.

    2014-12-01

    Generation of Extremely Low Frequency (ELF) and Very Low Frequency (VLF) signals through ionospheric modification has been practiced for many years. Heating the lower ionosphere with high power HF waves allows for modulation of natural current systems. Our experiments were carried out at the High Frequency Active Auroral Research Program (HAARP) facility in Alaska, USA. In this experiment, the ionosphere was heated with a vertical amplitude modulating signal and the modulation frequency was changed sequentially within an array of 40 frequencies followed by a frequency ramp. The observed magnetic field amplitude and polarization of the generated ELF/VLF signals were analyzed for multiple sites and as a function of modulation frequency. Our three observation sites: Chistochina, Paxson and Paradise are located within 36km (azimuth 47.7°), 50.2km (azimuth -20°) and 99km (azimuth 80.3°) respectively. We show that the peak amplitudes observed as a function of frequency result from vertical resonance in the Earth-ionosphere waveguide and can be used to diagnose the D-region profile. Polarization analysis showed that out of the three sites Paxson shows the highest circularity in the magnetic field polarization, compared to Chistochina and Paradise which show highly linear polarizations. The experimental results were compared with a theoretical simulation model results and it was clear that in both cases, the modulated Hall current dominates the observed signals at Chistochina and Paradise sites and at Paxson there is an equal contribution from Hall and Pedersen currents. The Chistochina site shows the highest magnetic field amplitudes in both experimental and simulation environments. Depending upon the experimental and simulation observations at the three sites, a radiation pattern for the HAARP ionospheric heater can be mapped

  4. High-frequency observations and source parameters of microearthquakes recorded at hard-rock sites

    USGS Publications Warehouse

    Cranswick, Edward; Wetmiller, Robert; Boatwright, John

    1985-01-01

    We have estimated the source parameters of 53 microearthquakes recorded in July 1983 which were aftershocks of the Miramichi, New Brunswick, earthquake that occurred on 9 January 1982. These events were recorded by local three-component digital seismographs at 400 sps/component from 2-Hz velocity transducers sited directly on glacially scoured crystalline basement outcrop. Hypocentral distances are typically less than 5 km, and the hypocenters and the seven digital seismograph stations established all lie essentially within the boundaries of a granitic pluton that encompasses the faults that ruptured during the main shock and major aftershocks. The P-wave velocity is typically 5 km/sec at the surface and at least 6 km/sec at depths greater than about 1 km.The events have S-wave corner frequencies in the band 10 to 40 Hz, and the calculated Brune model seismic moments range from 1015 to 1018 dyne-cm. The corresponding stress drops are generally less than 1.0 bars, but there is considerable evidence that the seismic-source signals have been modified by propagation and/or site-effects. The data indicate: (a) there is a velocity discontinuity at 0.5 km depth; (b) the top layer has strong scattering/attenuating properties; (c) some source-receiver paths differentiate the propagated signal; (d) there is a hard-rock-site P-wave “fmax” between 50 and 100 Hz; and (e) some hard-rock sites are characterized by P-wave resonance frequencies in the range 50 to 100 Hz. Comparison of this dataset with the January 1982 New Brunswick digital seismograms which were recorded at sites underlain by several meters of low-velocity surface sediments suggests that some of the hard-rock-site phenomena listed above can be explained in terms of a layer-over-a-half-space model. For microearthquakes, this result implies that spectrally determined source dimension scales with site dimension (thickness of the layer). More generally, it emphasizes that it is very difficult to accurately observe

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

    PubMed

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

    2015-05-01

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

  6. The Burden of JAK2V617F Mutated Allele in Turkish Patients With Myeloproliferative Neoplasms

    PubMed Central

    Yonal-Hindilerden, Ipek; Daglar-Aday, Aynur; Akadam-Teker, Basak; Yilmaz, Ceylan; Nalcaci, Meliha; Yavuz, Akif Selim; Sargin, Deniz

    2015-01-01

    Background Studies regarding the impact of JAK2V617F allele burden on phenotypic properties and clinical course in Philadelphia-negative myeloproliferative neoplasms (Ph-negative MPNs) have reported variable results. We aimed to analyze the association of mutated JAK2V617F allele burden with laboratory characteristics and clinical phenotype in Turkish patients (107 essential thrombocythemia (ET) and 77 primary myelofibrosis (PMF)). Methods Peripheral blood samples of 184 patients with Ph-negative MPNs were analyzed for JAK2V617F allele status and burden. JAK2 MutaScreen assay (Ipsogen, Luminy Biotech, Marseille, France) was used to detect the JAK2V617F status and quantitative JAK2V617F allele burdens in genomic DNA using TaqMan allelic discrimination. Results Frequency of JAK2V617F-positive patients with high mutation load (allele burden > 50%) was higher in PMF compared to ET (23.4% and 4.7%, respectively; P = 0.001). We found significant association between ET patients with high JAK2V617F allele burden and lower hemoglobin (Hgb) and hematocrit (Hct), higher LDH levels and more prevalent massive splenomegaly (P = 0.001, P = 0.001, P = 0.012 and P = 0.015, respectively). ET patients with high mutation load displayed higher prevalence of bleeding compared to low mutation load and wild-type mutational status (P = 0.003). Rate of DVT was significantly higher in ET patients with mutant allele burden in upper half compared to lower half and wild-type (P = 0.029). We observed significant association between PMF patients with high JAK2V617F allele burden and higher Hgb, Hct levels and leukocyte counts (P = 0.003, P = 0.021 and P = 0.001, respectively). Conclusions Our study demonstrated JAK2V617F allele burden correlates with clinical features in ET and PMF. We conclude quantification of JAK2V617F mutation contributes to the workup of Ph-negative MPNs. PMID:25584101

  7. The Miniature Radio Frequency instrument's (Mini-RF) global observations of Earth's Moon

    NASA Astrophysics Data System (ADS)

    Cahill, Joshua T. S.; Thomson, B. J.; Patterson, G. Wesley; Bussey, D. Benjamin J.; Neish, Catherine D.; Lopez, Norberto R.; Turner, F. Scott; Aldridge, T.; McAdam, M.; Meyer, H. M.; Raney, R. K.; Carter, L. M.; Spudis, P. D.; Hiesinger, H.; Pasckert, J. H.

    2014-11-01

    Radar provides a unique means to analyze the surface and subsurface physical properties of geologic deposits, including their wavelength-scale roughness, the relative depth of the deposits, and some limited compositional information. The NASA Lunar Reconnaissance Orbiter's (LRO) Miniature Radio Frequency (Mini-RF) instrument has enabled these analyses on the Moon at a global scale. Mini-RF has accumulated ∼67% coverage of the lunar surface in S-band (12.6 cm) radar with a resolution of 30 m/pixel. Here we present new Mini-RF global orthorectified uncontrolled S-band maps of the Moon and use them for analysis of lunar surface physical properties. Reported here are readily apparent global- and regional-scale differences in lunar surface physical properties that suggest three distinct terranes, namely: a (1) Nearside Radar Dark Region; (2) Orientale basin and continuous ejecta; and the (3) Highlands Radar Bright Region. Integrating these observations with new data from LRO's Diviner Radiometer rock abundance maps, as well Clementine and Lunar Prospector derived compositional values show multiple distinct lunar surface terranes and sub-terranes based upon both physical and compositional surface properties. Previous geochemical investigations of the Moon suggested its crust is best divided into three to four basic crustal provinces or terranes (Feldspathic Highlands Terrane (-An and -Outer), Procellarum KREEP Terrane, and South Pole Aitken Terrane) that are distinct from one another. However, integration of these geochemical data sets with new geophysical data sets allows us to refine these terranes. The result shows a more complex view of these same crustal provinces and provides valuable scientific and hazard perspectives for future targeted human and robotic exploration.

  8. The Miniature Radio Frequency Instruments (Mini-RF) Global Observations of Earth's Moon

    NASA Technical Reports Server (NTRS)

    Cahill, Joshua T. S.; Thomson, B. J.; Patterson, G. Wesley; Bussey, D. Benjamin J.; Neish, Catherine D.; Lopez, Norberto R.; Turner, F. Scott; Aldridge, T.; McAdam, M.; Meyer, H. M.; Raney, R. K.; Carter, L. M.; Spudis, P. D.; Hiesinger, H.; Pasckert, J. H.

    2014-01-01

    Radar provides a unique means to analyze the surface and subsurface physical properties of geologic deposits, including their wavelength-scale roughness, the relative depth of the deposits, and some limited compositional information. The NASA Lunar Reconnaissance Orbiter's (LRO) Miniature Radio Frequency (Mini-RF) instrument has enabled these analyses on the Moon at a global scale. Mini-RF has accumulated 67% coverage of the lunar surface in S-band (12.6 cm) radar with a resolution of 30 m/pixel. Here we present new Mini-RF global orthorectified uncontrolled S-band maps of the Moon and use them for analysis of lunar surface physical properties. Reported here are readily apparent global- and regional-scale differences in lunar surface physical properties that suggest three distinct terranes, namely: a (1) Nearside Radar Dark Region; (2) Orientale basin and continuous ejecta; and the (3) Highlands Radar Bright Region. Integrating these observations with new data from LRO's Diviner Radiometer rock abundance maps, as well Clementine and Lunar Prospector derived compositional values show multiple distinct lunar surface terranes and sub-terranes based upon both physical and compositional surface properties. Previous geochemical investigations of the Moon suggested its crust is best divided into three to four basic crustal provinces or terranes (Feldspathic Highlands Terrane (-An and -Outer), Procellarum KREEP Terrane, and South Pole Aitken Terrane) that are distinct from one another. However, integration of these geochemical data sets with new geophysical data sets allows us to refine these terranes. The result shows a more complex view of these same crustal provinces and provides valuable scientific and hazard perspectives for future targeted human and robotic exploration.

  9. PCR/oligonucleotide probe typing of HLA class II alleles in a Filipino population reveals an unusual distribution of HLA haplotypes

    SciTech Connect

    Bugawan, T.L.; Chang, J.D.; Erlich, H.A. ); Klitz, W. )

    1994-02-01

    The authors have analyzed the distribution of HLA class II alleles and haplotypes in a Filipino population by PCR amplification of the DRB1, DQB1, and DPB1 second-exon sequences from buccal swabs obtained from 124 family members and 53 unrelated individuals. The amplified DNA was typed by using nonradioactive sequence-specific oligonucleotide probes. Twenty-two different DRB1 alleles, including the novel Filipino *1105, and 46 different DRB1/DQB1 haplotypes, including the unusual DRB1*0405-DQB1*0503, were identified. An unusually high frequency (f = .383) of DPB1*0101, a rare allele in other Asian populations, was also observed. In addition, an unusual distribution of DRB1 alleles and haplotypes was seen in this population, with DR2 (f = .415) and DRB1*1502-DQB1*0502 (f = .233) present at high frequencies. This distribution of DRB1 alleles differs from the typical HLA population distribution, in which the allele frequencies are more evenly balanced. The distribution of HLA class II alleles and haplotypes in this Filipino population is different from that of other Asian and Pacific groups: of those populations studied to date, the Indonesian population is the most similar. DRB1*1502-DQB1*0502 was in strong linkage disequilibrium (D[prime] = .41) with DPB 1*0101 (f = .126, for the extended haplotype), which is consistent with selection for this DR, DQ, DP haplotype being responsible for the high frequency of these three class II alleles in this populations. 30 refs., 2 figs., 6 tabs.

  10. Radio-Frequency Pulses Emitted by Intracloud Lightning, as Observed From Space by the FORTE Satellite

    NASA Astrophysics Data System (ADS)

    Jacobson, A. R.

    2002-12-01

    The FORTE satellite has been used to trigger upon, and record, radio-frequency signals and optical signals from lightning. This talk will present recent results on the pulse characteristics, remote-sensing utility, and meteorological setting of two distinct types of radio-frequency impulses usually accompanying intracloud discharges. Emphasis will be given to implications of our recent FORTE results for future global lightning and severe-convective-storm monitoring, being proposed for the radio-frequency sensors on the Global Positioning System satellites.

  11. Allelic loss in colorectal carcinoma

    SciTech Connect

    Kern, S.E.; Fearon, E.R.; Tersmette, K.W.F.; Enterline, J.P.; Vogelstein, B.; Hamilton, S.R. ); Leppert, M.; Nakamura, Yusuke; White, R. )

    1989-06-02

    Clinical and pathological associations with molecular genetic alterations were studied in colorectal carcinomas from 83 patients. Fractional allelic loss, a measure of allelic deletions throughout the genome, and allelic deletions of specific chromosomal arms (the short arm of 17 and long arm of 18) each provided independent prognostic information by multivariate analysis when considered individually with Dukes' classification. Distant metastasis was significantly associated with high fractional allelic loss and with deletions of 17p and 18q. Mutations of ras proto-oncogenes and deletions of 5q had no prognostic importance. Statistically significant associations were also found between allelic losses and a family history of cancer, left-sided tumor location, and absence of extracellular tumor mucin. Allelic deletion analysis thus identified subsets of colorectal carcinoma with increased predilection for distant metastasis and cancer-related death. Further studies may define a subset of genetic alterations that can be used clinically to help assess prognosis.

  12. Distribution of apolipoprotein E alleles in coras and huicholes from Nayarit and Nahuas and Mestizos from Veracruz, Mexico.

    PubMed

    Cruz-Fuentes, Carlos S; González-Sobrino, Blanca Zoila; Gómez-Sanchez, Ariadna; Martínez Rueda, Hortencia; Chávez-Eakle, Rosa Aurora; Serrano Sánchez, Carlos

    2005-12-01

    We report allele frequencies for the most common polymorphism of the APOE gene in Mexican individuals from two regions not previously described: Coras and Huicholes from Nayarit, and Nahuas and mestizos from Veracruz. We also report APOE allele frequencies for inhabitants of Mexico City. These descriptive data underscore the allelic heterogeneity for this particular locus in Mexico.

  13. Enhanced frequency spectra of winds at the mesoscale based on radar profiler observations

    NASA Technical Reports Server (NTRS)

    Nastrom, G. D.; Gage, K. S.

    1990-01-01

    Frequency spectra of horizontal winds in the troposphere and stratosphere, over a range of periods and frequencies, have been studied by means of two radar profilers, located at Plattenville, Colorado, and Poker Flat, Alaska, to determine if the spectra deviations from a consistent power law behavior can be verified in a statistical sense. At Plattenville, the spectrum of both zonal and meridional winds in the troposphere is found to obey a low-frequency regime at periods longer than a few hours and a high-frequency regime at periods less than 1/2 hour. The energy levels in the high-frequency regime are enhanced over those obtained by extrapolation of the low-frequency regime by a factor of 4. At Poker Flat, a similar pattern is found in the stratosphere, and the magnitude of the enhancement factor is 1.7. It is suggested that the enhanced amplitudes reflect the effects of upward-propagating gravity waves launched by the flow over a rough terrain, and that they influence the dynamics of the large-scale circulation to a great extent.

  14. Crop-to-weed introgression has impacted allelic composition of johnsongrass populations with and without recent exposure to cultivated sorghum.

    PubMed

    Morrell, P L; Williams-Coplin, T D; Lattu, A L; Bowers, J E; Chandler, J M; Paterson, A H

    2005-06-01

    Sorghum halepense L. (johnsongrass) is one of the world's most noxious weeds, and a paradigm for the potential dangers of crop-weed hybridization. Introduced into the southeastern United States about 200 years ago, S. halepense is a close relative of cultivated sorghum (Sorghum bicolor). Both artificial crossing and experimental field studies have demonstrated the potential for S. halepensex S. bicolor hybrid formation, but no prior study has addressed the long-term persistence of sorghum genes in johnsongrass populations. We surveyed 283 loci (on all 10 sorghum linkage groups) to identify 77 alleles at 69 loci that are found in US sorghum cultivars but are absent from a worldwide sampling of johnsongrass genotypes. These putatively cultivar-specific alleles were present in up to 32.3% of individuals in johnsongrass populations adjacent to long-term sorghum production fields in Texas and Nebraska. Lower frequencies of cultivar-specific alleles at smaller numbers of loci are found in johnsongrass populations from New Jersey and Georgia with no recent exposure to cultivated sorghum, suggesting that introgressed sorghum alleles may be dispersed across long distances. The number of cultivar-specific alleles and extensive multilocus patterns of cultivar-specific allelic composition observed at both linked and unlinked loci in the johnsongrass populations, are inconsistent with alternatives to introgression such as convergence, or joint retention of ancestral polymorphisms. Naturalized johnsongrass populations appear to provide a conduit by which transgenes from sorghum could become widely disseminated.

  15. THE LOW-FREQUENCY CHARACTERISTICS OF PSR J0437–4715 OBSERVED WITH THE MURCHISON WIDE-FIELD ARRAY

    SciTech Connect

    Bhat, N. D. R.; Ord, S. M.; Tremblay, S. E.; Tingay, S. J.; Oronsaye, S.; Emrich, D.; Deshpande, A. A.; Van Straten, W.; Briggs, F.; Bernardi, G.; Bowman, J. D.; Cappallo, R. J.; Corey, B. E.; Goeke, R.; Hewitt, J. N.; Greenhill, L. J.; Kasper, J. C.; Hazelton, B. J.; Johnston-Hollitt, M.; Kaplan, D. L.; and others

    2014-08-20

    We report on the detection of the millisecond pulsar PSR J0437–4715 with the Murchison Wide-field Array (MWA) at a frequency of 192 MHz. Our observations show rapid modulations of pulse intensity in time and frequency that arise from diffractive scintillation effects in the interstellar medium (ISM), as well as prominent drifts of intensity maxima in the time-frequency plane that arise from refractive effects. Our analysis suggests that the scattering screen is located at a distance of ∼80-120 pc from the Sun, in disagreement with a recent claim that the screen is closer (∼10 pc). Comparisons with higher frequency data from Parkes reveal a dramatic evolution of the pulse profile with frequency, with the outer conal emission becoming comparable in strength to that from the core and inner conal regions. As well as demonstrating the high time resolution science capabilities currently possible with the MWA, our observations underscore the potential to conduct low-frequency investigations of timing-array millisecond pulsars, which may lead to increased sensitivity in the detection of nanoHertz gravitational waves via the accurate characterization of ISM effects.

  16. Observation of millimeter-wave oscillations from resonant tunneling diodes and some theoretical considerations of ultimate frequency limits

    NASA Technical Reports Server (NTRS)

    Sollner, T. C. L. G.; Brown, E. R.; Goodhue, W. D.; Le, H. Q.

    1987-01-01

    Recent observations of oscillation frequencies up to 56 GHz in resonant tunneling structures are discussed in relation to calculations by several authors of the ultimate frequency limits of these devices. It is found that calculations relying on the Wentzel-Kramers-Brillouin (WKB) approximation give limits well below the observed oscillation frequencies. Two other techniques for calculating the upper frequency limit were found to give more reasonable results. One method employs the solution of the time-dependent Schroedinger equation obtained by Kundrotas and Dargys (1986); the other uses the energy width of the transmission function for electrons through the double-barrier structure. This last technique is believed to be the most accurate since it is based on general results for the lifetime of any resonant state. It gives frequency limits on the order of 1 THz for two recently fabricated structures. It appears that the primary limitation of the oscillation frequency for double-barrier resonant-tunneling diodes is imposed by intrinsic device circuit parameters and by the transit time of the depletion layer rather than by time delays encountered in the double-barrier region.

  17. 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

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

    PubMed

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

    2015-09-01

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

  19. 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.

  20. Spatial frequency characteristics at image decision-point locations for observers with different radiological backgrounds in lung nodule detection

    NASA Astrophysics Data System (ADS)

    Pietrzyk, Mariusz W.; Manning, David J.; Dix, Alan; Donovan, Tim

    2009-02-01

    Aim: The goal of the study is to determine the spatial frequency characteristics at locations in the image of overt and covert observers' decisions and find out if there are any similarities in different observers' groups: the same radiological experience group or the same accuracy scored level. Background: The radiological task is described as a visual searching decision making procedure involving visual perception and cognitive processing. Humans perceive the world through a number of spatial frequency channels, each sensitive to visual information carried by different spatial frequency ranges and orientations. Recent studies have shown that particular physical properties of local and global image-based elements are correlated with the performance and the level of experience of human observers in breast cancer and lung nodule detections. Neurological findings in visual perception were an inspiration for wavelet applications in vision research because the methodology tries to mimic the brain processing algorithms. Methods: The wavelet approach to the set of postero-anterior chest radiographs analysis has been used to characterize perceptual preferences observers with different levels of experience in the radiological task. Psychophysical methodology has been applied to track eye movements over the image, where particular ROIs related to the observers' fixation clusters has been analysed in the spaces frame by Daubechies functions. Results: Significance differences have been found between the spatial frequency characteristics at the location of different decisions.

  1. Development of novel associations between MHC alleles and susceptibility to parasitic infections in an isolated population of an endangered mammal.

    PubMed

    Biedrzycka, Aleksandra; Kloch, Agnieszka

    2016-10-01

    The role of pathogens in dynamics of endangered species is not fully understood, and the effect of infection often interacts with other processes affecting those species, such as fragmentation and isolation or loss of genetic variation. Small, isolated populations are prone to losing functional alleles due to demographic processes and genetic drift, which may diminish their ability to resist infection if immune genes are affected. Demographic processes may also alter the selective pressure exerted by a parasite, as they influence the rate of parasite transmission between individuals. In the present paper we studied changes in parasite infection levels and genetic variability in an isolated population of spotted suslik (Spermophillus suslicus). Over a three-year period (approx. three generations), when the population size remained relatively stable, we observed a considerable increase in parasite prevalence and infection intensity, followed by the development of novel associations between MHC DRB alleles and parasite burden. Contrary to expectations, the change in MHC allele frequency over time was not consistent with the effect of the allele - for instance, Spsu-DRB*07, associated with higher intensity of infection with a nematode Capillaria sp., increased in frequency from 11.8 to 20.2%. Yet, we found no signatures of selection in the studied loci. Our results show that an isolated, stable population may experience a sudden increase in parasitic infections, resulting in a development of novel associations between MHC alleles and parasite susceptibility/resistance, even though no signatures of selection can be found.

  2. The observed human sperm mutation frequency cannot explain the achondroplasia paternal age effect.

    PubMed

    Tiemann-Boege, Irene; Navidi, William; Grewal, Raji; Cohn, Dan; Eskenazi, Brenda; Wyrobek, Andrew J; Arnheim, Norman

    2002-11-12

    The lifelong spermatogonial stem cell divisions unique to male germ cell production are thought to contribute to a higher mutation frequency in males. The fact that certain de novo human genetic conditions (e.g., achondroplasia) increase in incidence with the age of the father is consistent with this idea. Although it is assumed that the paternal age effect is the result of an increasing frequency of mutant sperm as a man grows older, no direct molecular measurement of the germ-line mutation frequency has been made to confirm this hypothesis. Using sperm DNA from donors of different ages, we determined the frequency of the nucleotide substitution in the fibroblast growth factor receptor 3 (FGFR3) gene that causes achondroplasia. Surprisingly, the magnitude of the increase in mutation frequency with age appears insufficient to explain why older fathers have a greater chance of having a child with this condition. A number of alternatives may explain this discrepancy, including selection for sperm that carry the mutation or an age-dependent increase in premutagenic lesions that remain unrepaired in sperm and are inefficiently detected by the PCR assay. PMID:12397172

  3. 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.

  4. Dual Frequency Radar Observations of Snow and Ice Properties: Esa's COREH2O Candidate Satellite Mission

    NASA Astrophysics Data System (ADS)

    Duguay, C.; Rott, H.; Cline, D. W.; Essery, R.; Etchevers, P.; Hajnsek, I.; Kern, M.; Macelloni, G.; Malnes, E.; Pulliainen, J. T.; Yueh, S. H.

    2012-12-01

    The satellite mission COld REgions Hydrology High-resolution Observatory (CoReH2O) is a candidate Earth Explorer mission within the Living Planet Programme of the European Space Agency. Detailed scientific and technical feasibility studies (Phase-A) for defining the satellite mission are going on. The mission will perform spatially detailed measurements of snow and ice in order to advance the modeling and prediction of water balance and streamflow in cold regions, and to improve the parameterization of snow and ice processes for climate models and numerical weather prediction. The primary snow and ice parameters to be delivered by the satellite are the area extent and mass (the water equivalent, SWE) of snow cover on land surfaces and the mass of winter snow accumulating on glaciers. In addition, the mission will make observations of various sea ice and lake ice parameters. The grid size of the final snow and ice products will vary between 200 m and 500 m, depending on the parameter and application. The sensor will be a dual-frequency dual-polarized SAR, operating at Ku-band (17.2 GHz) and X-band (9.6 GHz), VV and VH polarizations, with a swath width of about 100 km. Two mission phases with different repeat cycles and coverage are proposed. During the first two years a three-day repeat cycle is planned providing frequent repeat coverage over limited areas, in order to match the time scale of meteorological forcing by typical mid- and high-latitude weather systems. This orbit addresses in particular the parameterization of snow and ice processes in hydrological models and mesoscale atmospheric circulation models. The second mission phase shall deliver near complete observations of the global snow and ice areas at a repeat cycle of 12 to 15 days. Primary motivations for this phase are the validation of continental-scale hydrological models and climate models, and the development of downscaling techniques for coarse resolution satellite snow measurements. A processing

  5. HLA class II allele polymorphism in an outbreak of chikungunya fever in Middle Andaman, India

    PubMed Central

    Chaaithanya, Itta Krishna; Muruganandam, Nagarajan; Anwesh, Maile; Rajesh, Reesu; Ghosal, Sruti R; Kartick, Chinnaiah; Prasad, Kadiyala Nageswara; Muthumani, Karuppiah; Vijayachari, Paluru

    2013-01-01

    A sudden upsurge of fever cases with joint pain was observed in the outpatient department, Community Health Centre, Rangat during July–August 2010 in Rangat Middle Andaman, India. The aetiological agent responsible for the outbreak was identified as chikungunya virus (CHIKV), by using RT-PCR and IgM ELISA. The study investigated the association of polymorphisms in the human leucocyte antigen class II genes with susceptibility or protection against CHIKV. One hundred and one patients with clinical features suggestive of CHIKV infection and 104 healthy subjects were included in the study. DNA was extracted and typed for HLA-DRB1 and DQB1 alleles. Based on the amino acid sequences of HLA-DQB1 retrieved from the IMGT/HLA database, critical amino acid differences in the specific peptide-binding pockets of HLA-DQB1 molecules were investigated. The frequencies of HLA-DRB1 alleles were not significantly different, whereas lower frequency of HLA-DQB1*03:03 was observed in CHIKV patients compared with the control population [P = 0·001, corrected P = 0·024; odds ratio (OR) = 0, 95% confidence interval (95% CI) 0·0–0·331; Peto's OR = 0·1317, 95% CI 0·0428–0·405). Significantly lower frequency of glutamic acid at position 86 of peptide-binding pocket 1 coding HLA-DQB1 genotypes was observed in CHIKV patients compared with healthy controls (P = 0·004, OR = 0·307, 95% CI 0·125–0·707). Computational binding predictions of CD4 epitopes of CHIKV by NetMHCII revealed that HLA-DQ molecules are known to bind more CHIKV peptides than HLA-DRB1 molecules. The results suggest that HLA-DQB1 alleles and critical amino acid differences in the peptide-binding pockets of HLA-DQB1 alleles might have role in influencing infection and pathogenesis of CHIKV. PMID:23710940

  6. Frequency Dependence of Short Period Seismic Noise from Two Decades of Observations at Warramunga Seismic Array (WRA), Australia

    NASA Astrophysics Data System (ADS)

    Gal, M.; Reading, A. M.; Ellingsen, S. P.; Koper, K. D.; Tkalcic, H.; Hemer, M. A.

    2014-12-01

    The analysis of the seismic ambient noise field has recently received increased attention owing to its success in mapping the Earth's shallow and deep structures. The origin of the passive seismic wavefield is associated with deep ocean and coastal regions where ocean waves, under certain conditions, can excite seismic waves (microseisms) that propagate as surface and body waves. Previous seismological studies mainly focused on the observation of the strongest microseisms that are associated with the frequency range 0.1-0.3Hz. In our study, we focus on short period microseisms (0.325-0.725Hz) and examine the frequency dependant wave field and temporal variations over two decades. We use data recorded over two decades (1991-2012) from the Warramunga array (WRA) in central Australia. The analysis is carried out using IAS Capon beamforming that shows robust estimates of slowness and backazimuth, and is able to resolve multiple wave arrivals. Continuous data records are divided into one hour long recordings and evaluated for multiple arrivals in 8 separate frequency bands. We find multiple surface and body wave sources, which display seasonality and frequency dependence and remain stationary for two decades. We observe, for surface waves, that Rayleigh waves dominate for low frequencies while higher frequencies show a transition to leaky Rayleigh waves. The strong stationarity of the signal over multiple years, supports the suggestion that bathymetry and other site effects, such as coast line geometry, create favourable conditions for the generation of ocean induced surface waves. For body waves, source locations are identified in deep ocean regions for low frequencies and in shallow waters for higher frequencies. We further discuss correlation between arrivals and a WAVEWATCH III ocean wave hindcast for strong events. Fig 1: a) Shows the slowness of strongest incoming arrivals for 1 hour of WRA data over two decades. b) Displays the surface waves paths of incoming

  7. Frequency of the sit to stand task: An observational study of free-living adults.

    PubMed

    Dall, Philippa M; Kerr, Andrew

    2010-01-01

    The sit to stand movement is a key determinant of functional independence. Knowledge of the frequency with which the sit to stand movement is performed throughout the day could inform workplace ergonomics, but has rarely been examined. Healthy adults (n=140) were recruited from the general population. Free-living activity for each participant was reported using an activity monitor. On average, participants performed 60 (+/-22) sit to stand movements each day. Participants in indoor sedentary occupations performed significantly more sit to stand movements per day than participants in outdoor active occupations (66 vs. 54; n=102; p=0.003). Participants (n=33) performed significantly more sit to stand movements on working days than on non-working days (65 vs. 55; p=0.018). This analysis provides contemporary data for sit to stand frequency in a predominantly working population, and demonstrates that work and employment have a significant effect on that frequency. PMID:19450792

  8. Allelic Richness following Population Founding Events – A Stochastic Modeling Framework Incorporating Gene Flow and Genetic Drift

    PubMed Central

    Greenbaum, Gili; Templeton, Alan R.; Zarmi, Yair; Bar-David, Shirli

    2014-01-01

    Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population's long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele's presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population's allele frequency spectrum to provide predictions for allele recovery. The model's analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the “One Migrant per Generation” rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution. PMID:25526062

  9. Allelic richness following population founding events--a stochastic modeling framework incorporating gene flow and genetic drift.

    PubMed

    Greenbaum, Gili; Templeton, Alan R; Zarmi, Yair; Bar-David, Shirli

    2014-01-01

    Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population's long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele's presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population's allele frequency spectrum to provide predictions for allele recovery. The model's analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the "One Migrant per Generation" rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution.

  10. Unique frequency distribution of ice and dust cloud observations over Gale Crater on Mars

    NASA Astrophysics Data System (ADS)

    de la Torre Juarez, M.; Cantor, B. A.

    2012-12-01

    A normalized cloud index was tested to detect clouds using the MARs Camera Imager (MARCI) on the Mars Reconaissance orbiter. The algorithm and its validation are described. After validation it was used to extract the frequency of ice and dust clouds over the region around Gale. The analysis suggests a higher frequency of hazes and ice clouds over this region than over the other three final candidate sites for landing the Mars Science Laboratory at Mawrth, Eberswalde and Holding and a different type of non-guassian distribution raising the question about what properties around Gale could be causing a different cloud cycle.

  11. The velocity and the density spectrum of the solar wind from simultaneous three-frequency IPS observations

    NASA Technical Reports Server (NTRS)

    Scott, S. L.; Rickett, B. J.; Armstrong, J. W.

    1983-01-01

    Density inhomogeneities in the solar wind cause fluctuations regarding the emission of small diameter radio sources. Such fluctuations are called interplanetary scintillation (IPS). IPS has been studied to obtain information on both the solar wind and on the radio sources. In the present investigation it is attempted to extract information about the solar wind from simultaneous IPS observations at three radio frequencies and a single antenna. Data were recorded at frequencies of 270 MHz, 340 MHz, and 470 MHz on a 91 m telescope. Five different radio sources were observed. The observations are compared with theoretical predictions for spectra, cross-spectra, and cross-correlations using weak scattering theory and various models for the wavenumber spectrum of density inhomogeneities in the solar wind. Good fits are obtained over the observed wavenumbers to a spectrum modeled as a power law.

  12. Optimized trigger for ultra-high-energy cosmic-ray and neutrino observations with the low frequency radio array

    NASA Astrophysics Data System (ADS)

    Singh, K.; Mevius, M.; Scholten, O.; Anderson, J. M.; van Ardenne, A.; Arts, M.; Avruch, M.; Asgekar, A.; Bell, M.; Bennema, P.; Bentum, M.; Bernadi, G.; Best, P.; Boonstra, A.-J.; Bregman, J.; van de Brink, R.; Broekema, C.; Brouw, W.; Brueggen, M.; Buitink, S.; Butcher, H.; van Cappellen, W.; Ciardi, B.; Coolen, A.; Damstra, S.; Dettmar, R.; van Diepen, G.; Dijkstra, K.; Donker, P.; Doorduin, A.; Drost, M.; van Duin, A.; Eisloeffel, J.; Falcke, H.; Garrett, M.; Gerbers, M.; Grießmeier, J.-M.; Grit, T.; Gruppen, P.; Gunst, A.; van Haarlem, M.; Hoeft, M.; Holties, H.; Hörandel, J.; Horneffer, L. A.; Huijgen, A.; James, C.; de Jong, A.; Kant, D.; Kooistra, E.; Koopman, Y.; Koopmans, L.; Kuper, G.; Lambropoulos, P.; van Leeuwen, J.; Loose, M.; Maat, P.; Mallary, C.; McFadden, R.; Meulman, H.; Mol, J.-D.; Morawietz, J.; Mulder, E.; Munk, H.; Nieuwenhuis, L.; Nijboer, R.; Norden, M. J.; Noordam, J.; Overeem, R.; Paas, H.; Pandey, V. N.; Pandey-Pommier, M.; Pizzo, R.; Polatidis, A.; Reich, W.; de Reijer, J.; Renting, A.; Riemers, P.; Roettgering, H.; Romein, J.; Roosjen, J.; Ruiter, M.; Schoenmakers, A.; Schoonderbeek, G.; Sluman, J.; Smirnov, O.; Stappers, B.; Steinmetz, M.; Stiepel, H.; Stuurwold, K.; Tagger, M.; Tang, Y.; Ter Veen, S.; Vermeulen, R.; de Vos, M.; Vogt, C.; van der Wal, E.; Weggemans, H.; Wijnholds, S.; Wise, M.; Wucknitz, O.; Yattawatta, S.; van Zwieten, J.

    2012-02-01

    When an ultra-high energy neutrino or cosmic-ray strikes the Lunar surface a radio-frequency pulse is emitted. We plan to use the LOFAR radio telescope to detect these pulses. In this work we propose an efficient trigger implementation for LOFAR optimized for the observation of short radio pulses.

  13. Biased Allelic Expression in Human Primary Fibroblast Single Cells

    PubMed Central

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

    2015-01-01

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

  14. Electromagnetic Waves with Frequencies Near the Local Proton Gryofrequency: ISEF-3 1 AU Observations

    NASA Technical Reports Server (NTRS)

    Tsurutani, B.

    1993-01-01

    Low Frequency electromagnetic waves with periods near the local proton gyrofrequency have been detected near 1 AU by the magnetometer onboard ISEE-3. For these 1 AU waves two physical processes are possible: solar wind pickup of nuetral (interstellar?) particles and generation by relativistic electron beams propagating from the Sun.

  15. Magnetic Force Nanoprobe for Direct Observation of Audio Frequency Tonotopy of Hair Cells.

    PubMed

    Kim, Ji-Wook; Lee, Jae-Hyun; Ma, Ji-Hyun; Chung, Eunna; Choi, Hongsuh; Bok, Jinwoong; Cheon, Jinwoo

    2016-06-01

    Sound perception via mechano-sensation is a remarkably sensitive and fast transmission process, converting sound as a mechanical input to neural signals in a living organism. Although knowledge of auditory hair cell functions has advanced over the past decades, challenges remain in understanding their biomechanics, partly because of their biophysical complexity and the lack of appropriate probing tools. Most current studies of hair cells have been conducted in a relatively low-frequency range (<1000 Hz); therefore, fast kinetic study of hair cells has been difficult, even though mammalians have sound perception of 20 kHz or higher. Here, we demonstrate that the magnetic force nanoprobe (MFN) has superb spatiotemporal capabilities to mechanically stimulate spatially-targeted individual hair cells with a temporal resolution of up to 9 μs, which is equivalent to approximately 50 kHz; therefore, it is possible to investigate avian hair cell biomechanics at different tonotopic regions of the cochlea covering a full hearing frequency range of 50 to 5000 Hz. We found that the variation of the stimulation frequency and amplitude of hair bundles creates distinct mechanical responsive features along the tonotopic axis, where the kinetics of the hair bundle recovery motion exhibits unique frequency-dependent characteristics: basal, middle, and apical hair bundles can effectively respond at their respective ranges of frequency. We revealed that such recovery kinetics possesses two different time constants that are closely related to the passive and active motilities of hair cells. The use of MFN is critical for the kinetics study of free-standing hair cells in a spatiotemporally distinct tonotopic organization.

  16. Low-radio-frequency eclipses of the redback pulsar J2215+5135 observed in the image plane with LOFAR

    NASA Astrophysics Data System (ADS)

    Broderick, J. W.; Fender, R. P.; Breton, R. P.; Stewart, A. J.; Rowlinson, A.; Swinbank, J. D.; Hessels, J. W. T.; Staley, T. D.; van der Horst, A. J.; Bell, M. E.; Carbone, D.; Cendes, Y.; Corbel, S.; Eislöffel, J.; Falcke, H.; Grießmeier, J.-M.; Hassall, T. E.; Jonker, P.; Kramer, M.; Kuniyoshi, M.; Law, C. J.; Markoff, S.; Molenaar, G. J.; Pietka, M.; Scheers, L. H. A.; Serylak, M.; Stappers, B. W.; ter Veen, S.; van Leeuwen, J.; Wijers, R. A. M. J.; Wijnands, R.; Wise, M. W.; Zarka, P.

    2016-07-01

    The eclipses of certain types of binary millisecond pulsars (i.e. `black widows' and `redbacks') are often studied using high-time-resolution, `beamformed' radio observations. However, they may also be detected in images generated from interferometric data. As part of a larger imaging project to characterize the variable and transient sky at radio frequencies <200 MHz, we have blindly detected the redback system PSR J2215+5135 as a variable source of interest with the Low-Frequency Array (LOFAR). Using observations with cadences of two weeks - six months, we find preliminary evidence that the eclipse duration is frequency dependent (∝ν-0.4), such that the pulsar is eclipsed for longer at lower frequencies, in broad agreement with beamformed studies of other similar sources. Furthermore, the detection of the eclipses in imaging data suggests an eclipsing medium that absorbs the pulsed emission, rather than scattering it. Our study is also a demonstration of the prospects of finding pulsars in wide-field imaging surveys with the current generation of low-frequency radio telescopes.

  17. Evidence for changes in the magnitude and frequency of observed rainfall vs. snowmelt driven floods in Norway

    NASA Astrophysics Data System (ADS)

    Vormoor, Klaus; Lawrence, Deborah; Schlichting, Lena; Wilson, Donna; Wong, Wai Kwok

    2016-07-01

    There is increasing evidence for recent changes in the intensity and frequency of heavy precipitation and in the number of days with snow cover in many parts of Norway. The question arises as to whether these changes are also discernable with respect to their impacts on the magnitude and frequency of flooding and on the processes producing high flows. In this study, we tested up to 211 catchments for trends in peak flow discharge series by applying the Mann-Kendall test and Poisson regression for three different time periods (1962-2012, 1972-2012, 1982-2012). Field-significance was tested using a bootstrap approach. Over threshold discharge events were classified into rainfall vs. snowmelt dominated floods, based on a simple water balance approach utilizing a nationwide 1 × 1 km2 gridded data set with daily observed rainfall and simulated snowmelt data. Results suggest that trends in flood frequency are more pronounced than trends in flood magnitude and are more spatially consistent with observed changes in the hydrometeorological drivers. Increasing flood frequencies in southern and western Norway are mainly due to positive trends in the frequency of rainfall dominated events, while decreasing flood frequencies in northern Norway are mainly the result of negative trends in the frequency of snowmelt dominated floods. Negative trends in flood magnitude are found more often than positive trends, and the regional patterns of significant trends reflect differences in the flood generating processes (FGPs). The results illustrate the benefit of distinguishing FGPs rather than simply applying seasonal analyses. The results further suggest that rainfall has generally gained an increasing importance for the generation of floods in Norway, while the role of snowmelt has been decreasing and the timing of snowmelt dominated floods has become earlier.

  18. Dynamics of insecticide resistance alleles in house fly populations from New York and Florida.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The frequency of insecticide resistance alleles for two genes (Vssc1 and CYP6D1) was studied in field collected populations of house flies from two different climates. While the frequency of these resistance alleles in flies at dairies from four states has recently been reported, there is no infor...

  19. Experimental observation of three-frequency quasiperiodic solution in a ring of unidirectionally coupled oscillators.

    PubMed

    Borkowski, L; Perlikowski, P; Kapitaniak, T; Stefanski, A

    2015-06-01

    The subject of the experimental research supported with numerical simulations presented in this paper is an analog electrical circuit representing the ring of unidirectionally coupled single-well Duffing oscillators. The research is concentrated on the existence of the stable three-frequency quasiperiodic attractor in this system. It is shown that such solution can be robustly stable in a wide range of parameters of the system under consideration in spite of a parameter mismatch which is unavoidable during experiment. PMID:26172771

  20. HMW and LMW glutenin alleles among putative tetraploid and hexaploid European spelt wheat (Triticum spelta L.) progenitors.

    PubMed

    Yan, Y; Hsam, S L K; Yu, J Z; Jiang, Y; Ohtsuka, I; Zeller, F J

    2003-11-01

    The allelic compositions of high- and low-molecular-weight subunits of glutenins (HMW-GS and LMW-GS) among European spelt ( Triticum spelta L.) and related hexaploid and tetraploid Triticum species were investigated by one- and two-dimensional polyacrylamide-gel electrophoresis (PAGE) and capillary electrophoresis (CE). A total of seven novel glutenin alleles (designated A1a*, B1d*, B1g*, B1f*, B1j*, D1a* at Glu-1 and A3h at the Glu-3 loci, respectively) in European spelt wheat were detected by SDS-PAGE, which were confirmed further by employing A-PAGE and CE methods. Particularly, two HMW-GS alleles, Glu-B1d* coding the subunits 6.1 and 22.1, and Glu-B1f* coding the subunits 13 and 22*, were found to occur in European spelt with frequencies of 32.34% and 5.11%, respectively. These two alleles were present in cultivated emmer (Triticum dicoccum), but they were not observed in bread wheat (Triticum aestivum L.). The allele Glu-B1g* coding for 13* and 19* subunits found in spelt wheat was also detected in club wheat (Triticum compactum L.). Additionally, two alleles coding for LMW-GS, Glu-A3h and Glu-B3d, occurred with high frequencies in spelt, club and cultivated emmer wheat, whereas these were not found or present with very low frequencies in bread wheat. Our results strongly support the secondary origin hypothesis, namely European spelt wheat originated from hybridization between cultivated emmer and club wheat. This is also confirmed experimentally by the artificial synthesis of spelt through crossing between old European emmer wheat, T. dicoccum and club wheat, T. compactum.

  1. Experimental observation of stimulated low-frequency Raman scattering in water suspensions of silver and gold nanoparticles.

    PubMed

    Tcherniega, N V; Zemskov, K I; Savranskii, V V; Kudryavtseva, A D; Olenin, A Y; Lisichkin, G V

    2013-03-15

    In this Letter we report on experimental observation of stimulated low-frequency Raman scattering (SLFRS) in gold and silver nanoparticle suspensions excited by 20 ns ruby laser pulses, SLFRS propagated in forward and backward directions with a maximum conversion efficiency up to 20%. Frequency shift for silver nanoparticle suspension was found to be 0.33 THz and for gold nanoparticle suspension 0.435 THz. This type of stimulated scattering of light can be used as an effective source of biharmonic pumping for solving a large number of practical tasks.

  2. Detection of Ancestry Informative HLA Alleles Confirms the Admixed Origins of Japanese Population

    PubMed Central

    Nakaoka, Hirofumi; Mitsunaga, Shigeki; Hosomichi, Kazuyoshi; Shyh-Yuh, Liou; Sawamoto, Taiji; Fujiwara, Tsutomu; Tsutsui, Naohisa; Suematsu, Koji; Shinagawa, Akira; Inoko, Hidetoshi; Inoue, Ituro

    2013-01-01

    The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago. PMID:23577161

  3. Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population.

    PubMed

    Nakaoka, Hirofumi; Mitsunaga, Shigeki; Hosomichi, Kazuyoshi; Shyh-Yuh, Liou; Sawamoto, Taiji; Fujiwara, Tsutomu; Tsutsui, Naohisa; Suematsu, Koji; Shinagawa, Akira; Inoko, Hidetoshi; Inoue, Ituro

    2013-01-01

    The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago. PMID:23577161

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

    PubMed Central

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

    1998-01-01

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

  5. Observations of low and intermediate-frequency-peaked BL Lacs above 100 GeV with VERITAS

    NASA Astrophysics Data System (ADS)

    Errando, M.

    2013-12-01

    Most of the ~ 50 blazars detected to date at TeV energies (E > 0.1 TeV) are high-frequency-peaked BL Lacs (HBLs). Only a handful episodic detections of low- and intermediate-frequency-peaked BL Lacs (LBL/IBLs, with synchrotron peak frequencies in the infrared and optical regime) have been reported by ground-based gamma-ray telescopes, typically during high-flux states. The VERITAS array located in southern Arizona has observed five known TeV LBL/IBLs since 2009: 3C 66A, WComae, PKS 1424+240, S5 0716+714 and BL Lacertae, with exposures of 5-10 hours/year, which so far resulted in the detection of a bright, sub-hour timescale gamma-ray flare of BL Lacertae in June 2011. We also report the detection and characterization of two new IBLs: VER J0521+211 and B2 1215+30.

  6. Direct observation of low frequency confined acoustic phonons in silver nanoparticles: Terahertz time domain spectroscopy.

    PubMed

    Kumar, Sunil; Kamaraju, N; Karthikeyan, B; Tondusson, M; Freysz, E; Sood, A K

    2010-07-01

    Terahertz time domain spectroscopy has been used to study low frequency confined acoustic phonons of silver nanoparticles embedded in poly(vinyl alcohol) matrix in the spectral range of 0.1-2.5 THz. The real and imaginary parts of the dielectric function show two bands at 0.60 and 2.12 THz attributed to the spheroidal and toroidal modes of silver nanoparticles, thus demonstrating the usefulness of terahertz time domain spectroscopy as a complementary technique to Raman spectroscopy in characterizing the nanoparticles.

  7. Mid-frequency sound propagation through internal waves at short range with synoptic oceanographic observations.

    PubMed

    Rouseff, Daniel; Tang, Dajun; Williams, Kevin L; Wang, Zhongkang; Moum, James N

    2008-09-01

    Preliminary results are presented from an analysis of mid-frequency acoustic transmission data collected at range 550 m during the Shallow Water 2006 Experiment. The acoustic data were collected on a vertical array immediately before, during, and after the passage of a nonlinear internal wave on 18 August, 2006. Using oceanographic data collected at a nearby location, a plane-wave model for the nonlinear internal wave's position as a function of time is developed. Experimental results show a new acoustic path is generated as the internal wave passes above the acoustic source.

  8. The Behavior Observation Scale for Autism (BOS): Relationship of Frequency of Behavior to IQ.

    ERIC Educational Resources Information Center

    Freeman, B. J.; And Others

    The Behavior Observation Scale (BOS) was administered to 53 autistic children, 35 mentally retarded children matched for MA, and 33 normal children (all 2 to 5 years old) in an attempt to quantify autistic behavior. Ss were observed 3 days for 3 minutes through a one way mirror in a playroom setting where occurrence of 67 behaviors on the BOS was…

  9. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck.

    PubMed

    Balick, Daniel J; Do, Ron; Cassa, Christopher A; Reich, David; Sunyaev, Shamil R

    2015-08-01

    Population bottlenecks followed by re-expansions have been common throughout history of many populations. The response of alleles under selection to such demographic perturbations has been a subject of great interest in population genetics. On the basis of theoretical analysis and computer simulations, we suggest that this response qualitatively depends on dominance. The number of dominant or additive deleterious alleles per haploid genome is expected to be slightly increased following the bottleneck and re-expansion. In contrast, the number of completely or partially recessive alleles should be sharply reduced. Changes of population size expose differences between recessive and additive selection, potentially providing insight into the prevalence of dominance in natural populations. Specifically, we use a simple statistic, [Formula: see text], where xi represents the derived allele frequency, to compare the number of mutations in different populations, and detail its functional dependence on the strength of selection and the intensity of the population bottleneck. We also provide empirical evidence showing that gene sets associated with autosomal recessive disease in humans may have a BR indicative of recessive selection. Together, these theoretical predictions and empirical observations show that complex demographic history may facilitate rather than impede inference of parameters of natural selection. PMID:26317225

  10. Association between AgI-CA alleles and severity of autosomal recessive proximal spina lmuscular atrophy

    SciTech Connect

    DiDonato, C.J.; Carpten, J.D.; Fuerst, P.; Ingraham, S.E.; Mendell, J.R.; Burghes, A.H.M.; Morgan, K.; Prescott, G.; Simard, L.R.; McPherson, J.D.

    1994-12-01

    The gene for autosomal recessive proximal spinal muscular atrophy (SMA) has been mapped to an 850-kb interval on 5q11.2-q13.3, between the centromeric D5S823 and telomeric D5S557 markers. We report a new complex marker, Ag1-CA, that lies in this interval, whose primers produce one, two, or rarely three amplification-fragment-length variants (AFLVs) per allele. Class I chromosomes are those which amplify a single AFLV allele, and class II chromosomes are those which amplify an allele with two or three AFLVs. Ag1-CA shows highly significant allelic association with type I SMA in both the French Canadian (Hopital Sainte-Justine (HSJ)) and American (Ohio State University (OSU)) populations (P < .0001). Significant association between the Ag1-CA genotype and disease severity was also observed. Type I patients were predominantly homozygous for class I chromosomes (P = .0003 OSU; P = 0.0012 HSJ), whereas the majority of type II patients were heterozygous for class I and II chromosomes (P = .0014 OSU; P = .001 HSJ). There was no significant difference in Ag1-CA genotype frequencies between type III patients (P = .5 OSU; P = .25 HSJ) and the paired normal chromosomes from both carrier parents. Our results indicate that Ag1-CA is the most closely linked marker to SMA and defines the critical candidate-gene region. Finally, we have proposed a model that should be taken into consideration when screening candidates SMA genes.

  11. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck

    PubMed Central

    Balick, Daniel J.; Do, Ron; Cassa, Christopher A.; Reich, David; Sunyaev, Shamil R.

    2015-01-01

    Population bottlenecks followed by re-expansions have been common throughout history of many populations. The response of alleles under selection to such demographic perturbations has been a subject of great interest in population genetics. On the basis of theoretical analysis and computer simulations, we suggest that this response qualitatively depends on dominance. The number of dominant or additive deleterious alleles per haploid genome is expected to be slightly increased following the bottleneck and re-expansion. In contrast, the number of completely or partially recessive alleles should be sharply reduced. Changes of population size expose differences between recessive and additive selection, potentially providing insight into the prevalence of dominance in natural populations. Specifically, we use a simple statistic, BR≡∑xipop1/∑xjpop2, where x i represents the derived allele frequency, to compare the number of mutations in different populations, and detail its functional dependence on the strength of selection and the intensity of the population bottleneck. We also provide empirical evidence showing that gene sets associated with autosomal recessive disease in humans may have a B R indicative of recessive selection. Together, these theoretical predictions and empirical observations show that complex demographic history may facilitate rather than impede inference of parameters of natural selection. PMID:26317225

  12. Intense low-frequency chorus waves observed by Van Allen Probes: Fine structures and potential effect on radiation belt electrons

    NASA Astrophysics Data System (ADS)

    Gao, Zhonglei; Su, Zhenpeng; Zhu, Hui; Xiao, Fuliang; Zheng, Huinan; Wang, Yuming; Shen, Chao; Wang, Shui

    2016-02-01

    Frequency distribution is a vital factor in determining the contribution of whistler mode chorus to radiation belt electron dynamics. Chorus is usually considered to occur in the frequency range 0.1-0.8fce_eq (with the equatorial electron gyrofrequency fce_eq). We here report an event of intense low-frequency chorus with nearly half of wave power distributed below 0.1fce_eq observed by Van Allen Probe A on 27 August 2014. This emission propagated quasi-parallel to the magnetic field and exhibited hiss-like signatures most of the time. The low-frequency chorus can produce the rapid loss of low-energy (˜0.1 MeV) electrons, different from the normal chorus. For high-energy (≥0.5 MeV) electrons, the low-frequency chorus can yield comparable momentum diffusion to that of the normal chorus but much stronger (up to 2 orders of magnitude) pitch angle diffusion near the loss cone.

  13. Nature's starships. I. Observed abundances and relative frequencies of amino acids in meteorites

    SciTech Connect

    Cobb, Alyssa K.; Pudritz, Ralph E. E-mail: pudritz@physics.mcmaster.ca

    2014-03-10

    The class of meteorites called carbonaceous chondrites are examples of material from the solar system which have been relatively unchanged from the time of their initial formation. These meteorites have been classified according to the temperatures and physical conditions of their parent planetesimals. We collate available data on amino acid abundance in these meteorites and plot the concentrations of different amino acids for each meteorite within various meteorite subclasses. We plot average concentrations for various amino acids across meteorites separated by subclass and petrologic type. We see a predominance in the abundance and variety of amino acids in CM2 and CR2 meteorites. The range in temperature corresponding to these subclasses indicates high degrees of aqueous alteration, suggesting aqueous synthesis of amino acids. Within the CM2 and CR2 subclasses, we identify trends in relative frequencies of amino acids to investigate how common amino acids are as a function of their chemical complexity. These two trends (total abundance and relative frequencies) can be used to constrain formation parameters of amino acids within planetesimals. Our organization of the data supports an onion shell model for the temperature structure of planetesimals. The least altered meteorites (type 3) and their amino acids originated near cooler surface regions. The most active amino acid synthesis likely took place at intermediate depths (type 2). The most altered materials (type 1) originated furthest toward parent body cores. This region is likely too hot to either favor amino acid synthesis or for amino acids to be retained after synthesis.

  14. Evaluation of Long-Term Cloud-Resolving Model Simulations Using Satellite Radiance Observations and Multi-Frequency Satellite Simulators

    NASA Technical Reports Server (NTRS)

    Matsui, Toshihisa; Zeng, Xiping; Tao, Wei-Kuo; Masunaga, Hirohiko; Olson, William S.; Lang, Stephen

    2008-01-01

    This paper proposes a methodology known as the Tropical Rainfall Measuring Mission (TRMM) Triple-Sensor Three-step Evaluation Framework (T3EF) for the systematic evaluation of precipitating cloud types and microphysics in a cloud-resolving model (CRM). T3EF utilizes multi-frequency satellite simulators and novel statistics of multi-frequency radiance and backscattering signals observed from the TRMM satellite. Specifically, T3EF compares CRM and satellite observations in the form of combined probability distributions of precipitation radar (PR) reflectivity, polarization-corrected microwave brightness temperature (Tb), and infrared Tb to evaluate the candidate CRM. T3EF is used to evaluate the Goddard Cumulus Ensemble (GCE) model for cases involving the South China Sea Monsoon Experiment (SCSMEX) and Kwajalein Experiment (KWAJEX). This evaluation reveals that the GCE properly captures the satellite-measured frequencies of different precipitating cloud types in the SCSMEX case but underestimates the frequencies of deep convective and deep stratiform types in the KWAJEX case. Moreover, the GCE tends to simulate excessively large and abundant frozen condensates in deep convective clouds as inferred from the overestimated GCE-simulated radar reflectivities and microwave Tb depressions. Unveiling the detailed errors in the GCE s performance provides the best direction for model improvements.

  15. Allelic association between marker loci.

    PubMed

    Lonjou, C; Collins, A; Morton, N E

    1999-02-16

    Allelic association has proven useful to refine the location of major genes prior to positional cloning, but it is of uncertain value for genome scans in complex inheritance. We have extended kinship theory to give information content for linkage and allelic association. Application to pairs of closely linked markers as a surrogate for marker x oligogene pairs indicates that association is largely determined by regional founders, with little effect of subsequent demography. Sub-Saharan Africa has the least allelic association, consistent with settlement of other regions by small numbers of founders. Recent speculation about substantial advantages of isolates over large populations, of constant size over expansion, and of F1 hybrids over incrosses is not supported by theory or data. On the contrary, fewer affected cases, less opportunity for replication, and more stochastic variation tend to make isolates less informative for allelic association, as they are for linkage.

  16. 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)

  17. The effect of the lunar cycle on frequency of births: a retrospective observational study in Indian population.

    PubMed

    Bharati, Saswata; Sarkar, Malay; Haldar, Partha Sarathi; Jana, Swapan; Mandal, Subrata

    2012-01-01

    For ancient period moon has been held responsible for many biological activities. That way, lunar cycle, by activity of moon, has been held responsible for increase in number of child birth. In this retrospective, observational study, we examined a total of 9890 full-term spontaneous deliveries as well as non-elective cesarean sections that occurred throughout 12 lunar months (February 7 th , 2008-January 25 th , 2009) in a rural medical college to evaluate the influence of the lunar position on the distribution of deliveries among Indian population. Student's 't' test and ANOVA were used for statistical analysis where each delivery was considered as a single measure. We found no significant differences in the frequency of births during various phase of lunar cycle regardless of route of delivery. Our observations do not support the hypothesis of a relationship between lunar cycle and the frequency of obstetric deliveries.

  18. Observation of fluctuation-driven particle flux reduction by low-frequency zonal flow in a linear magnetized plasma

    SciTech Connect

    Chen, R.; Xie, J. L. Yu, C. X.; Liu, A. D.; Lan, T.; Li, H.; Liu, W. D.; Zhang, S. B.; Kong, D. F.; Hu, G. H.

    2015-01-15

    Low-frequency zonal flow (ZF) has been observed in a linear magnetic plasma device, exhibiting significant intermittency. Using the conditional analysis method, a time-averaged fluctuation-induced particle flux was observed to consistently decrease as ZF increased in amplitude. A dominant fraction of the flux, which is driven by drift-wave harmonics, is reversely modulated by ZF in the time domain. Spectra of the flux, together with each of the related turbulence properties, are estimated subject to two conditions, i.e., when potential fluctuation series represents a strong ZF intermittency or a very weak ZF component. Comparison of frequency-domain results demonstrates that ZF reduces the cross-field particle transport primarily by suppressing the density fluctuation as well as decorrelating density and potential fluctuations.

  19. The Impact of a Modified Cooperative Learning Technique on the Grade Frequencies Observed in a Preparatory Chemistry Course

    NASA Astrophysics Data System (ADS)

    Hayes Russell, Bridget J.

    This dissertation explored the impact of a modified cooperative learning technique on the final grade frequencies observed in a large preparatory chemistry course designed for pre-science majors. Although the use of cooperative learning at all educational levels is well researched and validated in the literature, traditional lectures still dominate as the primary methodology of teaching. This study modified cooperative learning techniques by addressing commonly cited reasons for not using the methodology. Preparatory chemistry students were asked to meet in cooperative groups outside of class time to complete homework assignments. A chi-square goodness-of-fit revealed that the final grade frequency distributions observed were different than expected. Although the distribution was significantly different, the resource investment using this particular design challenged the practical significance of the findings. Further, responses from a survey revealed that the students did not use the suggested group functioning methods that empirically are known to lead to more practically significant results.

  20. CYP2D6: novel genomic structures and alleles

    PubMed Central

    Kramer, Whitney E.; Walker, Denise L.; O’Kane, Dennis J.; Mrazek, David A.; Fisher, Pamela K.; Dukek, Brian A.; Bruflat, Jamie K.; Black, John L.

    2010-01-01

    Objective CYP2D6 is a polymorphic gene. It has been observed to be deleted, to be duplicated and to undergo recombination events involving the CYP2D7 pseudogene and surrounding sequences. The objective of this study was to discover the genomic structure of CYP2D6 recombinants that interfere with clinical genotyping platforms that are available today. Methods Clinical samples containing rare homozygous CYP2D6 alleles, ambiguous readouts, and those with duplication signals and two different alleles were analyzed by long-range PCR amplification of individual genes, PCR fragment analysis, allele-specific primer extension assay, and DNA sequencing to characterize alleles and genomic structure. Results Novel alleles, genomic structures, and the DNA sequence of these structures are described. Interestingly, in 49 of 50 DNA samples that had CYP2D6 gene duplications or multiplications where two alleles were detected, the chromosome containing the duplication or multiplication had identical tandem alleles. Conclusion Several new CYP2D6 alleles and genomic structures are described which will be useful for CYP2D6 genotyping. The findings suggest that the recombination events responsible for CYP2D6 duplications and multiplications are because of mechanisms other than interchromosomal crossover during meiosis. PMID:19741566

  1. Observations on the magnitude-frequency distribution of Earth-crossing asteroids

    NASA Technical Reports Server (NTRS)

    Shoemaker, Eugene M.; Shoemaker, Carolyn S.

    1987-01-01

    During the past decade, discovery of Earth-crossing asteroids has continued at the pace of several per year; the total number of known Earth crossers reached 70 as of September, 1986. The sample of discovered Earth crossers has become large enough to provide a fairly strong statistical basis for calculations of mean probabilities of asteroid collision with the Earth, the Moon, and Venus. It is also now large enough to begin to address the more difficult question of the magnitude-frequency distribution and size distribution of the Earth-crossing asteroids. Absolute V magnitude, H, was derived from reported magnitudes for each Earth crosser on the basis of a standard algorithm that utilizes a physically realistic phase function. The derived values of H range from 12.88 for (1627) Ivar to 21.6 for the Palomar-Leiden object 6344, which is the faintest and smallest asteroid discovered.

  2. Observations of low-frequency inertia-gravity waves in the lower stratosphere over Arecibo

    NASA Technical Reports Server (NTRS)

    Cornish, C. R.; Larsen, M. F.

    1989-01-01

    Results are presented of a detailed analysis of the horizontal wind data in the subtropical upper troposphere and lower stratosphere, obtained with the 430-MHz radar at Arecibo (Puerto Rico) in May 1982 and April 1983. Both sets of observations displayed a slowly varying anticyclonically rotating persistent structure in the wind field just above the tropopause, of the type that would be expected if the oscillations were associated with quasi-inertial period waves. The quasi-inertial period structure in the Arecibo observations appears to be typical of the results of a number of other studies, indicating that quasi-inertial period waves are a ubiquitous feature in the lower stratosphere, similar to what is observed in the oceans.

  3. Low-frequency radio observations of SN 2011dh and the evolution of its post-shock plasma properties

    NASA Astrophysics Data System (ADS)

    Yadav, Naveen; Ray, Alak; Chakraborti, Sayan

    2016-06-01

    We present late time, low-frequency observations of SN 2011dh made using the Giant Metrewave Radio Telescope (GMRT). Our observations at 325, 610 and 1280 MHz conducted between 93 and 421 d after the explosion supplement the millimeter and centimetre wave observations conducted between 4 and 15 d after explosion using the Combined Array for Research in Millimeter-wave Astronomy (CARMA) and extensive radio observations (1.0-36.5 GHz) conducted between 16 and 93 d after explosion using Jansky Very Large Array (JVLA). We fit a synchrotron self absorption model (SSA) to the 610 and 1280 MHz radio light curves. We use it to determine the radius (Rp) and magnetic field (Bp) at 173 and 323 d after the explosion. A comparison of the peak radio luminosity Lop with the product of the peak frequency νp and time to peak tp shows that the supernova evolves between the epochs of CARMA, JVLA and GMRT observations. It shows a general slowing down of the expansion speed of the radio emitting region on a time-scale of several hundred days during which the shock is propagating through a circumstellar medium set up by a wind with a constant mass-loss parameter, dot{M}/{v}_w. We derive the mass-loss parameter (A⋆) based on 610 and 1280 MHz radio light curves, which are found to be consistent with each other within error limits.

  4. Comparison of signal to noise ratios from spatial and frequency domain formulations of nonprewhitening model observers in digital mammography

    SciTech Connect

    Sisini, Francesco; Zanca, Federica; Marshall, Nicholas W.; Taibi, Angelo; Cardarelli, Paolo; Bosmans, Hilde

    2012-09-15

    Purpose: Image quality indices based upon model observers are promising alternatives to laborious human readings of contrast-detail images. This is especially appealing in digital mammography as limiting values for contrast thresholds determine, according to some international protocols, the acceptability of these systems in the radiological practice. The objective of the present study was to compare the signal to noise ratios (SNR) obtained with two nonprewhitening matched filter model observer approaches, one in the spatial domain and the other in the frequency domain, and with both of them worked out for disks as present in the CDMAM phantom. Methods: The analysis was performed using images acquired with the Siemens Novation and Inspiration digital mammography systems. The spatial domain formulation uses a series of high dose CDMAM images as the signal and a routine exposure of two flood images to calculate the covariance matrix. The frequency domain approach uses the mathematical description of a disk and modulation transfer function (MTF) and noise power spectrum (NPS) calculated from images. Results: For both systems most of the SNR values calculated in the frequency domain were in very good agreement with the SNR values calculated in the spatial domain. Both the formulations in the frequency domain and in the spatial domain show a linear relationship between SNR and the diameter of the CDMAM discs. Conclusions: The results suggest that both formulations of the model observer lead to very similar figures of merit. This is a step forward in the adoption of figures of merit based on NPS and MTF for the acceptance testing of mammography systems.

  5. Applications of high-frequency resolution, wide-field VLBI: observations of nearby star-forming galaxies & habitable exoplanetary candidates

    NASA Astrophysics Data System (ADS)

    Rampadarath, Hayden

    2014-04-01

    Until recently, the maximum observable field of view of Very Long Baseline Interferometric (VLBI) observations was limited, predominantly, by the ability to process large volumes of data. However, the availability of software correlators and high performance computing have provided the means to overcome these restrictions, giving rise to the technique of wide-field VLBI. This thesis reports on the application of this technique to investigate two different science cases: (1) to explore the use of VLBI for targeted searches for extra-terrestrial intelligence (SETI); (2) to investigate the compact radio source populations, supernovae, and star formation rates and the interstellar media of nearby star-forming galaxies. Radio sources detected with VLBI will display characteristic variations as a function of time and frequency that are dependent on their locations with respect to the observing phase centre. Thus, a planet with a radio emitting civilisation, bright enough to be detected, can be identified and separated from human generated signals through VLBI observations. This idea was tested on a VLBI observation of the planetary system Gliese 581. The dataset was searched for candidate SETI signals, in both time and frequency, with amplitudes greater than five times the baseline sensitivity on all baselines. Candidate signals were selected and through the use of automated, statistical data analysis techniques were ruled out as originating from the Gliese 581 system. The results of this study place an upper limit of 7 MW/Hz on the power output of any isotropic emitter located in the Gliese 581 system, within this frequency range. While the study was unable to identify any signals originating from Gliese 581, the techniques presented are applicable to the next-generation interferometers, such as the long baselines of the Square Kilometre Array.

  6. Color vision pigment frequencies in wild tamarins (Saguinus spp.).

    PubMed

    Surridge, A K; Suárez, S S; Buchanan-Smith, H M; Smith, A C; Mundy, N I

    2005-12-01

    The adaptive importance of polymorphic color vision found in many New World and some prosimian primates has been discussed for many years. Polymorphism is probably maintained in part through a heterozygote advantage for trichromatic females, as such individuals are observed to have greater foraging success when selecting ripe fruits against a background of forest leaves. However, recent work also suggests there are some situations in which dichromatic individuals may have an advantage, and that variation in color vision among individuals possessing different alleles may also be significant. Alleles that confer a selective advantage to individuals are expected to occur at a higher frequency in populations than those that do not. Therefore, analyzing the frequencies of color vision alleles in wild populations can add to our understanding of the selective advantages of some color vision phenotypes over others. With this aim, we used molecular techniques to determine the frequencies of color vision alleles in 12 wild tamarin groups representing three species of the genus Saguinus. Our results show that allele frequencies are not equal, possibly reflecting different selective regimes operating on different color vision phenotypes.

  7. Color vision pigment frequencies in wild tamarins (Saguinus spp.).

    PubMed

    Surridge, A K; Suárez, S S; Buchanan-Smith, H M; Smith, A C; Mundy, N I

    2005-12-01

    The adaptive importance of polymorphic color vision found in many New World and some prosimian primates has been discussed for many years. Polymorphism is probably maintained in part through a heterozygote advantage for trichromatic females, as such individuals are observed to have greater foraging success when selecting ripe fruits against a background of forest leaves. However, recent work also suggests there are some situations in which dichromatic individuals may have an advantage, and that variation in color vision among individuals possessing different alleles may also be significant. Alleles that confer a selective advantage to individuals are expected to occur at a higher frequency in populations than those that do not. Therefore, analyzing the frequencies of color vision alleles in wild populations can add to our understanding of the selective advantages of some color vision phenotypes over others. With this aim, we used molecular techniques to determine the frequencies of color vision alleles in 12 wild tamarin groups representing three species of the genus Saguinus. Our results show that allele frequencies are not equal, possibly reflecting different selective regimes operating on different color vision phenotypes. PMID:16342074

  8. Intense Low-frequency Chorus Waves Observed by Van Allen Probes: Fine Structures and Potential Effect on Radiation Belt Electrons

    NASA Astrophysics Data System (ADS)

    Gao, Z.; Su, Z.; Zhu, H.

    2015-12-01

    Whistler-mode chorus emission in the low-density plasmatrough contributes significantly to the radiation belt electron dynamics. Chorus was usually considered to occur in the frequency range 0.1-0.8 fce (with the equatorial electron gyrofrequency fce ). We here report an event of intense low-frequency chorus with nearly half of wave power distributed below 0.1 fce observed by the Van Allen Probes on 27 August 2014. This emission exhibited little discrete rising tones but mainly the hiss-like signatures, had the high ellipticity of ˜1 and propagated quasi-parallel to the magnetic field. Compared with the typical chorus, the low-frequency chorus can produce weaker (2 times at ~ MeV and even up to several orders of magnitude at ~0.1MeV) momentum diffusion of the near-equatorially trapped electrons, but much stronger (1-2 orders of magnitude) pitch-angle diffusion near the loss cone. The acceleration and particularly loss effect of such intense low-frequency chorus may need to be taken into account in future radiation belt models.

  9. Geotail observations of spiky electric fields and low-frequency waves in the plasma sheet and plasma sheet boundary

    NASA Technical Reports Server (NTRS)

    Cattell, C.; Mozer, F.; Tsuruda, K.; Hayakawa, H.; Nakamura, M.; Okada, T.; Kokubun, S.; Yamamoto, T.

    1994-01-01

    Electric field data from the Geotail spacecraft provide an opportunity to extend the observations of spiky fields made by International Sun Earth Explorer-1 (ISEE-1) to a region of the magnetosphere where quasistatic electric field measurements have not previously been msde, to examine their possible importance in the dynamics of the middle and distant tail, and to test some hypotheses about their formation. In this paper, examples of large fields in the plasma sheet and its boundary at radial distances up to approximately 90 R(sub E) are presented. It is shown that three different types of large electric fields can occur: (1) spiky fields; (2) 'DC' fields; and (3) waves at frequencies comparable to the lower hybrid frequency. There is usually a gradation between (1) and (3), and often large electric field spikes are embedded in regions of lower amplitude waves. The waves tend to occur in short (few to 10's of seconds) packets whose start and stop times are not always correlated with changes in the magnetic field and/or density (as indicated by the spacecraft potential). The peak frequency is often less than but comparable to the lower hybrid frequency in agreement with theories of lower hybrid drift waves in the magnetotail. The largest spikes are not always associated with the largest changes in the spacecraft potential and/or magnetic field. It is suggested that the spiky fields may represent the nonlinear development of the waves.

  10. 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

  11. Analysis of simple tandem repeat (STR) marker allele distributions in a Balinese population

    SciTech Connect

    Morell, R.; Ashler, J.H.; Friedman, T.B.

    1994-09-01

    Genotypes for 53 simple tandem repeat (STR) markers distributed at greater than 39 cM intervals throughout the genome were determined for 46 individuals from the village of Bengkala, Bali. This village dates to at least the thirteenth century, has approximately 2,200 individuals and has an oral and written tradition suggesting genetic bottlenecks. The allele frequency distributions in Bengkala were compared with distributions obtained by typing individuals in the CEPH data base using a Kolmogorov-Smirnov two sample test. Twenty-eight of the 53 markers showed differences (p<0.05) in distribution between the two populations. Allele frequencies of tetranucleotide STRs were much more similar between the two populations than were those of dinucleotide STRs (p < 0.0043). This may be due to the higher mutation rate of tetranucleotide STRs, combining with selection on repeat lengths, to produce a {open_quotes}stable{close_quotes} allele distribution. Population heterogeneity in Bengkala was indicated by an excess of observed homozygosity, deviations from Hardy-Weinberg equilibrium at seven loci, and significant genotypic disequilibrium between physically unlinked loci. These analyses serve as a resource to map a gene causing non-syndromal autosomal recessive deafness in Bengkala, and to corroborate the anthropological study of the history and social structure of the village.

  12. No association between an allele at the D sub 2 dopamine receptor gene (DRD2) and alcoholism

    SciTech Connect

    Gelernter, J.; Krystal, J.; Kennedy, J.L. West Haven Dept. of Veterans Affairs Medical Center, CT ); O'Malley, S.; Risch, N.; Merikangas, K.; Kidd, K.K. ); Kranzler, H.R. )

    1991-10-02

    The author attempted to replicate a positive allelic association between the A1 allele of DRD2 (the D{sub 2} dopamine receptor locus) and alcoholism that has been reported. They compared allele frequencies at the previously described Taq I restriction fragment length polymorphism system of DRD2 in alcoholics and random population controls.

  13. The nature of the low-frequency emission of M 51. First observations of a nearby galaxy with LOFAR

    NASA Astrophysics Data System (ADS)

    Mulcahy, D. D.; Horneffer, A.; Beck, R.; Heald, G.; Fletcher, A.; Scaife, A.; Adebahr, B.; Anderson, J. M.; Bonafede, A.; Brüggen, M.; Brunetti, G.; Chyży, K. T.; Conway, J.; Dettmar, R.-J.; Enßlin, T.; Haverkorn, M.; Horellou, C.; Iacobelli, M.; Israel, F. P.; Junklewitz, H.; Jurusik, W.; Köhler, J.; Kuniyoshi, M.; Orrú, E.; Paladino, R.; Pizzo, R.; Reich, W.; Röttgering, H. J. A.

    2014-08-01

    Context. Low-frequency radio continuum observations (<300 MHz) can provide valuable information on the propagation of low-energy cosmic ray electrons (CRE). Nearby spiral galaxies have hardly been studied in this frequency range because of the technical challenges of low-frequency radio interferometry. This is now changing with the start of operations of LOFAR. Aims: We aim to study the propagation of low-energy CRE in the interarm regions and the extended disk of the nearly face-on spiral galaxy Messier 51. We also search for polarisation in M 51 and other extragalactic sources in the field. Methods: The grand-design spiral galaxy M 51 was observed with the LOFAR High Frequency Antennas (HBA) and imaged in total intensity and polarisation. This observation covered the frequencies between 115 MHz and 175 MHz with 244 subbands of 8 channels each, resulting in 1952 channels. This allowed us to use RM synthesis to search for polarisation. Results: We produced an image of total emission of M 51 at the mean frequency of 151 MHz with 20'' resolution and 0.3 mJy rms noise, which is the most sensitive ima