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Sample records for allele frequencies observed

  1. Frequency of FCGR3B Alleles in Thai Blood Donors

    PubMed Central

    Kaset, Chollanot; Leetrakool, Nipapan; Intharanut, Kamphon

    2013-01-01

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

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

    PubMed Central

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

    1993-01-01

    We summarize available data on the frequencies of alleles at microsatellite loci in human populations and compare observed distributions of allele frequencies to those generated by a simulation of the stepwise mutation model. We show that observed frequency distributions at 108 loci are consistent with the results of the model under the assumption that mutations cause an increase or decrease in repeat number by one and under the condition that the product Nu, where N is the effective population size and u is the mutation rate, is larger than one. We show that the variance of the distribution of allele sizes is a useful estimator of Nu and performs much better than previously suggested estimators for the stepwise mutation model. In the data, there is no correlation between the mean and variance in allele size at a locus or between the number of alleles and mean allele size, which suggests that the mutation rate at these loci is independent of allele size. PMID:8454213

  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. 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.

  5. Robust identification of local adaptation from allele frequencies.

    PubMed

    Günther, Torsten; Coop, Graham

    2013-09-01

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

  6. 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

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

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-02

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

  8. 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.

  9. Fast spatial ancestry via flexible allele frequency surfaces

    PubMed Central

    Rañola, John Michael; Novembre, John; Lange, Kenneth

    2014-01-01

    Motivation: Unique modeling and computational challenges arise in locating the geographic origin of individuals based on their genetic backgrounds. Single-nucleotide polymorphisms (SNPs) vary widely in informativeness, allele frequencies change non-linearly with geography and reliable localization requires evidence to be integrated across a multitude of SNPs. These problems become even more acute for individuals of mixed ancestry. It is hardly surprising that matching genetic models to computational constraints has limited the development of methods for estimating geographic origins. We attack these related problems by borrowing ideas from image processing and optimization theory. Our proposed model divides the region of interest into pixels and operates SNP by SNP. We estimate allele frequencies across the landscape by maximizing a product of binomial likelihoods penalized by nearest neighbor interactions. Penalization smooths allele frequency estimates and promotes estimation at pixels with no data. Maximization is accomplished by a minorize–maximize (MM) algorithm. Once allele frequency surfaces are available, one can apply Bayes’ rule to compute the posterior probability that each pixel is the pixel of origin of a given person. Placement of admixed individuals on the landscape is more complicated and requires estimation of the fractional contribution of each pixel to a person’s genome. This estimation problem also succumbs to a penalized MM algorithm. Results: We applied the model to the Population Reference Sample (POPRES) data. The model gives better localization for both unmixed and admixed individuals than existing methods despite using just a small fraction of the available SNPs. Computing times are comparable with the best competing software. Availability and implementation: Software will be freely available as the OriGen package in R. Contact: ranolaj@uw.edu or klange@ucla.edu Supplementary information: Supplementary data are available at

  10. HLA-DRB1 and -DRB3 allele frequencies and haplotypic associations in Koreans.

    PubMed

    Song, Eun Young; Park, Hyejin; Roh, Eun Youn; Park, Myoung Hee

    2004-03-01

    We have investigated the frequencies of human leukocyte antigen-DRB1 (HLA-DRB1) and -DRB3 alleles and DRB1-DRB3 haplotypic associations in 800 Koreans. DRB1 genotyping was done using polymerase chain reaction-sequence-specific oligonucleotide (PCR-SSO) and PCR-single strand conformation polymorphism (SSCP) methods. DRB3 genotyping was done on 447 samples carrying DRB3-associated DRB1 alleles (DRB1*03, *11, *12, *13, and *14) using PCR-SSCP method. The allele frequencies of DRB3*0101, DRB3*0202, and DRB3*0301 were 0.073, 0.136, and 0.120, respectively, and we found one case of a probable new allele (DRB3*01new, 0.001). DRB1-DRB3 haplotypes with frequency (HF) > 0.005 exhibited strong associations between DRB3*0101 and DRB1*1201, *1301, and *1403; between DRB3*0301 and DRB1*1202 and *1302; between DRB3*0202 and DRB1*0301, *1101, *1401, *1405, and *1406 alleles. Most of the DRB1 alleles with frequency > 0.005 were exclusively associated with particular DRB3 alleles with relative linkage disequilibrium values of 1.0, except for DRB1*1201, *1202 and *1301; the rare presence (HF < 0.005) of DRB3*0202 associations were observed for these DRB1 alleles. We also investigated and presented rare DRB1-DRB3 associations in additional 6000 Koreans. Comparison with other ethnic groups revealed that DRB1*0301 and *1301 related DRB1-DRB3 haplotypes vary among different populations, in that Koreans and other Asian populations show less diversity compared with Caucasoids or African Americans.

  11. 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

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

    PubMed

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

    2016-10-31

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

  13. Resistance allele frequency to bt cotton in field populations of helicoverpa armigera (Lepidoptera: Noctuidae) in China.

    PubMed

    Liu, Fengyi; Xu, Zhiping; Chang, Juhua; Chen, Jin; Meng, Fengxia; Zhu, Yu Cheng; Shen, Jinliang

    2008-06-01

    Resistance evolution in target insects to Bacillus thurningiensis (Bt) cotton, Gossypium hirsutum L., is a main threat to Bt cotton technology. An increasing trend of population density of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) has been observed since 2001 in Qiuxian County (Hebei, China), where Bt cotton has been planted dominantly since 1998. This region was selected in 2006 and 2007 for estimating frequency of gene alleles conferring resistance to Bt cotton by screening the F1 progeny from single-pair cross between field-collected male and laboratory female of the Bt-resistant strain of H. armigera (F1 screen). F1 offspring from each single-pair line were screened for resistance alleles based on larval growth, development, and survival on Bt cotton leaves for 5 d. Two-year results indicated that approximately equal to 20% of field-collected males carried resistance alleles. The conservative estimate of the resistance allele frequency was 0.094 (95% CI, 0.044-0.145) for 2006 and 0.107 (95% CI, 0.055-0.159) for 2007. This is the first report of resistance allele frequency increase to such a high level in the field in China. Long-term adoption of Bt sprays, dominant planting of single-toxin-producing Bt cotton, and lack of conventional cotton refuge system might accelerate the resistance evolution in the region.

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

    PubMed

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

    2009-02-01

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

  15. FINDbase: a worldwide database for genetic variation allele frequencies updated

    PubMed Central

    Georgitsi, Marianthi; Viennas, Emmanouil; Antoniou, Dimitris I.; Gkantouna, Vassiliki; van Baal, Sjozef; Petricoin, Emanuel F.; Poulas, Konstantinos; Tzimas, Giannis; Patrinos, George P.

    2011-01-01

    Frequency of INherited Disorders database (FIND base; http://www.findbase.org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. In addition to the regular data content updates, we report the following significant advances: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for 144 markers in 14 genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection, built around Microsoft’s PivotViewer software (http://www.getpivot.com), based on Microsoft Silverlight technology (http://www.silverlight.net) that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics, a new open-access scientific journal, which would serve as a prime example of a non-profit model for sustainable database funding. PMID:21113021

  16. 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.

  17. Determination of arylsulfatase A pseudodeficiency allele and haplotype frequency in the Tunisian population.

    PubMed

    Ben Halim, Nizar; Dorboz, Imen; Kefi, Rym; Kharrat, Najla; Eymard-Pierre, Eleonore; Nagara, Majdi; Romdhane, Lilia; Ben Alaya-Bouafif, Nissaf; Rebai, Ahmed; Miladi, Najoua; Boespflug-Tanguy, Odile; Abdelhak, Sonia

    2016-03-01

    Arylsulfatase A (ASA) is a lysosomal enzyme involved in the catabolism of cerebroside sulfate. ASA deficiency is associated with metachromatic leukodystrophy (MLD). Low ASA activities have also been reported in a more common condition with no apparent clinical consequences termed ASA pseudo-deficiency (ASA-PD) which is associated with two linked mutations in the ASA gene (c.1049A>G and c.*96A>G). This study aimed to investigate the frequency of the two ASA-PD variants and their linkage disequilibrium (LD) among Tunisians. ASA-PD variants were detected in 129 healthy Tunisians and their frequencies were compared to those described worldwide. The frequency of the PD allele was estimated at 17.4% for the overall sample, with c.1049A>G and c.*96A>G frequencies of 25.6 and 17.4%, respectively. This study also revealed a high LD between the two ASA-PD variants (r(2) = 0.61). Inter-population analysis revealed similarities in the ASA-PD genetic structure between Tunisians and populations from Middle East with c.*96A>G frequencies being the highest in the world. A significant North vs. South genetic differentiation in the ASA-PD frequency was also observed in Tunisian population who seems genetically intermediate between Africans, Middle-Easterners and Europeans. This is the first report on the allele frequency of the ASA-PD in North Africa, revealing a relatively high frequency of the PD allele among Tunisians. This study gives also evidence on the importance of discriminating ASA-PD allele from pathological mutations causing MLD and supporting enzymatic activity testing with both sulfatiduria determination and genetic testing in the differential diagnosis of MLD in the Tunisian population.

  18. Recovering frequencies of known haplotype blocks from single-nucleotide polymorphism allele frequencies.

    PubMed Central

    Pe'er, Itsik; Beckmann, Jacques S

    2004-01-01

    Prospects for large-scale association studies rely on economical methods and powerful analysis. Representing available SNPs by small subsets and measuring allele frequencies on pooled DNA samples each improve genotyping cost effectiveness, while haplotype analysis may highlight associations in otherwise underpowered studies. This manuscript provides the mathematical framework to integrate these methodologies. PMID:15126415

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  1. Allele frequencies of microsatellite loci for genetic characterization of a Sicilian bovine population.

    PubMed

    Cosenza, M; Reale, S; Lupo, T; Vitale, F; Caracappa, S

    2015-01-30

    Short tandem repeats are used as an effective method to trace DNA markers in genotyping. Using a standardized kit, we tested 11 microsatellite markers recommended by the International Society for Animal Genetics (ISAG) in a sample of 495 Sicilian cattle. The aim of this study was to investigate the allele frequencies in the Sicilian cattle population to provide a reference database and at the same time to assess the use of the ISAG microsatellite panel for pedigree analysis. DNA samples were collected from blood and amplified in an 11-plex polymerase chain reaction (PCR); PCR products were injected in a 3130 Genetic Analyzer. All loci showed high mean polymorphism information content (0.768), and the observed mean heterozygosity was less than the expected value (0.732 vs 0.794, respectively). The exact test for Hardy-Weinberg proportions, allele number, and inbreeding coefficient were calculated. Our results indicated that equilibrium was not always maintained. The observed mean homozygote value exceeded the expected value (132.81 vs 102.14), but no evidence for allele dropout was found. These results could be explained by a non-random mating; further studies using a larger number of animals could confirm or invalidate this hypothesis. The probability of identity and exclusion of a locus were also estimated and proved to be useful in paternity testing. The ISAG microsatellite panel is useful to screen the Sicilian bovine kinship. Currently, an allele frequency database is being constructed.

  2. 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.

  3. 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).

  4. 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.

  5. Allele frequency distribution for 15 autosomal STR loci in Afridi Pathan population of Uttar Pradesh, India.

    PubMed

    Noor, Sabahat; Ali, Shahnaz; Eaaswarkhanth, Muthukrishnan; Haque, Ikramul

    2009-11-01

    Allele frequencies of the 15 autosomal short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO D19S433, vWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818 and FGA were determined in Afridi Pathan population of Uttar Pradesh, India. All the 15 STR loci studied were found to be highly polymorphic with respect to observed heterozygosity values. Adherence to the expectations of the Hardy-Weinberg equilibrium (HWE) was confirmed for all the loci with an exception of TPOX and FGA. The allele 12 in CSF1PO was found to be most frequent. The power of discrimination was found to be high ranging from a minimum of 0.858 for the locus CSFIPO to maximum of 0.962 for the locus FGA, thereby facilitating the validation and efficiency of these STR markers in human identification. Population differentiation test between the studied and neighboring populations revealed significant differences at several loci suggesting the endogamous nature of the studied population. To the best of our knowledge, Afridi Pathan population has not been explored genetically for generating forensic data on STR markers. Therefore, STR allele frequency data of this unique population is a valuable contribution to the existing DNA database on Indian populations.

  6. 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

  7. 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.

  8. Genotype and allele frequencies of isoniazid-metabolizing enzymes NAT2 and GSTM1 in Latvian tuberculosis patients.

    PubMed

    Igumnova, Viktorija; Capligina, Valentina; Krams, Alvils; Cirule, Andra; Elferts, Didzis; Pole, Ilva; Jansone, Inta; Bandere, Dace; Ranka, Renate

    2016-07-01

    Pharmacogenomic testing of tuberculosis drug-metabolizing enzyme genes was proposed as a strategy to identify patients at risk for suboptimal responses to medications. However, variations of the genotype frequencies among ethnic groups exist and new alleles are been identified. The aim of this study was to identify polymorphisms of genes encoding metabolic enzymes NAT2 and GSTM1 in tuberculosis patients in Latvia and to estimate the frequency of NAT2 slow acetylator and GSTM1 null genotypes. In total, 85 DNA samples were genotyped, all individuals were Caucasian. An ethnic heterogeneity reflecting the multiethnic population of the country was observed. 49 patients were Latvians, 30 were Russians and 6 of other ethnicity. In total, 7 NAT2 alleles were identified: *4, *5, *6, *7, *11, *12, * and *13. The most frequent was the slow acetylation allele NAT2*6 (frequency 0.388) followed by the slow acetylation allele NAT2*5 and the rapid acetylation allele NAT2*4 (frequencies 0.306 and 0.194, respectively). The predominance of slow (51.8%) and intermediate (43.5%) acetylators compared with rapid acetylators (4.7%) was observed. The GSTM1 null genotype was detected in 48.2% of tuberculosis patients. When subgroup analysis was performed according to ethnicity, the results showed that neither NAT2 allele frequencies nor GSTM1 null genotype frequency did not differ significantly in TB patients of Latvian or Russian ethnicity. Overall, genotyping results were similar with previous reports of a NAT2 gene variation and GSTM1 null genotype frequency in Caucasians. Our findings have a contribution for the pharmacogenetics-based tuberculosis therapy in Latvia in future.

  9. 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

  10. 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.

  11. Comparison of Prion Allele Frequency found in Suffolk and Targhee Sheep

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Scrapie is a class of Transmissible Spongiform Encephalopathy that affects sheep and goats. The objective of this study was to compare genotypic and allelic frequencies among USSES Targhee and Suffolk sheep. A total of 122 sheep were genotyped for codon 171 with allele specific primers in 2 separate...

  12. Determination of allele frequency in pooled DNA: comparison of three PCR-based methods.

    PubMed

    Wilkening, Stefan; Hemminki, Kari; Thirumaran, Ranjit Kumar; Bermejo, Justo Lorenzo; Bonn, Stefan; Försti, Asta; Kumar, Rajiv

    2005-12-01

    Determination of allele frequency in pooled DNA samples is a powerful and efficient tool for large-scale association studies. In this study, we tested and compared three PCR-based methods for accuracy, reproducibility, cost, and convenience. The methods compared were: (i) real-time PCR with allele-specific primers, (ii) real-time PCR with allele-specific TaqMan probes, and (iii) quantitative sequencing. Allele frequencies of three single nucleotide polymorphisms in three different genes were estimated from pooled DNA. The pools were made of genomic DNA samples from 96 cases with basal cell carcinoma of the skin and 96 healthy controls with known genotypes. In this study, the allele frequency estimation made by real-time PCR with allele-specific primers had the smallest median deviation (MD) from the real allele frequency with 1.12% (absolute percentage points) and was also the cheapest method. However; this method required the most time for optimization and showed the highest variation between replicates (SD = 6.47%). Quantitative sequencing, the simplest method, was found to have intermediate accuracies (MD = 1.44%, SD = 4.2%). Real-time PCR with TaqMan probes, a convenient but very expensive method, had an MD of 1.47% and the lowest variation between replicates (SD = 3.18%).

  13. Frequency of the delta ccr5 deletion allele in the urban Brazilian population.

    PubMed

    Passos, G A; Picanço, V P

    1998-04-01

    Studies on screening genes conferring resistance to HIV-1 and AIDS onset have shown a direct relationship between a 32 base pair (bp) deletion in the CCR5 beta-chemokine receptor gene (delta ccr5 mutant allele) and long survival of HIV-1 infected individuals bearing this mutation. These findings led to an interest in studies of delta ccr5 allele distribution in human populations. In the present study, polymerase chain reactions (PCR) in genomic DNA samples, using specific CCR5 oligonucleotide primers surrounding the breakpoint deletion, detected a 193-bp product from the normal CCR5 allele and a 161-bp product from the 32-bp deletion allele. In an investigation of the urban Brazilian population we detected a 93% frequency of normal CCR5/CCR5 homozygous individuals and a 7% frequency of CCR5/delta ccr5 heterozygous individuals. The frequency of the delta ccr5 mutant allele in this population is 0.035; however, no homozygous delta ccr5 individual has been detected thus far. This is the first evidence for the contribution of the delta ccr5 allele to the genetic background of the urban Brazilian population, which is characterized by intense ethnic admixture. These findings open perspectives for further studies on the relationship between delta ccr5 allele frequency and AIDS onset in high-risk HIV-1 exposures individuals.

  14. High-Throughput SNP Allele-Frequency Determination in Pooled DNA Samples by Kinetic PCR

    PubMed Central

    Germer, Søren; Holland, Michael J.; Higuchi, Russell

    2000-01-01

    We have developed an accurate, yet inexpensive and high-throughput, method for determining the allele frequency of biallelic polymorphisms in pools of DNA samples. The assay combines kinetic (real-time quantitative) PCR with allele-specific amplification and requires no post-PCR processing. The relative amounts of each allele in a sample are quantified. This is performed by dividing equal aliquots of the pooled DNA between two separate PCR reactions, each of which contains a primer pair specific to one or the other allelic SNP variant. For pools with equal amounts of the two alleles, the two amplifications should reach a detectable level of fluorescence at the same cycle number. For pools that contain unequal ratios of the two alleles, the difference in cycle number between the two amplification reactions can be used to calculate the relative allele amounts. We demonstrate the accuracy and reliability of the assay on samples with known predetermined SNP allele frequencies from 5% to 95%, including pools of both human and mouse DNAs using eight different SNPs altogether. The accuracy of measuring known allele frequencies is very high, with the strength of correlation between measured and known frequencies having an r2 = 0.997. The loss of sensitivity as a result of measurement error is typically minimal, compared with that due to sampling error alone, for population samples up to 1000. We believe that by providing a means for SNP genotyping up to thousands of samples simultaneously, inexpensively, and reproducibly, this method is a powerful strategy for detecting meaningful polymorphic differences in candidate gene association studies and genome-wide linkage disequilibrium scans. PMID:10673283

  15. Observations Suggesting Allelism of the Achondroplasia and Hypochondroplasia Genes

    PubMed Central

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

    1973-01-01

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

  16. Statistical Inference in the Wright-Fisher Model Using Allele Frequency Data.

    PubMed

    Tataru, Paula; Simonsen, Maria; Bataillon, Thomas; Hobolth, Asger

    2016-08-02

    The Wright-Fisher model provides an elegant mathematical framework for understanding allele frequency data. In particular, the model can be used to infer the demographic history of species and identify loci under selection. A crucial quantity for inference under the Wright-Fisher model is the distribution of allele frequencies (DAF). Despite the apparent simplicity of the model, the calculation of the DAF is challenging. We review and discuss strategies for approximating the DAF, and how these are used in methods that perform inference from allele frequency data. Various evolutionary forces can be incorporated in the Wright-Fisher model, and we consider these in turn. We begin our review with the basic bi-allelic Wright-Fisher model where random genetic drift is the only evolutionary force. We then consider mutation, migration, and selection. In particular, we compare diffusion-based and moment-based methods in terms of accuracy, computational efficiency, and analytical tractability. We conclude with a brief overview of the multi-allelic process with a general mutation model. [Allele frequency, diffusion, inference, moments, selection, Wright-Fisher.].

  17. 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.

  18. Frequency of the arylsulphatase A pseudodeficiency allele in the Spanish population.

    PubMed

    Chabás, A; Castellvi, S; Bayés, M; Balcells, S; Grinberg, D; Vilageliu, L; Marfany, G; Lissens, W; Gonzàlez-Duarte, R

    1993-12-01

    Pseudodeficiency in arylsulphatase A (ASA) is a relatively frequent condition in healthy individuals. It produces a reduction in enzyme activity similar to that found in metachromatic leukodystrophy (MLD). Unambiguous discrimination between the two conditions cannot be achieved through conventional enzyme activity assays. A PCR method has been developed which detects the pseudodeficiency (pd) allele using a single pair of primers encompassing the mutation site and hair follicles as the source of DNA. The frequency of this allele in the Spanish population has been evaluated and correlations between different genotypes and ASA activity levels have been established. Ten out of 55 individuals were heterozygous for the ASA pd allele, while two were homozygous. The allele frequency was thus 12.7%.

  19. Effects of allele frequency estimation on genomic predictions and inbreeding coefficients

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic calculations often require estimating allele frequencies, which differ across time due to selection and drift. Data were 50,000 simulated markers and 39,985 actual markers for 2391 genotyped Holstein bulls. Gene content of relatives and gene frequencies in the base (founder) population were ...

  20. 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.

  1. Using maximum likelihood to estimate population size from temporal changes in allele frequencies.

    PubMed Central

    Williamson, E G; Slatkin, M

    1999-01-01

    We develop a maximum-likelihood framework for using temporal changes in allele frequencies to estimate the number of breeding individuals in a population. We use simulations to compare the performance of this estimator to an F-statistic estimator of variance effective population size. The maximum-likelihood estimator had a lower variance and smaller bias. Taking advantage of the likelihood framework, we extend the model to include exponential growth and show that temporal allele frequency data from three or more sampling events can be used to test for population growth. PMID:10353915

  2. Allele and genotype frequencies of CYP2B6 in a Turkish population.

    PubMed

    Yuce-Artun, Nazan; Kose, Gulcin; Suzen, H Sinan

    2014-06-01

    Increasing interest in cytochrome P450 2B6 (CYP2B6) genetic polymorphism was stimulated by revelations of a specific CYP2B6 genotype significantly affecting the metabolism of various drugs in common clinical use in terms of increasing drug efficacy and avoiding adverse drug reactions. The present study aimed to determine the frequencies of CYP2B6*4 CYP2B6*5, CYP2B6*6, CYP2B6*7 and CYP2B6*9 alleles in healthy Turkish individuals (n = 172). Frequencies of three single nucleotide polymorphisms were 516G>T (28%), 785A>G (33%), and 1459C>T (12%). The frequencies of CYP2B6*1, *4, *5, *6, *7, and *9 alleles were 54.3 (95% CI 49.04-59.56), 6.4% (95% CI 3.81-8.99), 11% (95% CI 7.69-14.31), 25.3% (95% CI 20.71-29.89), 0.87% (95% CI -0.11-1.85) and 2.0% (95% CI 0.52-3.48), respectively. Allele *6 was more frequent (25.3%) than the other variant alleles in Turkish subjects. The frequencies of CYP2B6*4, *5, *6, *7, and *9 alleles were similar to European populations but significantly different from that reported for Asian populations. This is the first study to document the frequencies of the CYP2B6*4, *5, *6, *7, *9 alleles in the healthy Turkish individuals and our results could provide clinically useful information on drug metabolism by CYP2B6 in Turkish population.

  3. Cytochrome P450 2D6 variants in a Caucasian population: Allele frequencies and phenotypic consequences

    SciTech Connect

    Sachse, C.; Brockmoeller, J.; Bauer, S.; Roots, I.

    1997-02-01

    Cytochrome P450 2D6 (CYP2D6) metabolizes many important drugs. CYP2D6 activity ranges from complete deficiency to ultrafast metabolism, depending on at least 16 different known alleles. Their frequencies were determined in 589 unrelated German volunteers and correlated with enzyme activity measured by phenotyping with dextromethorphan or debrisoquine. For genotyping, nested PCR-RFLP tests from a PCR amplificate of the entire CYP2D6 gene were developed. The frequency of the CYP2D6*1 allele coding for extensive metabolizer (EM) phenotype was .364. The alleles coding for slightly (CYP2D6*2) or moderately (*9 and *10) reduced activity (intermediate metabolizer phenotype [IM]) showed frequencies of .324, .018, and .015, respectively. By use of novel PCR tests for discrimination, CYP2D6 gene duplication alleles were found with frequencies of.005 (*1 x 2), .013 (* 2 x 2), and .001 (*4 x 2). Frequencies of alleles with complete deficiency (poor metabolizer phenotype [PM]) were .207 (*4), .020 (*3 and *5), .009 (*6), and .001 (*7, *15, and *16). The defective CYP2D6 alleles *8, *11, *12, *13, and *14 were not found. All 41 PMs (7.0%) in this sample were explained by five mutations detected by four PCR-RFLP tests, which may suffice, together with the gene duplication test, for clinical prediction of CYP2D6 capacity. Three novel variants of known CYP2D6 alleles were discovered: *1C (T{sub 1957}C), *2B (additional C{sub 2558}T), and *4E (additional C{sub 2938}T). Analysis of variance showed significant differences in enzymatic activity measured by the dextromethorphan metabolic ratio (MR) between carriers of EN/PM (mean MR = .006) and IM/PM (mean MR = .014) alleles and between carriers of one (mean MR = .009) and two (mean MR = .003) functional alleles. The results of this study provide a solid basis for prediction of CYP2D6 capacity, as required in drug research and routine drug treatment. 35 refs., 4 figs., 5 tabs.

  4. Natural Selection VS. Random Drift: Evidence from Temporal Variation in Allele Frequencies in Nature

    PubMed Central

    Mueller, Laurence D.; Barr, Lorraine G.; Ayala, Francisco J.

    1985-01-01

    We have obtained monthly samples of two species, Drosophila pseudoobscura and Drosophila persimilis, in a natural population from Napa County, California. In each species, about 300 genes have been assayed by electrophoresis for each of seven enzyme loci in each monthly sample from March 1972 to June 1975. Using statistical methods developed for the purpose, we have examined whether the allele frequencies at different loci vary in a correlated fashion. The methods used do not detect natural selection when it is deterministic (e.g., overdominance or directional selection), but only when alleles at different loci vary simultaneously in response to the same environmental variations. Moreover, only relatively large fitness differences (of the order of 15%) are detectable. We have found strong evidence of correlated allele frequency variation in 13–20% of the cases examined. We interpret this as evidence that natural selection plays a major role in the evolution of protein polymorphisms in nature. PMID:4054608

  5. Estimation of the frequency of hexosaminidase a variant alleles in the American Jewish population.

    PubMed

    Greenberg, D A; Kaback, M M

    1982-05-01

    There appear to be several alleles of the hexosaminidase A (HEX A) gene that lead to different clinical syndromes. In addition to the infantile-onset Tay-Sachs disease (TSD), there is a juvenile-onset and an adult-onset form, which are also characterized by low HEX A levels. There are also apparently healthy adults with low HEX A activity. Based primarily on data from population screening for TSD carrier status, we estimate the allele frequency of the combined variant alleles for which data are available to be about 4.5 x 10(-4) and the frequency of adults showing zero HEX A levels (when tested using artificial substrate) to be about 1:67,000. The implications for population screening and prenatal diagnosis are discussed.

  6. Monooxygenase Levels and Knockdown Resistance (kdr) Allele Frequencies in Anopheles gambiae and Anopheles arabiensis in Kenya

    PubMed Central

    Chen, Hong; Githeko, Andrew K; Githure, John I; Mutunga, James; Zhou, Guofa; Yan, Guiyun

    2013-01-01

    Pyrethroid-treated bed nets and indoor spray are important components of malaria control strategies in Kenya. Information on resistance to pyrethroid insecticides in Anopheles gambiae and An. arabiensis populations is essential to the selection of appropriate insecticides and the management of insecticide resistance. Monooxygenase activity and knockdown resistance (kdr) allele frequency are biochemical and molecular indicators of mosquito resistance to pyrethroids. This study determined baseline information on monooxygenase activity and kdr allele frequency in anopheline mosquitoes in the western region, the Great Rift Valley-central province region, and the coastal region of Kenya. A total of 1990 field-collected individuals, representing 12 An. gambiae and 22 An. arabiensis populations was analyzed. We found significant among-population variation in monooxygenase activity in An. gambiae and An. arabiensis and substantial variability among individuals within populations. Nine out of 12 An. gambiae populations exhibited significantly higher average monooxygenase activity than the susceptible Kisumu reference strain. The kdr alleles (L1014S) were detected in three An. gambiae populations, and one An. arabiensis population in western Kenya, but not in the Rift Valley-central region and the coastal Kenya region. All genotypes with the kdr alleles were heterozygous, and the conservative estimation of kdr allele frequency was below 1% in these four populations. Information on monooxygenase activity and kdr allele frequency reported in this study provided baseline data for monitoring insecticide resistance changes in Kenya during the era when large-scale insecticide-treated bednet and indoor residual spray campaigns were being implemented. PMID:18402140

  7. Genome Wide Allele Frequency Fingerprints (GWAFFs) of Populations via Genotyping by Sequencing

    PubMed Central

    Byrne, Stephen; Czaban, Adrian; Studer, Bruno; Panitz, Frank; Bendixen, Christian; Asp, Torben

    2013-01-01

    Genotyping-by-Sequencing (GBS) is an excellent tool for characterising genetic variation between plant genomes. To date, its use has been reported only for genotyping of single individuals. However, there are many applications where resolving allele frequencies within populations on a genome-wide scale would be very powerful, examples include the breeding of outbreeding species, varietal protection in outbreeding species, monitoring changes in population allele frequencies. This motivated us to test the potential to use GBS to evaluate allele frequencies within populations. Perennial ryegrass is an outbreeding species, and breeding programs are based upon selection on populations. We tested two restriction enzymes for their efficiency in complexity reduction of the perennial ryegrass genome. The resulting profiles have been termed Genome Wide Allele Frequency Fingerprints (GWAFFs), and we have shown how these fingerprints can be used to distinguish between plant populations. Even at current costs and throughput, using sequencing to directly evaluate populations on a genome-wide scale is viable. GWAFFs should find many applications, from varietal development in outbreeding species right through to playing a role in protecting plant breeders’ rights. PMID:23469194

  8. 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

    2016-03-08

    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.

  9. 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.

  10. 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

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

    PubMed Central

    Mattei, Josiemer; Parnell, Laurence D; Lai, Chao-Qiang; Garcia-Bailo, Bibiana; Adiconis, Xian; Shen, Jian; Arnett, Donna; Demissie, Serkalem; Tucker, Katherine L; Ordovas, Jose M

    2009-01-01

    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 pressures. Such genetic information is limited in Puerto Ricans, the second largest Hispanic ethnic group in the US, and a group with high prevalence of chronic disease. We determined allele frequencies and population differentiation for 101 single nucleotide polymorphisms (SNPs) in 30 genes involved in major metabolic and disease-relevant pathways in Puerto Ricans (n = 969, ages 45–75 years) and compared them to similarly aged non-Hispanic whites (NHW) (n = 597). Results Minor allele frequency (MAF) distributions for 45.5% of the SNPs assessed in Puerto Ricans were significantly different from those of NHW. Puerto Ricans carried risk alleles in higher frequency and protective alleles in lower frequency than NHW. Patterns of population differentiation showed that Puerto Ricans had SNPs with exceptional FST values in intronic, non-synonymous and promoter regions. NHW had exceptional FST values in intronic and promoter region SNPs only. Conclusion These observations may serve to explain and broaden studies on the impact of gene polymorphisms on chronic diseases affecting Puerto Ricans. PMID:19682384

  12. 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).

  13. 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

  14. Insecticide Resistance Allele Frequencies in Anopheles gambiae before and after Anti-Vector Interventions in Continental Equatorial Guinea

    PubMed Central

    Reddy, Michael R.; Godoy, Adrian; Dion, Kirstin; Matias, Abrahan; Callender, Kevin; Kiszewski, Anthony E.; Kleinschmidt, Immo; Ridl, Frances C.; Powell, Jeffrey R.; Caccone, Adalgisa; Slotman, Michel A.

    2013-01-01

    Anti-malaria interventions that rely on insecticides can be compromised by insecticide-resistance alleles among malaria vectors. We examined frequency changes of resistance alleles at two loci, knockdown resistance (kdr) and acetylcholinesterase-1 (ace-1), which confer resistance to pyrethroids and DDT, and carbamates, respectively. A total of 7,059 Anopheles gambiae sensu stricto mosquitoes were analyzed from multiple sites across continental Equatorial Guinea. A subset of sites included samples collected pre-intervention (2007) and post-intervention (2009–2011). Both L1014S and L1014F resistance alleles were observed in almost all pre-intervention collections. In particular, L1014F was already at substantial frequencies in M form populations (17.6–74.6%), and at high frequencies (> 50%) in all but two S form populations. Comparison before and throughout anti-vector interventions showed drastic increases in L1014F, presumably caused by intensified selection pressure imposed by pyrethroids used in vector control efforts. In light of these findings, inclusion of other insecticide classes in any anti-vector intervention can be considered prudent. PMID:23438768

  15. Allele frequency of antiretroviral host factor TRIMCyp in wild-caught cynomolgus macaques (Macaca fascicularis)

    PubMed Central

    Saito, Akatsuki; Kawamoto, Yoshi; Higashino, Atsunori; Yoshida, Tomoyuki; Ikoma, Tomoko; Suzaki, Yuriko; Ami, Yasushi; Shioda, Tatsuo; Nakayama, Emi E.; Akari, Hirofumi

    2012-01-01

    A recent study showed that the frequency of an antiretroviral factor TRIM5 gene-derived isoform, TRIMCyp, in cynomolgus macaques (Macaca fascicularis) varies widely according to the particular habitat examined. However, whether the findings actually reflect the prevalence of TRIMCyp in wild cynomolgus macaques is still uncertain because the previous data were obtained with captive monkeys in breeding and rearing facilities. Here, we characterized the TRIM5 gene in cynomolgus macaques captured in the wild, and found that the frequency of the TRIMCyp allele was comparable to those in captive monkeys. This suggests that the previous results with captive monkeys do indeed reflect the natural allele frequency and that breeding and rearing facilities may not affect the frequency of TRIM5 alleles. Interestingly, the prevalence of a minor haplotype of TRIMCyp in wild macaques from the Philippines was significantly lower than in captive ones, suggesting that it is advantageous for wild monkeys to possess the major haplotype of TRIMCyp. Overall, our results add to our understanding of the geographic and genetic prevalence of cynomolgus macaque TRIMCyp. PMID:22969754

  16. 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.

  17. Preferred frequencies for SETI observations

    NASA Astrophysics Data System (ADS)

    Zuckerman, B.

    1983-10-01

    The proper radio bands for observing and transmitting signals to and from other star systems in a search for extraterrestrial intelligence. It is assumed that other civilizations will have developed the energies and other resources of their solar systems, and that they will use electromagnetic radiation as a communications medium. The sizes of the space based antennas that other civilizations might have built are discussed in terms of the resulting interferometers, the possible wavelengths used, and the technological bases assumed. It is suggested that transmissions might be most effective if confined to a few microns bandwidth to which the galaxy is largely transparent. However, no universal, 'magic' frequency can presently be identified, although nondirectional emissions may congregate around the 'water hole' of radio frequencies in the universe.

  18. 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

  19. Genotypic and allelic frequencies of gene polymorphisms associated with meat tenderness in Nellore beef cattle.

    PubMed

    Carvalho, M E; Eler, J P; Bonin, M N; Rezende, F M; Biase, F H; Meirelles, F V; Regitano, L C A; Coutinho, L L; Balieiro, J C C; Ferraz, J B S

    2017-02-16

    The objectives of this study were to characterize the allelic and genotypic frequencies of polymorphisms in the µ-calpain and calpastatin genes, and to assess their association with meat tenderness and animal growth in Nellore cattle. We evaluated 605 Nellore animals at 24 months of age, on average, at slaughter. The polymorphisms were determined for the molecular markers CAPN316, CAPN530, CAPN4751, CAPN4753, and UOGACAST1. Analyses of meat tenderness at 7, 14, and 21 days of maturation were performed in samples of longissimus thoracis obtained between the 12th and 13th rib and sheared using a Warner Bratzler Shear Force. Significant effects were observed for meat tenderness at days 7, 14, and 21 of maturation for the marker CAPN4751, at day 21 for the marker CAPN4753, and at days 14 and 21 for the marker UOGCAST1. For genotypic combinations of markers, the results were significant for the combination CAPN4751/UOGCAST1 in the three maturation periods and CAPN4753/UOGCAST1 at days 14 and 21 of maturation.

  20. The joint allele frequency spectrum of multiple populations: a coalescent theory approach.

    PubMed

    Chen, Hua

    2012-03-01

    The allele frequency spectrum is a series of statistics that describe genetic polymorphism, and is commonly used for inferring population genetic parameters and detecting natural selection. Population genetic theory on the allele frequency spectrum for a single population has been well studied using both coalescent theory and diffusion equations. Recently, the theory was extended to the joint allele frequency spectrum (JAFS) for three populations using diffusion equations and was shown to be very useful in inferring human demographic history. In this paper, I show that the JAFS can be analytically derived with coalescent theory for a basic model of two isolated populations and then extended to multiple populations and various complex scenarios, such as those involving population growth and bottleneck, migration, and positive selection. Simulation study is used to demonstrate the accuracy and applicability of the theoretical model. The coalescent theory-based approach for the JAFS can characterize the demographic history with comprehensive statistical models as the diffusion approach does, and in addition gains several novel advantages: the computational complexity of calculating the JAFS with coalescent theory is reduced, and thus it is feasible to analytically obtain the JAFS for multiple populations; the hitchhiking effect can be efficiently modeled in coalescent theory, enabling the development of methodologies for detecting selection via multi-population polymorphism data. As an alternative to the diffusion approximation approach, the coalescent theory for the JAFS also provides a foundation for population genetic inference with the advent of large-scale genomic polymorphism data.

  1. 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.

  2. 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.

  3. Genotype and allele frequencies of drug-metabolizing enzymes and drug transporter genes affecting immunosuppressants in the Spanish white population.

    PubMed

    Bosó, Virginia; Herrero, María J; Buso, Enrique; Galán, Juan; Almenar, Luis; Sánchez-Lázaro, Ignacio; Sánchez-Plumed, Jaime; Bea, Sergio; Prieto, Martín; García, María; Pastor, Amparo; Sole, Amparo; Poveda, José Luis; Aliño, Salvador F

    2014-04-01

    Interpatient variability in drug response can be widely explained by genetically determined differences in metabolizing enzymes, drug transporters, and drug targets, leading to different pharmacokinetic and/or pharmacodynamic behaviors of drugs. Genetic variations affect or do not affect drug responses depending on their influence on protein activity and the relevance of such proteins in the pathway of the drug. Also, the frequency of such genetic variations differs among populations, so the clinical relevance of a specific variation is not the same in all of them. In this study, a panel of 33 single nucleotide polymorphisms in 14 different genes (ABCB1, ABCC2, ABCG2, CYP2B6, CYP2C19, CYP2C9, CYP3A4, CYP3A5, MTHFR, NOD2/CARD15, SLCO1A2, SLCO1B1, TPMT, and UGT1A9), encoding for the most relevant metabolizing enzymes and drug transporters relating to immunosuppressant agents, was analyzed to determine the genotype profile and allele frequencies in comparison with HapMap data. A total of 570 Spanish white recipients and donors of solid organ transplants were included. In 24 single nucleotide polymorphisms, statistically significant differences in allele frequency were observed. The largest differences (>100%) occurred in ABCB1 rs2229109, ABCG2 rs2231137, CYP3A5 rs776746, NOD2/CARD15 rs2066844, TPMT rs1800462, and UGT1A9 rs72551330. In conclusion, differences were recorded between the Spanish and other white populations in terms of allele frequency and genotypic distribution. Such differences may have implications in relation to dose requirements and drug-induced toxicity. These data are important for further research to help explain interindividual pharmacokinetic and pharmacodynamic variability in response to drug therapy.

  4. Analysis of HLA DQ alpha allele and genotype frequencies in populations from Florida.

    PubMed

    Crouse, C A; Feuer, W J; Nippes, D C; Hutto, S C; Barnes, K S; Coffman, D; Livingston, S H; Ginsberg, L; Glidewell, D E

    1994-05-01

    HLA DQ alpha allele and genotype frequencies for Caucasian, African American, Haitian, and Hispanic populations in Florida have been estimated. The Florida laboratories involved in these studies collected donor samples from a variety of sites including clinical laboratories, victim and suspect standards, blood banks, county jail detainees, and laboratory personnel. We have determined that the Caucasian and African American DQ alpha genotype frequencies do not deviate significantly from Hardy-Weinberg expectations and as a result of this heterogeneity analyses, data from the four Florida Caucasian populations may be combined and data from the four Florida African American populations may be combined to form two large HLA DQ alpha genotype frequency databanks. Further, data from the Florida Haitian population may be combined with the Florida African American population. Comparison of the combined Florida Caucasian populations, combined Florida African American populations, the Palm Beach Sheriff's Office (PBSO) Hispanic, and PBSO Haitian population with other databases does not support combination because allele frequency distributions are heterogeneous.

  5. 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.

  6. Upper bounds on FST in terms of the frequency of the most frequent allele and total homozygosity: the case of a specified number of alleles.

    PubMed

    Edge, Michael D; Rosenberg, Noah A

    2014-11-01

    FST is one of the most frequently-used indices of genetic differentiation among groups. Though FST takes values between 0 and 1, authors going back to Wright have noted that under many circumstances, FST is constrained to be less than 1. Recently, we showed that at a genetic locus with an unspecified number of alleles, FST for two subpopulations is strictly bounded from above by functions of both the frequency of the most frequent allele (M) and the homozygosity of the total population (HT). In the two-subpopulation case, FST can equal one only when the frequency of the most frequent allele and the total homozygosity are 1/2. Here, we extend this work by deriving strict bounds on FST for two subpopulations when the number of alleles at the locus is specified to be I. We show that restricting to I alleles produces the same upper bound on FST over much of the allowable domain for M and HT, and we derive more restrictive bounds in the windows M∈[1/I,1/(I-1)) and HT∈[1/I,I/(I(2)-1)). These results extend our understanding of the behavior of FST in relation to other population-genetic statistics.

  7. 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...

  8. No differences of butyrylcholinesterase protein activity and allele frequency in Lewy body diseases.

    PubMed

    Maetzler, Walter; Keller, Stefanie; Michelis, Joan; Koehler, Niklas; Stransky, Elke; Becker, Clemens; Schulte, Claudia; Melms, Arthur; Gasser, Thomas; Berg, Daniela

    2009-08-01

    Butyrylcholinesterase (BChE) genotypes and protein (BuChE) activity, especially in combination with Apolipoprotein E4 (ApoE4), have been investigated as risk factors for developing Alzheimer disease (AD) and may be associated with the rate of progression of cognitive decline. Despite similar pathologic (e.g. amyloid deposition) and neurochemical (e.g. cholinergic deficits) aspects between AD and Lewy body diseases (LBD), scarce data is obtainable about BChE genotypes and BuChE activity in LBD. We measured BuChE activity levels in serum and cerebrospinal fluid (CSF) of 114 LBD subjects (59 of them were demented) and 31 elderly controls. We found higher CSF BuChE activity in males compared to females, and a negative correlation of serum BuChE activity with age and cognitive function. Demented LBD patients, non-demented LBD patients and controls did not differ significantly with regard to serum and CSF BuChE activity. Furthermore, BChE K variant and ApoE4 allele frequencies were determined. The BChE K variant was significantly associated with lower serum activity; the same trend was observable in CSF. The subgroups did not differ significantly with regard to BChE K/ApoE4 occurrence. These data confirm and extend previous results on the relationship between BChE gene and BuChE activity, and argue rather against a major impact of BuChE on LBD-associated pathologies.

  9. 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.

  10. Lower Frequency of HLA-DRB1 Type 1 Diabetes Risk Alleles in Pediatric Patients with MODY

    PubMed Central

    López-Euba, Tamara; Velayos, Teresa; Martínez de LaPiscina, Idoia; Bilbao, José Ramón; Rica, Itxaso; Castaño, Luis

    2017-01-01

    Objective The aim of this study was to determine the frequency of susceptible HLA-DRB1 alleles for type 1 diabetes in a cohort of pediatric patients with a confirmed genetic diagnosis of MODY. Materials and Methods 160 families with a proband diagnosed with type 1 diabetes and 74 families with a molecular diagnosis of MODY (61 GCK-MODY and 13 HNF1A-MODY) were categorized at high definition for HLA-DRB1 locus. According to the presence or absence of the susceptible HLA-DRB1 alleles for type 1 diabetes, we considered three different HLA-DRB1 genotypes: 0 risk alleles (no DR3 no DR4); 1 risk allele (DR3 or DR4); 2 risk alleles (DR3 and/or DR4). Results Compared with type 1 diabetes, patients with MODY carried higher frequency of 0 risk alleles, OR 22.7 (95% CI: 10.7–48.6) and lower frequency of 1 or 2 risk alleles, OR 0.53 (95% CI: 0.29–0.96) and OR 0.06 (95% CI: 0.02–0.18), respectively. Conclusions The frequency of HLA-DRB1 risk alleles for type 1 diabetes is significantly lower in patients with MODY. In children and adolescents with diabetes, the presence of 2 risk alleles (DR3 and/or DR4) reduces the probability of MODY diagnosis, whereas the lack of risk alleles increases it. Therefore, we might consider that HLA-DRB1 provides additional information for the selection of patients with high probability of monogenic diabetes. PMID:28052112

  11. Inheritance of Cry1F resistance, cross-resistance and frequency of resistant alleles in Spodoptera frugiperda (Lepidoptera: Noctuidae).

    PubMed

    Vélez, A M; Spencer, T A; Alves, A P; Moellenbeck, D; Meagher, R L; Chirakkal, H; Siegfried, B D

    2013-12-01

    Transgenic maize, Zea maize L., expressing the Cry1F protein from Bacillus thuringiensis has been registered for Spodoptera frugiperda (J. E. Smith) control since 2003. Unexpected damage to Cry1F maize was reported in 2006 in Puerto Rico and Cry1F resistance in S. frugiperda was documented. The inheritance of Cry1F resistance was characterized in a S. frugiperda resistant strain originating from Puerto Rico, which displayed >289-fold resistance to purified Cry1F. Concentration-response bioassays of reciprocal crosses of resistant and susceptible parental populations indicated that resistance is recessive and autosomal. Bioassays of the backcross of the F1 generation crossed with the resistant parental strain suggest that a single locus is responsible for resistance. In addition, cross-resistance to Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry2Aa and Vip3Aa was assessed in the Cry1F-resistant strain. There was no significant cross-resistance to Cry1Aa, Cry1Ba and Cry2Aa, although only limited effects were observed in the susceptible strain. Vip3Aa was highly effective against susceptible and resistant insects indicating no cross-resistance with Cry1F. In contrast, low levels of cross-resistance were observed for both Cry1Ab and Cry1Ac. Because the resistance is recessive and conferred by a single locus, an F1 screening assay was used to measure the frequency of Cry1F-resistant alleles from populations of Florida and Texas in 2010 and 2011. A total frequency of resistant alleles of 0.13 and 0.02 was found for Florida and Texas populations, respectively, indicating resistant alleles could be found in US populations, although there have been no reports of reduced efficacy of Cry1F-expressing plants.

  12. 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

  13. Estimating Selection Coefficients in Spatially Structured Populations from Time Series Data of Allele Frequencies

    PubMed Central

    Mathieson, Iain; McVean, Gil

    2013-01-01

    Inferring the nature and magnitude of selection is an important problem in many biological contexts. Typically when estimating a selection coefficient for an allele, it is assumed that samples are drawn from a panmictic population and that selection acts uniformly across the population. However, these assumptions are rarely satisfied. Natural populations are almost always structured, and selective pressures are likely to act differentially. Inference about selection ought therefore to take account of structure. We do this by considering evolution in a simple lattice model of spatial population structure. We develop a hidden Markov model based maximum-likelihood approach for estimating the selection coefficient in a single population from time series data of allele frequencies. We then develop an approximate extension of this to the structured case to provide a joint estimate of migration rate and spatially varying selection coefficients. We illustrate our method using classical data sets of moth pigmentation morph frequencies, but it has wide applications in settings ranging from ecology to human evolution. PMID:23307902

  14. Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans

    PubMed Central

    Pritchard, Jonathan K.

    2016-01-01

    The site frequency spectrum (SFS) has long been used to study demographic history and natural selection. Here, we extend this summary by examining the SFS conditional on the alleles found at the same site in other species. We refer to this extension as the “phylogenetically-conditioned SFS” or cSFS. Using recent large-sample data from the Exome Aggregation Consortium (ExAC), combined with primate genome sequences, we find that human variants that occurred independently in closely related primate lineages are at higher frequencies in humans than variants with parallel substitutions in more distant primates. We show that this effect is largely due to sites with elevated mutation rates causing significant departures from the widely-used infinite sites mutation model. Our analysis also suggests substantial variation in mutation rates even among mutations involving the same nucleotide changes. In summary, we show that variable mutation rates are key determinants of the SFS in humans. PMID:27977673

  15. 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

  16. Polymorphism of the bovine POU1F1 gene: allele frequencies and effects on milk production in three Iranian native breeds and Holstein cattle of Iran.

    PubMed

    Zakizadeh, S; Reissmann, M; Rahimi, G; Javaremi, A Nejati; Reinecke, P; Mirae-Ashtiani, S R; Shahrbabak, M Moradi

    2007-08-01

    The aim of this study was to estimate the allele frequencies in polymorphic site of exon six of POU1F1 gene in three Iranian native and Holstein cattle. Genomic DNA was extracted from 3 Iranian native cattle breeds, including 97 Mazandarani, 87 Sarabi, 112 Golpaygani and also 110 Holstein cattle. A 451 bp fragment of intron 5 and exon 6 were amplified and digested with HinfI restriction enzyme. Frequencies of allele A were 0.37, 0.27, 0.34 and 0.21 for Mazandarani, Sarabi, Golpaygani and Holstein cattle, respectively. Significant differences in genotype frequencies were found between Mazandarani or Golpaygani and Holstein cattle. No significant differences in genotype frequencies were found between Sarabi and Holstein cattle. Transition A to G in nucleotide 1256 is responsible for HinfI(-) allele. No significant association was observed between POU1F1 polymorphism and milk production. Differences in allelic frequency between native Bos indicus breeds (Mazandarani, Golpaygani) and Holstein at the present study might be due to differences in origin breeds, low number of samples and/or as the effect of natural selection in native breeds.

  17. 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.

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

    PubMed Central

    Cornuet, J. M.; Luikart, G.

    1996-01-01

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

  19. Frequency detection of imidacloprid resistance allele in Aphis gossypii field populations by real-time PCR amplification of specific-allele (rtPASA).

    PubMed

    Zhang, Jing; Cui, Li; Xu, Xibao; Rui, Changhui

    2015-11-01

    The Aphis gossypii Glover (Hemiptera: Aphididae) is one of the most serious pests worldwide, and imidacloprid has been widely used to control this insect pest. Just like other classes of insecticides, the resistance to imidacloprid has been found in A. gossypii. An amino acid mutation (R81T) in the nicotinic acetylcholine receptor (nAChR) beta1 subunit was detected in the imidacloprid-resistant A. gossypii collected from Langfang (LF) and Dezhou (DZ) cities. To estimate the R81T mutation frequency of A. gossypii field populations, a simple, rapid and accurate rtPASA (real-time PCR amplification of specific allele) protocol was developed. The performance of the rtPASA protocol was evaluated by comparing with the data generated by a cPASA (competitive PCR amplification of specific allele) method from 50 individual genotypes. The R81T allele frequencies of the LF population (34.7%±1.3%) and DZ population (45.2%±5.2%) estimated by the rtPASA protocol matched the frequencies (LF 38.1%, DZ 48.2%) deduced by the cPASA method in specimens. The results indicated that the rtPASA format was applicable for the detection of mutation associated with imidacloprid resistance and will allow rapid and efficient monitoring of A. gossypii resistance in field populations in a high throughput format.

  20. 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.

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

    PubMed Central

    Racimo, Fernando

    2016-01-01

    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

  2. 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.

  3. 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.

  4. 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

  5. Allele and genotype frequencies of polymorphisms in cytokine genes in ethnic Russian individuals from Moscow, Russia.

    PubMed

    Shadrina, Alexandra; Voronina, Elena; Zolotukhin, Igor; Filipenko, Maxim

    2017-02-01

    Two hundred and twenty eight ethnic Russian individuals from Moscow, Russia, were genotyped at 14 single nucleotide polymorphisms CCL2 A-2578G; VEGFA C-2578A, G-634C, and C+936T; TNF G+419A and G-308A; IL1A G-889A; IL1RN T+1018C; IL6G-174C and G-572C; IFNG T+874A; IL1B C-511T; IL10 A+1082G; TGFB1 C-509T. Genotypes were determined using real-time polymerase chain reaction with TaqMan probes and polymerase chain reaction followed by melting analysis of dual-labeled probe. Genotype distribution was in accordance with Hardy-Weinberg equilibrium for all studied polymorphisms. Genotype data are available in the Allele Frequencies Net Database under identifier AFND 3367 and the population name "Russia Moscow Cytokine".

  6. Utilizing Ethnic-Specific Differences in Minor Allele Frequency to Recategorize Reported Pathogenic Deafness Variants

    PubMed Central

    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.

    2014-01-01

    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

  7. Analysis and frequency of bovine lymphocyte antigen (BoLA-DRB3) alleles in Iranian Holstein cattle.

    PubMed

    Nassiry, M R; Shahroodi, F Eftekhar; Mosafer, J; Mohammadi, A; Manshad, E; Ghazanfari, S; Mohammad Abadi, M R; Sulimova, G E

    2005-06-01

    The bovine lymphocyte antigen (BoLA-DRB3) gene encodes cell surface glycoproteins that initiate immune response by presenting processed antigenic peptides to CD4 T helper cells. DRB3 is the most polymorphic bovine MHC class II gene which encodes the peptide-binding groove. DRB3 gene has been extensively evaluated as a candidate marker for association with various bovine diseases and immunological traits. This study describes genetic variability in the BoLA-DRB3 in Iranian Holstein cattle. This is the first study of the DNA polymorphism of the BoLA-DRB3 gene in Iranian Holstein cattle. Hemi-nested PCR-RFLP method is used for identification the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the studied herd (26 alleles). Almost 67% of the alleles were accounted for four alleles (BoLA-DRB3.2*8, *24, *11 and *16) in Iranian Holstein cattle. The DRB3.2*8 allele frequency (26.6%) was higher than the others. The frequencies of the DRB3.2*54, *37, *36, *28, *25, *14, *13, *10, *1 alleles were lower than 1%. Significant distinctions have been found between Iranian Holstein cattle and other cattle breeds studied. In Iranian Holstein cattle the alleles (BoLA-DRB3.2*22, *2 and *16) associated with a lower risk of cystic ovarian disease in Holstein cattle are found. The alleles associated with the resistance to mastitis and to bovine leukemia virus infection BoLA-DRB3.2*11 and *23 are detected with the frequencies 10.4% and 4.4%, respectively. Thus in the Iranian Holstein cows studied are found alleles which are associated with resistance to various diseases. The method of DNA-typing of animals can be used in agricultural practice for BoLA-DRB3 allele genotyping of cattle in order to reduce spreading of alleles providing susceptibility to mastitis or leukemia in cattle herds.

  8. 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

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

    PubMed

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

    2016-11-04

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

  10. 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

  11. Alarmingly High Segregation Frequencies of Quinolone Resistance Alleles within Human and Animal Microbiomes Are Not Explained by Direct Clinical Antibiotic Exposure

    PubMed Central

    Field, Wesley; Hershberg, Ruth

    2015-01-01

    Antibiotic resistance poses a major threat to human health. It is therefore important to characterize the frequency of resistance within natural bacterial environments. Many studies have focused on characterizing the frequencies with which horizontally acquired resistance genes segregate within natural bacterial populations. Yet, very little is currently understood regarding the frequency of segregation of resistance alleles occurring within the housekeeping targets of antibiotics. We surveyed a large number of metagenomic datasets extracted from a large variety of host-associated and non host-associated environments for such alleles conferring resistance to three groups of broad spectrum antibiotics: streptomycin, rifamycins, and quinolones. We find notable segregation frequencies of resistance alleles occurring within the target genes of each of the three antibiotics, with quinolone resistance alleles being the most frequent and rifamycin resistance alleles being the least frequent. Resistance allele frequencies varied greatly between different phyla and as a function of environment. The frequency of quinolone resistance alleles was especially high within host-associated environments, where it averaged an alarming ∼40%. Within host-associated environments, resistance to quinolones was most often conferred by a specific resistance allele. High frequencies of quinolone resistance alleles were also found within hosts that were not directly treated with antibiotics. Therefore, the high segregation frequency of quinolone resistance alleles occurring within the housekeeping targets of antibiotics in host-associated environments does not seem to be the sole result of clinical antibiotic usage. PMID:26019163

  12. Alarmingly High Segregation Frequencies of Quinolone Resistance Alleles within Human and Animal Microbiomes Are Not Explained by Direct Clinical Antibiotic Exposure.

    PubMed

    Field, Wesley; Hershberg, Ruth

    2015-05-26

    Antibiotic resistance poses a major threat to human health. It is therefore important to characterize the frequency of resistance within natural bacterial environments. Many studies have focused on characterizing the frequencies with which horizontally acquired resistance genes segregate within natural bacterial populations. Yet, very little is currently understood regarding the frequency of segregation of resistance alleles occurring within the housekeeping targets of antibiotics. We surveyed a large number of metagenomic datasets extracted from a large variety of host-associated and non host-associated environments for such alleles conferring resistance to three groups of broad spectrum antibiotics: streptomycin, rifamycins, and quinolones. We find notable segregation frequencies of resistance alleles occurring within the target genes of each of the three antibiotics, with quinolone resistance alleles being the most frequent and rifamycin resistance alleles being the least frequent. Resistance allele frequencies varied greatly between different phyla and as a function of environment. The frequency of quinolone resistance alleles was especially high within host-associated environments, where it averaged an alarming ∼ 40%. Within host-associated environments, resistance to quinolones was most often conferred by a specific resistance allele. High frequencies of quinolone resistance alleles were also found within hosts that were not directly treated with antibiotics. Therefore, the high segregation frequency of quinolone resistance alleles occurring within the housekeeping targets of antibiotics in host-associated environments does not seem to be the sole result of clinical antibiotic usage.

  13. Allele frequencies of D21S11, FGA, TH01, and VWA in populations of the Balkans.

    PubMed

    Huckenbeck, W; Scheil, H G; Schmidt, H D; Efremovska, L; Mikerezi, I

    2004-12-01

    This study is part of an extensive investigation of the genetic relationship between Balkan populations, especially the Aromuns. Allele frequencies of four STRs (D21S11, FGA, TH01, VWA) from Macedonians (Skopje), Gramostian Aromuns from the Stip region (Macedonia), Moskopolian Aromuns from Krusevo (Macedonia), and Musequiar Aromuns from Dukasi (Albania) are presented.

  14. 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.

  15. 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.

  16. Inferring microevolutionary patterns from allele-size frequency distributions of minisatellite loci: a worldwide study of the APOB 3' hypervariable region polymorphism.

    PubMed

    Destro-Bisol, G; Capelli, C; Belledi, M

    2000-10-01

    The availability of numerous population and molecular data makes the apolipoprotein B 3' hypervariable region (APOB 3' HVR) polymorphism ideal for a pilot study of the relationships between the allele-size frequency distributions (referred to as allele-size distributions) of minisatellite loci and the microevolutionary processes underlying their present-day polymorphism in human populations. In this paper, we present a worldwide APOB 3' HVR study, based on published and unpublished data, which refers to 36 populations. We systematically compare APOB 3' HVR within-group diversity (in terms of heterozygosity, number of alleles, and allele-size variance) in numerous human populations, including African, European, Asian, Amerindian, Australomelanesian, and Polynesian groups. Overall, our analyses indicate a greater APOB 3' HVR diversity in Africans than non-Africans. Then, we compare APOB 3' HVR allele-size distributions. The APOB 3' HVR allele-size distribution is found to be quasi-unimodal in Africans and bimodal or nonunimodal in non-African populations. The analysis of the distribution of pairwise comparisons suggests that Africans expanded earlier and/or that their ancestral population was larger than other continental groups. As a final step, we examine APOB 3' HVR interpopulational relationships by using three genetic distances. The F(ST) genetic distance, which assumes genetic drift as being the agent that differentiates populations, provides results that are more congruent with established anthropological knowledge than mutation-based distances (D(SW) and R(ST)). We hypothesize that the ancestral population was characterized by a high heterozygosity, an extended range of allele size, and a quasi-unimodal allele-size distribution centered on allele *37, features persisting in examined African populations. Sampling processes during "out-of-Africa" migrations would be responsible for the decrease in APOB 3' HVR gene diversity and the nonunimodal allele

  17. Allele frequencies of three factor VIII gene polymorphisms in Iranian populations and their application in hemophilia A carrier detection.

    PubMed

    Azimifar, S Babak; Seyedna, S Yoosef; Zeinali, Sirous

    2006-05-01

    Hemophilia A is an X-linked recessive bleeding disorder caused by a quantitative or qualitative deficiency of blood coagulation factor VIII (FVIII). ARMS (amplification refractory mutation system) primers were designed to determine allele frequencies of three FVIII gene linked markers, IVS7 nt 27 G/A SNP, BclI/intron 18, and HindIII/intron 19 among 85 normal Iranian women from unrelated families. Then same method was applied to perform carrier detection for hemophilia A families. The allele frequencies of IVS7 nt 27 "G"/"A" allele, BclI "T"/"A" allele, and HindIII "C"/"T" allele among normal women were 0.88/0.12, 0.52/0.48, and 0.48/0.52, respectively. The three polymorphisms were found to be in strong linkage disequilibrium, which decreased the overall heterozygosity to 51%. Twenty-one women from 15 unrelated hemophilia A families were referred to us for hemophilia A carrier detection. Taking advantage of these three biallelic polymorphisms in conjunction with multiallelic St14 VNTR (locus DXS52), IVS13 (CA)n STR, and IVS22 (CA)n STR, carrier status was determined in 16 women (16/21 or 76% of the at-risk women) from 11 families (11/15 or 73% of the families). The used ARMS methods are rapid and can easily be applied in conjunction with other FVIII gene linked polymorphisms for indirect mutation detection of hemophilia A where they are informative.

  18. Allele and genotype frequencies of CYP2B6 and CYP2C19 polymorphisms in Egyptian agricultural workers.

    PubMed

    Ellison, Corie A; Abou El-Ella, Soheir S; Tawfik, Maha; Lein, Pamela J; Olson, James R

    2012-01-01

    Genetic variability in cytochrome P-450 (CYP) has the potential to modify pharmacological and toxicological responses to many chemicals. Both CYP2B6 and CYP2C19 are pharmacologically and toxicologically relevant due to their ability to metabolize multiple drugs and environmental contaminants, including the organophosphorus (OP) pesticide chlorpyrifos. The aim of this study was to determine the prevalence of CYP2B6 and CYP2C19 variants in an indigenous Egyptian population (n = 120) that was shown to be occupationally exposed to chlorpyrifos. Further, the genotyping data was compared for Egyptians with previously studied populations to determine between population differences. Allelic frequencies were CYP2B6 1459C > T (3.8%), CYP2B6 785A > G (30.4%), CYP2B6 516G > T (28.8%), CYP2C19 681G > A (3.8%), and CYP2C19 431G > A (0%). The most prevalent CYP2B6 genotype combinations were CYP2B6 *1/*1 (44%), *1/*6 (38%), *6/*6 (8%), and *1/*5 (6%). The frequency of the CYP2C19 genotype combinations were CYP2C19 *1/*1 (93%), *1/*2 (6%), and *2/*2 (1%). The frequency of the CYP2B6 516G > T and CYP2B6 785A > G polymorphisms in this Egyptian cohort is similar to that found North American and European populations but significantly different from that reported for West African populations, while that of CYP2B6 1459C > T is similar to that found in Africans and African Americans. The observed frequency of CYP2C19 681G > A in Egyptians is similar to that of African pygmies but significantly different from other world populations, while CYP2C19 431 G > A was significantly different from that of African pygmies but similar to other world populations.

  19. Frequency Specific Effects of ApoE ε4 Allele on Resting-State Networks in Nondemented Elders

    PubMed Central

    Liang, Ying; Li, Zhenzhen; Neuroimaging Initiative, Alzheimer's Disease

    2017-01-01

    We applied resting-state functional magnetic resonance imaging (fMRI) to examine the Apolipoprotein E (ApoE) ε4 allele effects on functional connectivity of the default mode network (DMN) and the salience network (SN). Considering the frequency specific effects of functional connectivity, we decomposed the brain network time courses into two bands: 0.01–0.027 Hz and 0.027–0.08 Hz. All scans were acquired by the Alzheimer's Disease Neuroscience Initiative (ADNI). Thirty-two nondemented subjects were divided into two groups based on the presence (n = 16) or absence (n = 16) of the ApoE ε4 allele. We explored the frequency specific effects of ApoE ε4 allele on the default mode network (DMN) and the salience network (SN) functional connectivity. Compared to ε4 noncarriers, the DMN functional connectivity of ε4 carriers was significantly decreased while the SN functional connectivity of ε4 carriers was significantly increased. Many functional connectivities showed significant differences at the lower frequency band of 0.01–0.027 Hz or the higher frequency band of 0.027–0.08 Hz instead of the typical range of 0.01–0.08 Hz. The results indicated a frequency dependent effect of resting-state signals when investigating RSNs functional connectivity.

  20. Human leukocyte antigen class II (DRB1 and DQB1) alleles and haplotypes frequencies in patients with pemphigus vulgaris among the Serbian population.

    PubMed

    Zivanovic, D; Bojic, S; Medenica, L; Andric, Z; Popadic, D

    2016-05-01

    The etiology of pemphigus vulgaris (PV) is multifactorial and includes genetic, environmental, hormonal, and immunological factors. Inheritance of certain Human class II leukocyte antigen (HLA) alleles is by far the best-established predisposing factor for the development of PV. Class II HLA alleles vary among racial/ethnic backgrounds. We have determined an association between HLA class II alleles and PV among the Serbian population. A total of 72 patients with confirmed diagnosis of PV were genotyped for HLA class II alleles. HLA frequencies were compared with unrelated healthy bone marrow donors. The statistical significance of differences between patients and controls was evaluated using Fisher's exact test. The DRB1*04 and DRB1*14 allelic groups were associated with PV (P adj = 4.45 × 10(-13) and 4.06 × 10(-19) respectively), while HLA-DRB1*11 was negatively associated with PV (P adj = 0.0067) suggesting a protective role. DRB1*04:02, DRB1*14:04, DQB1*03:02 and DQB1*05:03 alleles were shown to be strongly associated with PV (P adj = 1.63 × 10(-12), 5.20 × 10(-7), 1.28 × 10(-6), and 4.44 × 10(-5), respectively). The frequency of HLA DRB1*04-DQB1*03 and HLA DRB1*14-DQB1*05 haplotypes in PV patients was significantly higher than in controls (31.3% vs 8.8%, P adj =7.66 × 10(-8) and 30.6% vs 6.3%, P adj = 3.22 × 10(-10), respectively). At high-resolution level, statistical significance was observed in HLA-DRB1*04:02-DQB1*03:02 and HLA-DRB1*14:04-DQB1*05:03 haplotypes (P adj = 5.55 × 10(-12), and P adj = 3.91 × 10(-6), respectively). Our findings suggest that HLA-DRB1*04:02, DRB1*14:04, HLA-DQB1* 03:02 and DQB1*05:03 alleles and HLA-DRB1*04:02-DQB1*03:02 and HLA-DRB1*14:04-DQB1*05:03 haplotypes are genetic markers for susceptibility for PV, while DRB1*11 allelic group appears protective in Serbian population.

  1. HLA-DRB and HLA-DQB Allele and Haplotype Frequencies in Iranian Patients with Recurrent Aphthous Stomatitis.

    PubMed

    Najafi, Shamsolmoulouk; Mohammadzadeh, Mahsa; Zare Bidoki, Alireza; Meighani, Ghasem; Aslani, Saeed; Mahmoudi, Mahdi; Rezaei, Nima

    Recurrent aphthous stomatitis (RAS) is known as the most common chronic disease of the oral cavity, which affects a range of 5-25% of the population. RAS appears to be associated with some human leukocyte antigen (HLA) class II alleles and haplotypes. This study attempts to survey the distribution of HLA-DRB and -DQB alleles among Iranian RAS patients and healthy controls. In order to evaluate the association of HLA-DR and DQ alleles and haplotypes, 54 patients with RAS and 100 unrelated healthy subjects as control group were investigated. Our data indicated that DRB1*13:17, DRB1*15:01, and DRB5*01 were significantly more frequent in RAS patients in comparison to controls. However, DRB3:01allele frequency was higher in the controls compared to the patients. The significantly frequent allele in the patients compared with the healthy subjects was HLA-DQB1*03:02. However, both HLA-DQB1*02:01 and HLA-DQB1*03:01 alleles were most frequent in the healthy individuals rather than the patients. The DRB*04/DQB1*03:01 and DRB*01:01/DQB1*02:01 haplotypes were significantly distributed in healthy subjects compared with patients. However, DRB*07:01/DQB1*03:02 haplotype was found to be significantly frequent in patients than controls. In respect of HLA genes, factors are involved in the incidence of RAS; various HLA-DRB and HLA-DQB1 alleles and the related haplotypes are suggested to be the three main RAS susceptibility factors in our population study.

  2. Genotype prevalence and allele frequencies of 5,10-methylenetetrahydrofolate reductase (MTHFR) C677T mutation in two caste groups of India.

    PubMed

    Rai, V; Yadav, U; Kumar, P

    2012-06-15

    The aim of the present study was to investigate the distribution of 5,10-methylenetetrahydrofolate reductase (MTHFR) polymorphism in two caste group populations of eastern Uttar Pradesh. This mutation has been suggested to be positively associated with the risk of several congenital and multifactorial disorders. Frequency of mutant T allele differs in various ethnic and geographical populations of the world. MTHFR C677T mutation analysis was carried out by PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) method and the samples studied were randomly selected from the healthy individuals belonging to two caste populations. In Brahmin samples, genotype frequencies of CC, CT and TT were 0.727, 0.25 and 0.023 respectively whereas in Rajput samples, CC genotype was observed in 88 samples, CT genotype in 25 and TT genotype was found in 2 samples. Frequency of mutant T allele was found to be 0.147 in Brahmin and 0.126 in Rajput populations. The percentage of CT genotype and C allele were high in both the populations.

  3. Prevalence of alpha-1 antitrypsin deficiency and allele frequency in patients with COPD in Brazil

    PubMed Central

    Russo, Rodrigo; Zillmer, Laura Russo; Nascimento, Oliver Augusto; Manzano, Beatriz; Ivanaga, Ivan Teruaki; Fritscher, Leandro; Lundgren, Fernando; Miravitlles, Marc; Gondim, Heicilainy Del Carlos; Santos, Gildo; Alves, Marcela Amorim; Oliveira, Maria Vera; de Souza, Altay Alves Lino; Sales, Maria Penha Uchoa; Jardim, José Roberto

    2016-01-01

    ABSTRACT Objective: To determine the prevalence of alpha 1-antitrypsin (AAT) deficiency (AATD), as well as allele frequency, in COPD patients in Brazil. Methods: This was a cross-sectional study involving 926 COPD patients 40 years of age or older, from five Brazilian states. All patients underwent determination of AAT levels in dried blood spot (DBS) samples by nephelometry. Those with DBS AAT levels ≤ 2.64 mg/dL underwent determination of serum AAT levels. Those with serum AAT levels of < 113 mg/dL underwent genotyping. In case of conflicting results, SERPINA1 gene sequencing was performed. Results: Of the 926 COPD patients studied, 85 had DBS AAT levels ≤ 2.64 mg/dL, and 24 (2.6% of the study sample) had serum AAT levels of < 113 mg/dL. Genotype distribution in this subset of 24 patients was as follows: PI*MS, in 3 (12.5%); PI*MZ, in 13 (54.2%); PI*SZ, in 1 (4.2%); PI*SS, in 1 (4.2%); and PI*ZZ, in 6 (25.0%). In the sample as a whole, the overall prevalence of AATD was 2.8% and the prevalence of the PI*ZZ genotype (severe AATD) was 0.8% Conclusions: The prevalence of AATD in COPD patients in Brazil is similar to that found in most countries and reinforces the recommendation that AAT levels be measured in all COPD patients. PMID:27812629

  4. 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

  5. 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.

  6. 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

  7. Polymorphism and predictability at the alpha-glycerophosphate dehydrogenase locus in Colias butterflies: gradients in allele frequency within single populations.

    PubMed

    Johnson, G B

    1976-06-01

    Heterozygosity at the alpha-glycerophosphate dehydrogenase locus of five species of Colias butterflies is widespread in montane populations; alpine and lowland populations are not heterozygous. Within a single demographically characterized population of C. meadii where the population extends from alpine down into montane habitats, a marked cline in allele frequency is seen. Such within-population clines suggest the involvement of strong selection across the marked ecological interface. Thermal factors are the most likely causative agents, but associative overdominance is not excluded.

  8. Allelic and genotype frequencies of catechol-O-methyltransferase (Val158Met) and CYP2D6*10 (Pro34Ser) single nucleotide polymorphisms in the Philippines

    PubMed Central

    Baclig, Michael O; Predicala, Rey Z; Mapua, Cynthia A; Lozano-Kühne, Jingky P; Daroy, Maria Luisa G; Natividad, Filipinas F; Javier, Francis O

    2012-01-01

    A hospital-based cross-sectional study was conducted to determine the allelic and genotype frequencies in the genes encoding for catechol-O-methyltransferase and CYP2D6*10 among healthy volunteers and patients clinically diagnosed with cancer pain. PCR-RFLP was used to identify COMT and CYP2D6*10 genotypes. Allelic frequencies among healthy volunteer Filipinos were 0.83 and 0.17 for the COMT Val and COMT Met alleles, respectively. Calculated frequencies in Hardy-Weinberg equilibrium (HWE) were 73% for COMT Val/Val, 26% for COMT Val/Met, and 1% for COMT Met/Met genotype. For CYP2D6*10, allelic frequencies in HWE among volunteers were 0.46 for the C allele and 0.54 for the T allele. Twenty percent were identified as homozygous for the wild-type C/C genotype, 56% were identified as heterozygous for the C/T genotype, and 24% were identified as homozygous for the T/T variant genotype. No significant differences in COMT and CYP2D6*10 allele frequencies between cancer patients and healthy volunteers were noted. Our data demonstrated that the allele frequencies of COMT and CYP2D6*10 in the Filipino healthy volunteers were similar with other Asians but markedly different from Caucasian populations. PMID:22724048

  9. Allelic and genotype frequencies of catechol-O-methyltransferase (Val158Met) and CYP2D6*10 (Pro34Ser) single nucleotide polymorphisms in the Philippines.

    PubMed

    Baclig, Michael O; Predicala, Rey Z; Mapua, Cynthia A; Lozano-Kühne, Jingky P; Daroy, Maria Luisa G; Natividad, Filipinas F; Javier, Francis O

    2012-01-01

    A hospital-based cross-sectional study was conducted to determine the allelic and genotype frequencies in the genes encoding for catechol-O-methyltransferase and CYP2D6*10 among healthy volunteers and patients clinically diagnosed with cancer pain. PCR-RFLP was used to identify COMT and CYP2D6*10 genotypes. Allelic frequencies among healthy volunteer Filipinos were 0.83 and 0.17 for the COMT Val and COMT Met alleles, respectively. Calculated frequencies in Hardy-Weinberg equilibrium (HWE) were 73% for COMT Val/Val, 26% for COMT Val/Met, and 1% for COMT Met/Met genotype. For CYP2D6*10, allelic frequencies in HWE among volunteers were 0.46 for the C allele and 0.54 for the T allele. Twenty percent were identified as homozygous for the wild-type C/C genotype, 56% were identified as heterozygous for the C/T genotype, and 24% were identified as homozygous for the T/T variant genotype. No significant differences in COMT and CYP2D6*10 allele frequencies between cancer patients and healthy volunteers were noted. Our data demonstrated that the allele frequencies of COMT and CYP2D6*10 in the Filipino healthy volunteers were similar with other Asians but markedly different from Caucasian populations.

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

    PubMed

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

    2015-11-11

    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.

  11. 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

  12. 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.

  13. Increase of TCR V beta accessibility within E beta regulatory region influences its recombination frequency but not allelic exclusion.

    PubMed

    Senoo, Makoto; Wang, Lili; Suzuki, Daisuke; Takeda, Naoki; Shinkai, Yoichi; Habu, Sonoko

    2003-07-15

    Seventy percent of the murine TCRbeta locus (475 kb) was deleted to generate a large deleted TCRbeta (beta(LD)) allele to investigate a possible linkage between germline transcription, recombination frequency, and allelic exclusion of the TCR Vbeta genes. In these beta(LD/LD) mice, the TCRbeta gene locus contained only four Vbeta genes at the 5' side of the locus, and consequently, the Vbeta10 gene was located in the original Dbeta1-Jbeta1cluster within the Ebeta regulatory region. We showed that the frequency of recombination and expression of the Vbeta genes are strongly biased to Vbeta10 in these mutant mice even though the proximity of the other three 5'Vbeta genes was also greatly shortened toward the Dbeta-Jbeta cluster and the Ebeta enhancer. Accordingly, the germline transcription of the Vbeta10 gene in beta(LD/LD) mice was exceptionally enhanced in immature double negative thymocytes compared with that in wild-type mice. During double negative-to-double positive transition of thymocytes, the level of Vbeta10 germline transcription was prominently increased in beta(LD/LD) recombination activating gene 2-deficient mice receiving anti-CD3epsilon Ab in vivo. Interestingly, however, despite the increased accessibility of the Vbeta10 gene in terms of transcription, allelic exclusion of this Vbeta gene was strictly maintained in beta(LD/LD) mice. These results provide strong evidence that increase of Vbeta accessibility influences frequency but not allelic exclusion of the TCR Vbeta rearrangement if the Vbeta gene is located in the Ebeta regulatory region.

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

    PubMed

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

    2007-12-01

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

  15. Plasminogen Activator Inhibitor-1 (PAI-1) gene 4G/5G alleles frequency distribution in the Lebanese population.

    PubMed

    Shammaa, Dina M R; Sabbagh, Amira S; Taher, Ali T; Zaatari, Ghazi S; Mahfouz, Rami A R

    2008-09-01

    Plasminogen activator inhibitor-1 (PAI-1) is an inhibitor of fibrinolysis. Increased plasma PAI-1 levels play an essential role in the pathogenesis of cardiovascular risk and other diseases associated with thrombosis. The 4G/5G polymorphism of the PAI-1 promoter region has been extensively studied in different populations. We studied 160 healthy unrelated Lebanese individuals using a reverse hybridization PCR assay to detect the 5G/5G, 4G/5G and, 4G/4G genotypes of the PAI-1 gene and the frequencies of the 4G and 5G alleles. We found that 4G/5G genotype was the most prevalent (45.6%) followed by 5G/5G (36.9%) and 4G/4G (17.5%). The frequencies of the 4G and 5G alleles were calculated to be 0.403 and 0.597, respectively. Compared to other ethnic communities, the Lebanese population was found to harbour a relatively high prevalence of the rare 4G allele. This, in turn, may predispose this population to develop cardiovascular diseases and other thrombotic clinical conditions. This study aids to enhance our understanding of the genetic features of the Lebanese population.

  16. 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.

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

    PubMed

    González-Galarza, Faviel F; Takeshita, Louise Y C; Santos, Eduardo J M; Kempson, Felicity; Maia, Maria Helena Thomaz; da Silva, Andrea Luciana Soares; Teles e Silva, André Luiz; 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.

  18. 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

  19. Maximum-likelihood and markov chain monte carlo approaches to estimate inbreeding and effective size from allele frequency changes.

    PubMed Central

    Laval, Guillaume; SanCristobal, Magali; Chevalet, Claude

    2003-01-01

    Maximum-likelihood and Bayesian (MCMC algorithm) estimates of the increase of the Wright-Malécot inbreeding coefficient, F(t), between two temporally spaced samples, were developed from the Dirichlet approximation of allelic frequency distribution (model MD) and from the admixture of the Dirichlet approximation and the probabilities of fixation and loss of alleles (model MDL). Their accuracy was tested using computer simulations in which F(t) = 10% or less. The maximum-likelihood method based on the model MDL was found to be the best estimate of F(t) provided that initial frequencies are known exactly. When founder frequencies are estimated from a limited set of founder animals, only the estimates based on the model MD can be used for the moment. In this case no method was found to be the best in all situations investigated. The likelihood and Bayesian approaches give better results than the classical F-statistics when markers exhibiting a low polymorphism (such as the SNP markers) are used. Concerning the estimations of the effective population size all the new estimates presented here were found to be better than the F-statistics classically used. PMID:12871924

  20. 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.

  1. 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.

  2. 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.

  3. Beta-thalassemia mutations in Rome. A high frequency of the IVSII-745 allele in subjects of latium origin.

    PubMed

    Massa, A; Cianciulli, P; Cianetti, L; Iazzone, R; Cenci, A; Sorrentino, F; Franco, G; Pecci, G; Papa, G; Peschle, C

    1994-01-01

    We studied the molecular bases of beta-thalassemia in Rome, a city centrally located in Latium, which is a region with a low incidence of beta-carriers. People also come to Rome from other regions for specific or prenatal diagnostic assessment. Only 11 patients (20%) out of 62 characterized beta-thalassemia subjects were of Latium family origin. They presented five mutations with an uncommonly high frequency of the IVSII-745 allele, that was found in homozygosis in 4 unrelated patients from a southeastern area in the province of Frosinone. These data may indicate a founder effect.

  4. 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

  5. Allele frequencies for 15 autosomal STR loci and haplotype data for 17 Y-STR loci in a population from Belize.

    PubMed

    Flores, Shahida; Sun, Jie; King, Jonathan; Eisenberg, Arthur; Budowle, Bruce

    2015-11-01

    Allele frequencies for 15 autosomal STR loci (N = 290) and haplotype data for 17 Y-STR loci (N = 157) were determined for an admixed population from Belize. There were no detectable departures from Hardy-Weinberg equilibrium expectations at any autosomal STR loci except for the D8S1179 locus (p = 0.002). The combined power of discrimination (PD) and combined power of exclusion (PE) were greater than 0.99999999 and 0.99999951, respectively. In addition, a total of 144 distinct Y-STR haplotypes were observed with 133 Y-STR haplotypes observed only once. The most common Y-STR haplotype was observed three times for two separate haplotypes. The various analyses of these forensically relevant STR loci showed that these markers are informative in the Belize population for forensic and parentage testing applications.

  6. Comprehensive genetic testing with ethnic-specific filtering by allele frequency in a Japanese hearing-loss population

    PubMed Central

    Moteki, Hideaki; Azaiez, Hela; Booth, Kevin T; Shearer, A Eliot; Sloan, Christina M; Kolbe, Diana L; Nishio, Shin-ya; Hattori, Mitsuru; Usami, Shin-ichi; Smith, Richard J H

    2016-01-01

    Recent advances in targeted genomic enrichment with massively parallel sequencing (TGE+MPS) have made comprehensive genetic testing for non-syndromic hearing loss (NSHL) possible. After excluding NSHL subjects with causative mutations in GJB2 and the MT-RNR1 (1555A>G) variant by Sanger sequencing, we completed TGE+MPS on 194 probands with presumed NSHL identified across Japan. We used both publicly available minor allele frequency (MAF) datasets and ethnic-specific MAF filtering against an in-house database of 200 normal-hearing Japanese controls. Ethnic-specific MAF filtering allowed us to re-categorize as common 203 variants otherwise annotated as rare or novel in non-Japanese ethnicities. This step minimizes false-positive results and improves the annotation of identified variants. Causative variants were identified in 27% of probands with solve rates of 35%, 35% and 19% for dominant, recessive and sporadic NSHL, respectively. Mutations in MYO15A and CDH23 follow GJB2 as the frequent causes of recessive NSHL; copy number variations in STRC are a major cause of mild-to-moderate NSHL. Ethnic-specific filtering by allele frequency is essential to optimize the interpretation of genetic data. PMID:26346818

  7. 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 Central

    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

  8. 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

  9. 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.

  10. High-Frequency Observations of Blazars

    NASA Technical Reports Server (NTRS)

    Marscher, A. P.; Marchenko-Jorstad, S. G.; Mattox, J. R.; Wehrle, A. E.; Aller, M. F.

    2000-01-01

    We report on the results of high-frequency VLBA observations of 42 gamma-ray bright blazars monitored at 22 and 43 GHz between 1993.9 and 1997.6. In 1997 the observations included polarization-sensitive imaging. The cores of gamma-ray blazars are only weakly polarized, with EVPAs (electric-vector position angles) usually within 40 deg of the local direction of the jet. The EVPAs of the jet components are usually within 20 deg of the local jet direction. The apparent speeds of the gamma-ray bright blazars are considerably faster than in the general population of bright compact radio sources. Two X-ray flares (observed with RXTE) of the quasar PKS 1510-089 appear to be related to radio flares, but with the radio leading the X-ray variations by about 2 weeks. This can be explained either by synchrotron self-Compton emission in a component whose variations are limited by light travel time or by the Mirror Compton model.

  11. High-Frequency Observations of Blazars

    NASA Technical Reports Server (NTRS)

    Marscher, A. P.; Marchenko-Jorstad, S. G.; Mattox, J. R.; Wehrle, A. E.; Aller, M. F.

    2000-01-01

    We report on the results of high-frequency VLBA observations of 42 gamma ray bright blazars monitored at 22 and 43 GHz between 1993.9 and 1997-6. In 1997 the observations included polarization-sensitive imaging. The cores of gamma ray blazars are only weakly polarized, with EVPAs (electric-vector position angles) usually within 40 degrees of the local direction of the jet. The EVPAs of the jet components are usually within 20 degrees of the local jet direction. The apparent speeds of the gamma ray bright blazars are considerably faster than in the general population of bright compact radio sources. Two X-ray flares (observed with RXTE) of the quasar PKS 1510-089 appear to be related to radio flares, but with the radio leading the X-ray variations by about 2 weeks. This can be explained either by synchrotron self-Compton emission in a component whose variations are limited by light travel time or by the Mirror Compton model.

  12. Highly Connected Populations and Temporal Stability in Allelic Frequencies of a Harvested Crab from the Southern Pacific Coast.

    PubMed

    Rojas-Hernandez, Noemi; Veliz, David; Riveros, Marcela P; Fuentes, Juan P; Pardo, Luis M

    2016-01-01

    For marine invertebrates with a benthic adult form and a planktonic larva phase, the connectivity among populations is mainly based on larval dispersal. While an extended larval phase will promote gene flow, other factors such as an intensive fishery and geographical barriers could lead to changes in genetic variability. In this study, the population genetic structure of the commercial crab Metacarcinus edwardsii was analyzed along 700 km of the Chilean coast. The analysis, based on eight microsatellite loci genotyped from megalopae and adult crabs, considered temporal and spatial patterns of genetic variation. The results showed no evidence of spatial patterns in genetic structure, suggesting high connectivity among the sampling sites. The temporal analysis showed no evidence of changes in allele frequencies and no evidence of a recent bottleneck. The lack of spatial structure and allele variation over time could be explained by the interaction of factors such as i) low reproductive variance due to the capability of females to store sperm in the seminal receptacle, which can be used for successive broods, ii) high larval dispersal and iii) high individual reproductive output. Using our data as priors, a genetic modelling approach coincided, predicting this temporal and spatial stability. The same analysis showed that a reduction in population size leads to the loss of genetic variability in populations, as well as of the genetic cohesiveness between populations, pointing out the importance management for species under exploitation, such as M. edwardsii.

  13. Genetic Diversity and Allelic Frequency of Glutamate-Rich Protein (GLURP) in Plasmodium falciparum Isolates from Sub-Saharan Africa

    PubMed Central

    Duru, Kimberley C; Thomas, Bolaji N

    2014-01-01

    Glutamate-rich protein is a Plasmodium falciparum (Pf) antigen found in all stages of the parasite and has been reported to induce clinical immunity. The R0 and R2 regions have been found to exhibit a high degree of conservation, therefore serving as a good vaccine design material. We assayed the genetic diversity of Pf glurp genes in the R0 and R2 regions, as well as evaluated the role of seasonality on allelic frequency. A total of 402 genomic DNA samples, extracted from filter paper blood samples, were screened by nested polymerase chain reaction (PCR) analysis of Pf glurp R0 and R2 regions, in addition to fragment analysis of the polymorphic regions to identify allelic diversity of the parasite population. We found an extensive heterogeneity in the R2 region in general, and this heterogeneity is seasonally dependent, indicative of region plasticity. The R0 region displayed genetic conservation, as expected. We conclude that positive genotyping results with glurp R0 region should be seen as indicative of an active Pf infection, requiring adequate treatment. In addition, we advocate extending the possibility that an R0 region genotypic positivity could serve as diagnostic tool, thereby reducing cases of untreated or poorly treated infection, contributory to recrudescence or treatment failure. PMID:25452699

  14. Highly Connected Populations and Temporal Stability in Allelic Frequencies of a Harvested Crab from the Southern Pacific Coast

    PubMed Central

    Rojas-Hernandez, Noemi; Veliz, David; Riveros, Marcela P; Fuentes, Juan P.; Pardo, Luis M.

    2016-01-01

    For marine invertebrates with a benthic adult form and a planktonic larva phase, the connectivity among populations is mainly based on larval dispersal. While an extended larval phase will promote gene flow, other factors such as an intensive fishery and geographical barriers could lead to changes in genetic variability. In this study, the population genetic structure of the commercial crab Metacarcinus edwardsii was analyzed along 700 km of the Chilean coast. The analysis, based on eight microsatellite loci genotyped from megalopae and adult crabs, considered temporal and spatial patterns of genetic variation. The results showed no evidence of spatial patterns in genetic structure, suggesting high connectivity among the sampling sites. The temporal analysis showed no evidence of changes in allele frequencies and no evidence of a recent bottleneck. The lack of spatial structure and allele variation over time could be explained by the interaction of factors such as i) low reproductive variance due to the capability of females to store sperm in the seminal receptacle, which can be used for successive broods, ii) high larval dispersal and iii) high individual reproductive output. Using our data as priors, a genetic modelling approach coincided, predicting this temporal and spatial stability. The same analysis showed that a reduction in population size leads to the loss of genetic variability in populations, as well as of the genetic cohesiveness between populations, pointing out the importance management for species under exploitation, such as M. edwardsii. PMID:27814382

  15. An analysis of HLA-A, -B, and -DRB1 allele and haplotype frequencies of 21,918 residents living in Liaoning, China.

    PubMed

    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.

  16. 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.

  17. Allele frequencies of the new European Standard Set (ESS) loci in a population of Apulia (Southern Italy).

    PubMed

    Piglionica, M; Baldassarra, S Lonero; Giardina, E; Tonino Marsella, L; Resta, N; Dell'Erba, A

    2013-02-01

    Allele frequencies of five miniSTRs loci (D1S1656, D2S441, D12S391, D10S1248 and D22S1045) included in the new European Standard Set (ESS) were calculated from a sample of 150 unrelated individuals from Apulia, a Region of Southern Italy. Two different PCR Amplification Kits were used, in order to evaluate the concordance of the genotypes. The results obtained with the two kits showed no differences in all genotype profiles. No deviation from Hardy-Weinberg expectations was detected at either locus. Moreover genetic analysis using Fst estimation showed no evidence for differentiation at the five new loci between Apulia and Italian populations. The high levels of polymorphisms of the analyzed markers in the Apulian population allow to confirm that these markers are useful tools in paternity and forensic analysis from degraded DNA samples.

  18. POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface.

    PubMed

    Takezaki, Naoko; Nei, Masatoshi; Tamura, Koichiro

    2010-04-01

    Currently, there is a demand for software to analyze polymorphism data such as microsatellite DNA and single nucleotide polymorphism with easily accessible interface in many fields of research. In this article, we would like to make an announcement of POPTREE2, a computer program package, that can perform evolutionary analyses of allele frequency data. The original version (POPTREE) was a command-line program that runs on the Command Prompt of Windows and Unix. In POPTREE2 genetic distances (measures of the extent of genetic differentiation between populations) for constructing phylogenetic trees, average heterozygosities (H) (a measure of genetic variation within populations) and G(ST) (a measure of genetic differentiation of subdivided populations) are computed through a simple and intuitive Windows interface. It will facilitate statistical analyses of polymorphism data for researchers in many different fields. POPTREE2 is available at http://www.med.kagawa-u.ac.jp/ approximately genomelb/takezaki/poptree2/index.html.

  19. 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.

  20. Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples

    PubMed Central

    Boitard, Simon; Kofler, Robert; Françoise, Pierre; Robelin, David; Schlötterer, Christian; Futschik, Andreas

    2013-01-01

    Due to its cost effectiveness, next generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for genome-wide estimation of allele frequencies in population samples. As the allele frequency spectrum provides information about past episodes of selection, Pool-seq is also a promising design for genomic scans for selection. However, no software tool has yet been developed for selection scans based on Pool-Seq data. We introduce Pool-hmm, a Python program for the estimation of allele frequencies and the detection of selective sweeps in a Pool-Seq sample. Pool-hmm includes several options that allow a flexible analysis of Pool-Seq data, and can be run in parallel on several processors. Source code and documentation for Pool-hmm is freely available at https://qgsp.jouy.inra.fr/. PMID:23311589

  1. 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

  2. dbQSNP: a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods.

    PubMed

    Tahira, Tomoko; Baba, Shingo; Higasa, Koichiro; Kukita, Yoji; Suzuki, Yutaka; Sugano, Sumio; Hayashi, Kenshi

    2005-08-01

    We present a database, dbQSNP (http://qsnp.gen.kyushu-u.ac.jp/), that provides sequence and allele frequency information for single-nucleotide polymorphisms (SNPs) located in the promoter regions of human genes, which were defined by the 5' ends of full-length cDNA clones. We searched for the SNPs in these regions by sequencing or single-strand conformation polymorphism (SSCP) analysis. The allele frequencies of the identified SNPs in two ethnic groups were quantified by SSCP analyses of pooled DNA samples. The accuracy of our estimation is supported by strong correlations between the frequencies in our data and those in other databases for the same ethnic groups. The frequencies vary considerably between the two ethnic groups studied, suggesting the need for population-based collections and allele frequency determination of SNPs, in, e.g., association studies of diseases. We show profiles of SNP densities that are characteristic of transcription start site regions. A fraction of the SNPs revealed a significantly different allele frequency between the groups, suggesting differential selection of the genes involved.

  3. 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.

  4. 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.

  5. Variation in meiotic recombination frequencies between allelic transgenes inserted at different sites in the Drosophila melanogaster genome.

    PubMed

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

    2013-08-07

    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.

  6. Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency.

    PubMed

    Hancock, Angela M; Witonsky, David B; Ehler, Edvard; Alkorta-Aranburu, Gorka; Beall, Cynthia; Gebremedhin, Amha; Sukernik, Rem; Utermann, Gerd; Pritchard, Jonathan; Coop, Graham; Di Rienzo, Anna

    2010-05-11

    Human populations use a variety of subsistence strategies to exploit an exceptionally broad range of ecoregions and dietary components. These aspects of human environments have changed dramatically during human evolution, giving rise to new selective pressures. To understand the genetic basis of human adaptations, we combine population genetics data with ecological information to detect variants that increased in frequency in response to new selective pressures. Our approach detects SNPs that show concordant differences in allele frequencies across populations with respect to specific aspects of the environment. Genic and especially nonsynonymous SNPs are overrepresented among those most strongly correlated with environmental variables. This provides genome-wide evidence for selection due to changes in ecoregion, diet, and subsistence. We find particularly strong signals associated with polar ecoregions, with foraging, and with a diet rich in roots and tubers. Interestingly, several of the strongest signals overlap with those implicated in energy metabolism phenotypes from genome-wide association studies, including SNPs influencing glucose levels and susceptibility to type 2 diabetes. Furthermore, several pathways, including those of starch and sucrose metabolism, are enriched for strong signals of adaptations to a diet rich in roots and tubers, whereas signals associated with polar ecoregions are overrepresented in genes associated with energy metabolism pathways.

  7. 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

  8. 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

  9. 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.

  10. OutLyzer: software for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice

    PubMed Central

    Muller, Etienne; Goardon, Nicolas; Brault, Baptiste; Rousselin, Antoine; Paimparay, Germain; Legros, Angelina; Fouillet, Robin; Bruet, Olivia; Tranchant, Aurore; Domin, Florian; San, Chankannira; Quesnelle, Céline; Frebourg, Thierry; Ricou, Agathe; Krieger, Sophie; Vaur, Dominique; Castera, Laurent

    2016-01-01

    Highlighting tumoral mutations is a key step in oncology for personalizing care. Considering the genetic heterogeneity in a tumor, software used for detecting mutations should clearly distinguish real tumor events of interest that could be predictive markers for personalized medicine from false positives. OutLyzer is a new variant-caller designed for the specific and sensitive detection of mutations for research and diagnostic purposes. It is based on statistic and local evaluation of sequencing background noise to highlight potential true positive variants. 130 previously genotyped patients were sequenced after enrichment by capturing the exons of 22 genes. Sequencing data were analyzed by HaplotypeCaller, LofreqStar, Varscan2 and OutLyzer. OutLyzer had the best sensitivity and specificity with a fixed limit of detection for all tools of 1% for SNVs and 2% for Indels. OutLyzer is a useful tool for detecting mutations of interest in tumors including low allele-frequency mutations, and could be adopted in standard practice for delivering targeted therapies in cancer treatment. PMID:27825131

  11. Phenol sulphotransferase SULT1A1 polymorphism: molecular diagnosis and allele frequencies in Caucasian and African populations.

    PubMed Central

    Coughtrie, M W; Gilissen, R A; Shek, B; Strange, R C; Fryer, A A; Jones, P W; Bamber, D E

    1999-01-01

    Sulphation, catalysed by members of the sulphotransferase (SULT) enzyme family, is an important component of the body's chemical defence mechanism, but also acts to bioactivate mutagens such as hydroxylated aryl and heterocyclic amines. A major human sulphotransferase, SULT1A1 (P-PST), metabolizes and/or bioactivates many drugs, iodothyronines and hydroxylated aromatic amines. The enzyme activity varies widely within the population and is under genetic control. We have developed an assay detecting a G-->A transition in SULT1A1 that causes an Arg213-->His substitution associated with low SULT activity and altered enzyme properties, and have used it to assess the SULT1A1 genotype in Caucasian (n=293) and African (Nigerian, n=52) populations. We show that the mutant SULT1A1*2 allele is present at frequencies of 0.321 and 0.269 in the Caucasian and African populations respectively. We also demonstrate a significant age-related difference in SULT1A1 genotype within our Caucasian population, with increasing incidence of SULT1A1*1 homozygosity and decreasing incidence of SULT1A1*2 homozygosity with increasing age, indicating a potential association of SULT1A1*1 allozyme(s) with protection against cell and/or tissue damage during aging. PMID:9854023

  12. 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

  13. A Model of Compound Heterozygous, Loss-of-Function Alleles Is Broadly Consistent with Observations from Complex-Disease GWAS Datasets

    PubMed Central

    Sanjak, Jaleal S.; Long, Anthony D.; Thornton, Kevin R.

    2017-01-01

    The genetic component of complex disease risk in humans remains largely unexplained. A corollary is that the allelic spectrum of genetic variants contributing to complex disease risk is unknown. Theoretical models that relate population genetic processes to the maintenance of genetic variation for quantitative traits may suggest profitable avenues for future experimental design. Here we use forward simulation to model a genomic region evolving under a balance between recurrent deleterious mutation and Gaussian stabilizing selection. We consider multiple genetic and demographic models, and several different methods for identifying genomic regions harboring variants associated with complex disease risk. We demonstrate that the model of gene action, relating genotype to phenotype, has a qualitative effect on several relevant aspects of the population genetic architecture of a complex trait. In particular, the genetic model impacts genetic variance component partitioning across the allele frequency spectrum and the power of statistical tests. Models with partial recessivity closely match the minor allele frequency distribution of significant hits from empirical genome-wide association studies without requiring homozygous effect sizes to be small. We highlight a particular gene-based model of incomplete recessivity that is appealing from first principles. Under that model, deleterious mutations in a genomic region partially fail to complement one another. This model of gene-based recessivity predicts the empirically observed inconsistency between twin and SNP based estimated of dominance heritability. Furthermore, this model predicts considerable levels of unexplained variance associated with intralocus epistasis. Our results suggest a need for improved statistical tools for region based genetic association and heritability estimation. PMID:28103232

  14. 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

  15. The Frequency of HLA-A, HLA-B, and HLA-DRB1 Alleles in Patients with Acute Lymphoblastic Leukemia in the Turkish Population: A Case-Control Study

    PubMed Central

    Patıroğlu, Türkan; Akar, H. Haluk

    2016-01-01

    We studied the frequencies of human leukocyte antigen alleles (A, B, and DRB1) in 90 patients with acute lymphoblastic leukemia (ALL) and then compared them with 126 controls in this study. Although the frequencies of the A*03 allele, the DRB1*03 allele, the DRB1*04 allele, the A*02/B*35/DRB1*13 haplotype, and homozygosity of A*02 were higher in patients (p=0.006, p=0.003, p=0.002, p=0.01, and p=0.02, respectively), the frequencies of the A*23, B*13, B*40, and DRB1*13 alleles were lower (p=0.002, p=0.07, p=0.002, and p=0.003, respectively) in patients than controls. The frequencies of the DRB1*04 and DRB1*07 alleles were higher in patients in the high-risk group and standard-risk group, respectively (p=0.009 and p=0.007, respectively). This study indicated that the frequency of the A*03 allele, the DRB1*03 allele, the DRB1*04 allele, the A*02/B*35/DRB1*13 haplotype, and A*02 homozygosity may play a predisposing role in patients with ALL in the Turkish population. The frequency of the DRB1*04 and DRB1*07 alleles may also be associated with high risk and standard risk in patients with ALL, respectively. PMID:27095065

  16. The Frequency of HLA-A, HLA-B, and HLA-DRB1 Alleles in Patients with Acute Lymphoblastic Leukemia in the Turkish Population: A Case-Control Study.

    PubMed

    Patıroğlu, Türkan; Akar, H Haluk

    2016-12-01

    We studied the frequencies of human leukocyte antigen alleles (A, B, and DRB1) in 90 patients with acute lymphoblastic leukemia (ALL) and then compared them with 126 controls in this study. Although the frequencies of the A*03 allele, the DRB1*03 allele, the DRB1*04 allele, the A*02/B*35/DRB1*13 haplotype, and homozygosity of A*02 were higher in patients (p=0.006, p=0.003, p=0.002, p=0.01, and p=0.02, respectively), the frequencies of the A*23, B*13, B*40, and DRB1*13 alleles were lower (p=0.002, p=0.07, p=0.002, and p=0.003, respectively) in patients than controls. The frequencies of the DRB1*04 and DRB1*07 alleles were higher in patients in the high-risk group and standard-risk group, respectively (p=0.009 and p=0.007, respectively). This study indicated that the frequency of the A*03 allele, the DRB1*03 allele, the DRB1*04 allele, the A*02/B*35/DRB1*13 haplotype, and A*02 homozygosity may play a predisposing role in patients with ALL in the Turkish population. The frequency of the DRB1*04 and DRB1*07 alleles may also be associated with high risk and standard risk in patients with ALL, respectively.

  17. 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

  18. Frequencies of cystic fibrosis mutations in the Maine population: high proportion of unknown alleles in individuals of French-Canadian ancestry.

    PubMed

    Bayleran, J K; Yan, H; Hopper, C A; Simpson, E M

    1996-08-01

    Cystic fibrosis (CF) is one of the most common severe autosomal recessive disorders in Caucasian populations. A mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene causes this disorder. Reported here is the first analysis of CF mutations in the Maine population. We have screened 263 CF chromosomes for 16 previously reported mutations. Analysis of DNA from 124 apparently unrelated CF patients and 15 obligate carrier parents (whose partner and affected child were unavailable for study) resulted in the identification of 91% of the CF alleles and complete genotyping of 85% of the patients. The frequencies (%) of these mutations in the Maine population are delta F508 (75% of the chromosomes), G85E (0.76), R117H (0.76), I148T (1.1), 621 + 1G --> T (1.1), 711 + 1G --> T (3.0), A455E (1.1), 1717-1G --> A (1.1), G542X (1.9), G551D (1.9), R560T (0.76), Y1092X (0.38), W1282X (0.38), and N1303K (1.5). The exon 10 mutation, delta I507, and the exon 11 mutation, R553X, were not observed. Surprisingly, whereas only 5% of the alleles remain unidentified in the non-French population, the unidentified proportion in the French population is 19%. CF testing for the Maine population will be further improved as the as yet unidentified CF mutations in this population are characterized.

  19. Allelic frequencies of 3' Ig heavy chain locus enhancer HS1,2-A associated with Ig levels in patients with schizophrenia and healthy control subjects

    PubMed Central

    Frezza, Domenico; Giambra, Vincenzo; Mattioli, Claudia; Piccoli, Katia; Massoud, Renato; Siracusano, Alberto; Giannantonio, Massimo Di; Birshtein, Barbara K.; Rubino, I. Alex

    2009-01-01

    Infectious and autoimmune pathogenic hypotheses of schizophrenia have been proposed, prompting searches for antibodies against viruses or brain structures, and for altered levels of immunoglobulins. Previous experiments have shown that allele frequencies of the Ig heavy chain 3' enhancer HS1,2*A are associated with several autoimmune diseases, suggesting a possible correlation between HS1,2 alleles and Ig production. To test this, we analyzed levels of serum Igs and HS1,2*A genotypes in two independent cohorts, one of 88 schizophrenic inpatients (24 women) and a second of 133 healthy subjects (59 women). Both groups were similar in the frequency of individuals with altered serum concentration of Ig classes and IgG subclasses (schizophrenia panel-80%; controls-68%). With the possible exception of a stabilizing effect of olanzapine, no psychopharmacological drug consumed during the month prior to serum sampling in the schizophrenia group significantly affected Ig levels. In both patient and control cohorts, an increased frequency of the HS1,2 *2A allele corresponded to increased Ig plasma levels, while an increased frequency of the HS1,2*1A allele corresponded to decreased Ig plasma levels. EMSA analysis with nuclear extracts from human B cells showed that the transcription factor SP1 bound to the polymorphic region of both HS1,2*1A and HS1,2*2A while NF-κB bound only to the HS1,2*2A. We predict that differences in transcription factor binding sites in the two allelic variants of the 3' IgH enhancer HS1,2 may provide a mechanism by which differences in Ig expression are affected. PMID:19309558

  20. Frequency of streptococcal upper respiratory tract infections and HLA-Cw*06 allele in 70 patients with guttate psoriasis from northern Poland

    PubMed Central

    Szczerkowska-Dobosz, Aneta; Rębała, Krzysztof; Wysocka, Joanna; Roszkiewicz, Jadwiga; Szczerkowska, Zofia; Placek, Waldemar

    2015-01-01

    Introduction The association of guttate psoriasis with a streptococcal throat infection and HLA-Cw*06 allele is well established in different populations. Nevertheless, only few studies on this form of disease have been performed in the Polish population. Aim To analyze the frequencies of streptococcal-induced guttate psoriasis and HLA-Cw*06 allele in 70 patients with guttate psoriasis originating from northern Poland. Material and methods Seventy patients with guttate psoriasis and 24 healthy volunteers were enrolled into the study. Both groups were sex- and age-matched. The evidence of streptococcal infection was based on the positive throat swabs and/or elevated ASO titers. The modified method, including PCR-SSP and PCR-RFLP, was applied to HLA-Cw*06 genotyping. Results HLA-Cw*06 allele was confirmed in 49 (70%) out of 70 patients, which is significantly higher than in the control population (30%) (p = 0.001). Evidence for streptococcal infection was found in 34 (48.5%) subjects with psoriasis. Twenty-seven of them (79%) carried HLA-Cw*06 allele. In 36 individuals in whom no evidence of streptococcal infection was found, 14 (39%) did not carry HLA-Cw*06 allele. Conclusions Our data confirm that HLA-Cw*06 is a major, but not imperative, genetic determinant for guttate psoriasis. PMID:26755910

  1. Simultaneous multi-frequency imaging observations of solar microwave bursts

    NASA Technical Reports Server (NTRS)

    Kundu, M. R.; White, S. M.; Schmahl, E. J.

    1989-01-01

    The results of simultaneous two-frequency imaging observations of solar microwave bursts with the Very Large Array are reviewed. Simultaneous 2 and 6 cm observations have been made of bursts which are optically thin at both frequencies, or optically thick at the lower frequency. In the latter case, the source structure may differ at the two frequencies, but the two sources usually seem to be related. However, this is not always true of simultaneous 6 and 20 cm observations. The results have implications for the analysis of nonimaging radio data of solar and stellar flares.

  2. Allelic and genotypic frequencies in polymorphic Booroola fecundity gene and their association with multiple birth and postnatal growth in Chhotanagpuri sheep

    PubMed Central

    Oraon, Thanesh; Singh, D. K.; Ghosh, Mayukh; Kullu, S. S.; Kumar, Rajesh; Singh, L. B.

    2016-01-01

    Aim: Chhotanagpuri breed of sheep reared for mutton in Jharkhand, India, having problem of low litter size and body weight. The response of genetic improvement for traits with low heritability through traditional selection method is time-consuming. Therefore, marker-assisted selection based on a polymorphism study of suitable candidate gene can response quickly. Thus, this study was aimed at identification of different allelic and genotypic frequencies of Booroola fecundity (FecB) gene and its association with multiple birth and postnatal growth in Chhotanagpuri sheep. Materials and Methods: DNA isolation and gene-specific amplification of FecB gene was performed from blood samples of from 92 Chhotanagpuri lambs maintained under similar feeding and management conditions. Custom nucleotide sequencing and single-strand conformational polymorphism analysis were performed to identify different genotypes with respect to the target gene. Statistical analysis was performed for determination of allelic and genotypic frequencies of FecB gene polymorphisms and its association with multiple birth and postnatal growth of lambs from birth to 52 weeks age. Results: “AA,” “AB,” and “BB” genotypes were found at locus-1 as it is polymorphic for FecB gene while locus-2 was found to be monomorphic for FecB gene. Higher frequency of “A” allele at locus-1 was found in single born lambs, whereas “B” allele was predominant among multiple born lambs. The lambs having “BB” genotype weighed significantly (p≤0.01) heavier than those of “AB” and “AA” genotype at 52 weeks of age. Conclusion: “BB” genotype has emerged as favored genotype for multiple births and better growth indicator. Therefore, homozygous lambs for “B” allele should be selected and utilized in breeding program for better growth rate. PMID:27956784

  3. HLA class II variation in the Gila River Indian Community of Arizona: alleles, haplotypes, and a high frequency epitope at the HLA-DR locus.

    PubMed

    Williams, R C; McAuley, J E

    1992-01-01

    A genetic distribution for the HLA class II loci is described for 349 "full-blooded" Pima and Tohono O'odham Indians (Pimans) in the Gila River Indian Community. A high frequency epitope in the *DRw52 family was defined by reactions with 31 alloantisera, which we have designated *DR3X6. It segregates as a codominant allele at HLA-DR with alleles *DR2, *DR4, and *DRw8, and has the highest frequency yet reported for an HLA-DR specificity, 0.735. It forms a common haplotype with *DRw52 and *DQw3 that is a valuable marker for genetic admixture and anthropological studies. Phenotype and allele frequencies, and haplotype frequencies for two and three loci, are presented. Variation at these loci is highly restricted, the mean heterozygosity for HLA-DR and HLA-DQ being 0.361. The Pimans represent a contemporary model for the Paleo-Indians who first entered North America 20,000 to 40,000 years ago.

  4. THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites

    PubMed Central

    Chang, Hsiao-Han; Worby, Colin J.; Yeka, Adoke; Nankabirwa, Joaniter; Kamya, Moses R.; Staedke, Sarah G.; Hubbart, Christina; Amato, Roberto; Kwiatkowski, Dominic P.

    2017-01-01

    As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring malaria epidemiology are urgent priorities. P. falciparum population genetic approaches offer promising tools for understanding transmission and spread of the disease, but a high prevalence of multi-clone or polygenomic infections can render estimation of even the most basic parameters, such as allele frequencies, challenging. A previous method, COIL, was developed to estimate complexity of infection (COI) from single nucleotide polymorphism (SNP) data, but relies on monogenomic infections to estimate allele frequencies or requires external allele frequency data which may not available. Estimates limited to monogenomic infections may not be representative, however, and when the average COI is high, they can be difficult or impossible to obtain. Therefore, we developed THE REAL McCOIL, Turning HEterozygous SNP data into Robust Estimates of ALelle frequency, via Markov chain Monte Carlo, and Complexity Of Infection using Likelihood, to incorporate polygenomic samples and simultaneously estimate allele frequency and COI. This approach was tested via simulations then applied to SNP data from cross-sectional surveys performed in three Ugandan sites with varying malaria transmission. We show that THE REAL McCOIL consistently outperforms COIL on simulated data, particularly when most infections are polygenomic. Using field data we show that, unlike with COIL, we can distinguish epidemiologically relevant differences in COI between and within these sites. Surprisingly, for example, we estimated high average COI in a peri-urban subregion with lower transmission intensity, suggesting that many of these cases were imported from surrounding regions with higher transmission intensity. THE REAL McCOIL therefore provides a robust tool for understanding the molecular epidemiology of malaria across transmission settings. PMID

  5. Pomology observations, morphometric analysis, ultrastructural study and allelic profiles of "olivastra Seggianese" endocarps from ancient olive trees (Olea europaea L.).

    PubMed

    Milanesi, Claudio; Sorbi, Andrea; Paolucci, Elisa; Antonucci, Francesca; Menesatti, Paolo; Costa, Corrado; Pallottino, Federico; Vignani, Rita; Cimato, Antonio; Ciacci, Andrea; Cresti, Mauro

    2011-01-01

    Preliminary studies of historical sources and remote sensing were used to identify ancient olive trees near archaeological sites and heritage buildings in the Orcia Valley (Siena, Italy). Distinctive characters were assessed by traditional pomological observation. Trees with similar characters were selected on the basis of the features of endocarps, the only structure that survives aerobic deterioration and conserves useful botanical information for centuries. Non-invasive morphometric analysis of endocarp size and shape established morphological variations in individuals of different populations. Plastid organization in the endocarp and location of DNA in the endocarp tegument were detected by morphological and ultrastructural observations using light and electron microscopy. Cytoplasmic markers with high polymorphism were used to test similarity of endocarp and leaf DNA within individuals and to confirm low variability and minimal divergence between individuals. The ancient trees studied showed the same allelic profiles and therefore belonged to a distinct cultivar. The traditional pomological descriptions of the trees, leaves and fruits, morphometric analysis of size, and shape elliptic Fourier analysis of endocarp outline, ultrastructural observations and allelic profiles of endocarp tegument delineated the general species-specific qualities of the cultivar "olivastra Seggianese" of the Orcia Valley.

  6. 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.

  7. Frequency distribution of Q188R, N314D, Duarte 1, and Duarte 2 GALT variant alleles in an Indian galactosemia population.

    PubMed

    Singh, Ramandeep; Thapa, Babu R; Kaur, Gurjit; Prasad, Rajendra

    2012-12-01

    Classical galactosemia is a genetic disorder caused by mutations in the galactose-1-phosphate uridyltransferase (GALT) gene. The Q188R and N314D mutations are the most frequently cited GALT gene mutations. N314D is further associated with two variants, Duarte 1 and Duarte 2. Nevertheless, no reports are available on the clinical and molecular spectrum of galactosemia from the Indian population. The present study was designed to establish the frequency of these two most common mutations and their variants in Indian galactosemia patients so as to determine a single most common mutation/polymorphism for establishing the DNA-based diagnosis of galactosemia. Three alleles were found to be present at a frequency of 0.036 (Q188R), 0.40 (N314D), and 0.39 (D2); no D1 alleles were found. A significantly higher frequency of the Duarte 2 allele in our population suggests the presence of a milder form of galactosemia, which can be well managed by early diagnosis and dietary management.

  8. Estimation of the 6-digit level allele and haplotype frequencies of HLA-A, -B, and -C in Koreans using ambiguity-solving DNA typing.

    PubMed

    Jun, J-H; Hwang, K; Kim, S-K; Oh, H-B; Cho, M-C; Lee, K-J

    2014-09-01

    Because Korean society is fast becoming multi-ethnic, the determination of ambiguous human leukocyte antigen (HLA) types using HLA allele frequencies is becoming less applicable. In this study, we focused on the development of new technical methods to directly resolve the ambiguities arising from HLA genotyping. One hundred and fifty unrelated healthy Korean adults were included in this study. All alleles from each HLA locus were first divided into 2-4 groups, with each group amplified in a single PCR tube (multi-group-specific amplification, MGSA). To resolve phase ambiguities, some allele groups were also amplified separately in small group-specific amplification (SGSA) tubes. In order to then resolve incomplete sequence ambiguities, primers for MGSA and SGSA were initially designed to cover additional exons. If needed, a heterozygous ambiguity resolving primer (HARP) or sequence specific primer (SSP) was also used. When MGSA and SGSA methods were applied, the rate of phase ambiguity was greatly reduced to an average of 6% (1.3% in HLA-A, 15.7% in -B, and 2.0% in -C). Additional HARP and SSP methods could resolve all the phase ambiguities. Using our proposed method, we also detected three alleles that have not been previously reported in Korea, C*04:82, C*07:18, and C*08:22, and report 6-digit level HLA allele and haplotype frequencies among Koreans. In conclusion, the use of MGSA/SGSA for the initial amplification step is a cost-effective method facilitating timely and accurate reporting, given the continuing increase in the ethnic diversity of the Korean population. The MGSA described here can be applicable to various populations and thus could be shared by the majority of HLA typing laboratories. However, efforts to solve HLA ambiguity should continue, because SGSA, HARPs and SSPs would be specific to a particular population.

  9. 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...

  10. 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

  11. 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.

  12. Somatic homologous recombination in planta: the recombination frequency is dependent on the allelic state of recombining sequences and may be influenced by genomic position effects.

    PubMed

    Swoboda, P; Hohn, B; Gal, S

    1993-02-01

    We have previously described a non-selective method for scoring somatic recombination in the genome of whole plants. The recombination substrate consists of a defective partial dimer of Cauliflower Mosaic Virus (CaMV) sequences, which can code for production of viable virus only upon homologous recombination; this leads to disease symptoms on leaves. Brassica napus plants (rapeseed) harbouring the recombination substrate as a transgene were used to examine the time in plant development at which recombination takes place. The analysis of three transgene loci revealed recombination frequencies specific for each locus. Recombination frequencies were increased if more than one transgene locus was present per genome, either in allelic (homozygosity of the transgene locus) or in non-allelic positions. In both cases, the overall recombination frequency was found to be elevated to approximately the sum of the frequencies for the individual transgene loci or slightly higher, suggesting that the respective transgene loci behave largely independently of each other. For all plants tested (single locus, two or multiple loci) maximal recombination frequencies were of the order of 10(-6) events per cell division.

  13. Neonatal screening for hereditary fructose intolerance: frequency of the most common mutant aldolase B allele (A149P) in the British population.

    PubMed

    James, C L; Rellos, P; Ali, M; Heeley, A F; Cox, T M

    1996-10-01

    Hereditary fructose intolerance (HFI) causes severe and sometimes fatal metabolic disturbances in infants and children but responds to dietary treatment. To determine the practicability of screening newborn infants for HFI, we have investigated the frequency of the most common and widespread mutant allele of aldolase B, A149P, in the neonatal population. The polymerase chain reaction was used to amplify aldolase B exon 5 genomic sequences in DNA present in dried blood specimens preserved on Guthrie cards. The A149P mutation was identified by discriminatory hybridisation to allele specific oligonucleotides and confirmed independently by digestion with the restriction endonuclease BsaHI. Twenty-seven A149P heterozygotes were identified by the molecular analysis of aldolase B genes in blood samples obtained from a random cohort of 2050 subjects born in 1994 and 1995, 1.32 +/- 0.49% (95% confidence level). Although no A149P homozygotes were identified, the data allow the frequency of 1 in 23,000 homozygotes for this allele to be predicted. Our findings have implications for establishing an interventional mass screening programme to identify newborn infants with HFI in the UK.

  14. Frequency Analysis of Photographic Observations of Pulsating Stars

    NASA Astrophysics Data System (ADS)

    Bezdenezhnyi, V. P.

    2001-12-01

    The Fourier analysis are performed for photoelectric and photographic B-observations (Goranskij and Shugarov, 1979) of RR Lyrae star RW Ari. Besides the main frequency f0 and four its first harmonics two more frequencies are found: f1=f0/3 and f2=0.711f0 c/d. It permits to identify frequencies: f0 as fs, introduced by us earlier (Bezdenezhnyi, 1997b) for RR Lyrae star T Sex, and f2 - as f1H. Such analysis of photographic author's observations of RR Lyrae star BK Dra is performed too. It is shown that BK Dra is a multiperiodic variable star. Its frequencies identifications are carried out and given. Three data sets of Cepheid V477 Oph: visual author's (Bezdenezhnyi and Mandel, 1977), photographic Mandel's (1970) observations and (O-C) - residuals (Hacke, 1988) show that V477 Oph apparently can be referred to bimodal Cepheids.

  15. 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.

  16. Association between a high-expressing interferon-gamma allele and a lower frequency of kidney angiomyolipomas in TSC2 patients.

    PubMed

    Dabora, Sandra L; Roberts, Penelope; Nieto, Andres; Perez, Ron; Jozwiak, Sergiusz; Franz, David; Bissler, John; Thiele, Elizabeth A; Sims, Katherine; Kwiatkowski, David J

    2002-10-01

    Tuberous sclerosis complex (TSC) is a familial hamartoma syndrome in which renal involvement is common and, at times, life threatening. We have investigated the potential effect of a non-TSC gene on renal disease in a cohort of 172 TSC patients with TSC2 mutations. Patients were genotyped for an interferon-gamma (IFN-gamma) microsatellite polymorphism, within intron 1, for which one common allele (allele 2, with 12 CA repeats) has been shown to have a higher expression of IFN-gamma. A chi(2) analysis was used to examine the association between IFN-gamma allele 2 and the development of kidney angiomyolipomas (KAMLs) in this TSC2 cohort. Because of the age-dependent development of KAMLs in TSC, we initially focused on the 127 patients who were >5 years old. Additional subgroup analyses were done to investigate the influence of age and gender. The transmission/disequilibrium test (TDT) was also performed in a subset of this cohort (46 probands) for whom parent and/or sibling samples were available for analysis. Both chi(2) analysis and TDT suggested an association between IFN-gamma allele 2 and the absence of KAMLs in patients who have known TSC2 mutations. Among the 127 patients who were >5 years old, KAMLs were present in 95 (75%) and were absent in 32 (25%). In the group with KAML present, the frequency of IFN-gamma allele 2 was 56%; in the group with KAML absent, the frequency of IFN-gamma allele 2 was significantly higher, at 78% (P=.02, by chi(2) analysis). The family-based TDT analysis gave similar results, with a TDT statistic (TDT chi2=5.45) corresponding to a P value of.02. Subgroup analyses show that both age and gender may influence the impact of this association. Although these results should be replicated in other populations with TSC, the present study suggests that modifier genes play a role in the variable expression of TSC and also suggests a potential therapy for KAMLs in patients with TSC.

  17. Polymorphisms and allele frequencies of glutathione S-transferases A1 and P1 genes in the Polish population.

    PubMed

    Skrzypczak-Zielinska, M; Zakerska-Banaszak, O; Tamowicz, B; Sobieraj, I; Drweska-Matelska, N; Szalata, M; Slomski, R; Mikstacki, A

    2015-03-31

    Glutathione S-transferases (GST) A1 and P1 are crucial enzymes involved in the biotransformation of drugs, carcinogens, and toxins, and their activity may influence drug response, susceptibility to diseases, and carcinogenesis. The genes encoding these enzymes, GSTA1 and GSTP1, have been examined in many studies because of their genetic variability, which may affect enzymatic activity. The goal of this study was to determine the distribution of the alleles GSTA1*A/*B and GSTP1*A, *B, and *C in the Polish population. A total of 160 subjects from the Polish population were genotyped for 2 polymorphisms (I105V and A114V) in the GSTP1 gene using pyrosequencing. The promoter region of the GSTA1 gene was screened using sequencing. The detected variants were subjected to haplotype analysis. We found that the distribution of the alleles GSTA1*A/*B and GSTP1*A, *B, and *C in the Polish population correspond to the results of studies in Caucasians. Furthermore, we identified additional single nucleotide polymorphisms, excluding 3 well-known changes (G-52A, C-69T, T-567G), which are linked to alleles GSTA1*A/*B, that affect enzyme activity. A total of 4 haplotypes were identified in 160 Polish individuals.

  18. 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

  19. Short communication: The combined use of linkage disequilibrium-based haploblocks and allele frequency-based haplotype selection methods enhances genomic evaluation accuracy in dairy cattle.

    PubMed

    Jónás, Dávid; Ducrocq, Vincent; Croiseau, Pascal

    2017-04-01

    The construction and use of haploblocks [adjacent single nucleotide polymorphisms (SNP) in strong linkage disequilibrium] for genomic evaluation is advantageous, because the number of effects to be estimated can be reduced without discarding relevant genomic information. Furthermore, haplotypes (the combination of 2 or more SNP) can increase the probability of capturing the quantitative trait loci effect compared with individual SNP markers. With regards to haplotypes, the allele frequency parameter is also of interest, because as a selection criterion, it allows the number of rare alleles to be reduced, and the effects of those alleles are usually difficult to estimate. We have proposed a simple pipeline that simultaneously incorporates linkage disequilibrium and allele frequency information in genomic evaluation, and here we present the first results obtained with this procedure. We used a population of 2,235 progeny-tested bulls from the Montbéliarde breed for the tests. Phenotype data were available in the form of daughter yield deviations on 5 production traits, and genotype data were available from the 50K SNP chip. We conducted a classical validation study by splitting the population into training (80% oldest animals) and validation (20% youngest animals) sets to emulate a real-life scenario in which the selection candidates had no available phenotype data. We measured all reported parameters for the validation set. Our results proved that the proposed method was indeed advantageous, and that the accuracy of genomic evaluation could be improved. Compared with results from a genomic BLUP analysis, correlations between daughter yield deviations (a proxy for true) and genomic estimated breeding values increased by an average of 2.7 percentage points for the 5 traits. Inflation of the genomic evaluation of the selection candidates was also significantly reduced. The proposed method outperformed the other SNP and haplotype-based tests we had evaluated in a

  20. Planetary and exoplanetary low frequency radio observations from the Moon

    NASA Astrophysics Data System (ADS)

    Zarka, P.; Bougeret, J.-L.; Briand, C.; Cecconi, B.; Falcke, H.; Girard, J.; Grießmeier, J.-M.; Hess, S.; Klein-Wolt, M.; Konovalenko, A.; Lamy, L.; Mimoun, D.; Aminaei, A.

    2012-12-01

    We analyze the planetary and exoplanetary science that can be carried out with precursor as well as future low frequency radio instruments on the Moon, assessing the limiting noise sources, comparing them to the average and peak spectra of all planetary radio components as they will be seen from the Lunar surface or orbit. We identify which objectives will be accessible with each class of instrument, and discuss the interest of these observations compared to observations by planetary probes and to ground-based observations by large low-frequency radio arrays. The interest of goniopolarimetry is emphasized for pathfinder missions.

  1. 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.

  2. 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

  3. 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.

  4. Contemporary evolution of sea urchin gamete-recognition proteins: experimental evidence of density-dependent gamete performance predicts shifts in allele frequencies over time.

    PubMed

    Levitan, Don R

    2012-06-01

    Species whose reproductive strategies evolved at one density regime might be poorly adapted to other regimes. Field and laboratory experiments on the sea urchin Strongylocentrotus franciscanus examined the influences of the two most common sperm-bindin alleles, which differ at two amino acid sites, on fertilization success. In the field experiment, the arginine/glycine (RG) genotype performed best at low densities and the glycine/arginine (GR) genotype at high densities. In the laboratory experiment, the RG genotype had a higher affinity with available eggs, whereas the GR genotype was less likely to induce polyspermy. These sea urchins can reach 200 years of age. The RG allele dominates in larger/old sea urchins, whereas smaller/younger sea urchins have near-equal RG and GR allele frequencies. A latitudinal cline in RG and GR genotypes is consistent with longer survival of sea urchins in the north and with predominance of RG genotypes in older individuals. The largest/oldest sea urchins were likely conceived at low densities, before sea-urchin predators, such as sea otters, were overharvested and sea-urchin densities exploded off the west coast of North America. Contemporary evolution of gamete-recognition proteins might allow species to adapt to shifts in abundances and reduces the risk of reproductive failure in altered populations.

  5. The frequency of different CGG-repeat alleles in the FMR-1 gene in the general population and special populations

    SciTech Connect

    Holden, J.J.A. |; Chalifoux, M.; Wing, M.

    1994-09-01

    The fragile X (FRAXA) syndrome is the most common inherited form of developmental disability and was the first genetic disorder in which the mechanism of mutation is triplet repeat expansion. The normal fragile X mental retardation-1 gene has 6-52 copies of the CGG-repeat; affected males have extensive amplification, coupled with methylation and gene inactivation; and carriers have between about 55 and 200 copies. There is some overlap in the 45-55 repeat range, with some alleles showing stable and othres unstable transmission. There have been several estimates of the incidence of the FRAXA syndrome, based on testing of special populations using chromosome analysis and the range is 1/750-1/2000. Because of the high burden associated with this syndrome, and in the face of discussions about population screening, it is important to know the actual incidence of mutations in this gene, as well as the distribution of unstable repeats above 45 copes. We have initiated a general population screening to examine 50,000 newborn samples using PCR, and have developed a rapid, inexpensive and reliable method for amplifying the CGG-repeat from Guthrie spots. In the first 1600 samples examined, we found 15 alleles with greater than 45 CGG-repeats, with the highest being 61 repeats.

  6. 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.

  7. Mutant allele frequencies among domestic cats in some eastern areas of Canada: regional homogeneity of factors in Canadian Atlantic Provinces and the French colony of Saint Pierre.

    PubMed

    Todd, N B; Todd, L M

    1976-01-01

    Surveys to determine mutant allele frequencies in domestic cats of the Canadian Atlantic Provinces (Halifax, Nova Scotia; Fredericton, New Brunswick; Charlottetown, Prince Edward Island; St. John's Newfoundland) and the French colony of Saint Pierre, Saint Pierre et Miquelon, reveal a general regional homogeneity for most factors. Despite diverse historical patterns of settlement, a strong common component of origin is indicated. This is tentatively identified as late 18th and early 19th century British. One mutant, polydactyly, which is of New England origin appears to have been distributed largely by loyalist refugees from New England at the time of the American Rebellion. No elements of a specific Acadian (French) character have yet been identified. Siamese cats have been "introduced" to the region in recent years and are now so abundant that they will undoubtedly cause a significant change in some mutant allele frequencies over the next few decades. Interregional exchanges of cats no doubt are contributing to homogenizing the populations of the area, but the practice of sterilization of pets offsets this to some degree.

  8. 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.

  9. The Adaptive Change of HLA-DRB1 Allele Frequencies Caused by Natural Selection in a Mongolian Population That Migrated to the South of China.

    PubMed

    Sun, Hao; Yang, Zhaoqing; Lin, Keqin; Liu, Shuyuan; Huang, Kai; Wang, Xiuyun; Chu, Jiayou; Huang, Xiaoqin

    2015-01-01

    Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA) alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT) was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another five ethnic groups. Meanwhile, 10 autosomal short tandem repeats (STRs) were genotyped to assess the influence of genetic background on HLA-DRB1 frequencies. The frequencies of certain alleles changed significantly in the Mongolian population that migrated to Yunnan. For example, DRB1*12:02:01 increased from 6.1% to 35.4%. STR analysis excluded the possibility of a recent bottleneck and indicated that 50% of the genetic consistency between northern and southern Mongolians; Tajima's D value for HLA-DRB1 exon2 and dN/dS analysis showed that the HLA-DRB1 genes in both Mongolian populations were under balancing selection. However, the sites under natural selection changed. We proposed that the dramatically change of HLA frequencies in southern Mongolian was caused by a combination of inter-population gene flow and natural selection. Certain diseases specific to the south of China, such as malaria, may be the driving force behind the enhanced DRB1*12:02:01 frequency.

  10. The Adaptive Change of HLA-DRB1 Allele Frequencies Caused by Natural Selection in a Mongolian Population That Migrated to the South of China

    PubMed Central

    Sun, Hao; Yang, Zhaoqing; Lin, Keqin; Liu, Shuyuan; Huang, Kai; Wang, Xiuyun; Chu, Jiayou; Huang, Xiaoqin

    2015-01-01

    Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA) alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT) was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another five ethnic groups. Meanwhile, 10 autosomal short tandem repeats (STRs) were genotyped to assess the influence of genetic background on HLA-DRB1 frequencies. The frequencies of certain alleles changed significantly in the Mongolian population that migrated to Yunnan. For example, DRB1*12:02:01 increased from 6.1% to 35.4%. STR analysis excluded the possibility of a recent bottleneck and indicated that 50% of the genetic consistency between northern and southern Mongolians; Tajima's D value for HLA-DRB1 exon2 and dN/dS analysis showed that the HLA-DRB1 genes in both Mongolian populations were under balancing selection. However, the sites under natural selection changed. We proposed that the dramatically change of HLA frequencies in southern Mongolian was caused by a combination of inter-population gene flow and natural selection. Certain diseases specific to the south of China, such as malaria, may be the driving force behind the enhanced DRB1*12:02:01 frequency. PMID:26230582

  11. 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.

  12. Observations of Fast Radio Bursts and perspectives at low frequencies

    NASA Astrophysics Data System (ADS)

    Zarka, P.; Mottez, F.

    2016-12-01

    We briefly summarize the characteristics of the elusive Fast Radio Bursts from existing observations. Then we emphasize the interest of low-frequency observations, e.g. with NenuFAR. In order to define the best observing parameters and detection scheme, we have built a simulation program of FRB at low-frequencies, that proceeds in 2 steps: (i) FRB generation and dilution in a dynamic spectrum with given characteristics, and (ii) definition of the FRB spectrum, and detection on the galactic radio background by means of parametric dedispersion. We carry on a preliminary simulation study, that allows us to draw first conclusions, among which the possibility to detect Lorimer-like FRB with NenuFAR.

  13. Comparison of HLA allelic imputation programs.

    PubMed

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

    2017-01-01

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

  14. Comparison of HLA allelic imputation programs

    PubMed Central

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

    2017-01-01

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

  15. 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

  16. Novel rapid genotyping assays for neuronal ceroid lipofuscinosis in Border Collie dogs and high frequency of the mutant allele in Japan.

    PubMed

    Mizukami, Keijiro; Chang, Hye-Sook; Yabuki, Akira; Kawamichi, Takuji; Kawahara, Natsuko; Hayashi, Daisuke; Hossain, Mohammad A; Rahman, Mohammad M; Uddin, Mohammad M; Yamato, Osamu

    2011-11-01

    Neuronal ceroid lipofuscinosis (NCL) constitutes a group of recessively inherited lysosomal storage diseases that primarily affect neuronal cells. Such diseases share certain clinical and pathologic features in human beings and animals. Neuronal ceroid lipofuscinosis in Border Collie dogs was first detected in Australia in the 1980s, and the pathogenic mutation was shown to be a nonsense mutation (c.619C>T) in exon 4 in canine CLN5 gene. In the present study, novel rapid genotyping assays including polymerase chain reaction (PCR)-restriction fragment length polymorphism, PCR primer-induced restriction analysis, mutagenically separated PCR, and real-time PCR with TaqMan minor groove binder probes, were developed. The utility of microchip electrophoresis was also evaluated. Furthermore, a genotyping survey was carried out in a population of Border Collies in Japan using these assays to determine the current allele frequency in Japan, providing information to control and prevent this disease in the next stage. All assays developed in the current study are available to discriminate these genotypes, and microchip electrophoresis showed a timesaving advantage over agarose gel electrophoresis. Of all assays, real-time PCR was the most suitable for large-scale examination because of its high throughput. The genotyping survey demonstrated that the carrier frequency was 8.1%. This finding suggested that the mutant allele frequency of NCL in Border Collies is high enough in Japan that measures to control and prevent the disease would be warranted. The genotyping assays developed in the present study could contribute to the prevention of NCL in Border Collies.

  17. 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.

  18. 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.

  19. Frequency of the CCR5 delta 32 mutant allele in HIV-1-positive patients, female sex workers, and a normal population in Taiwan.

    PubMed

    Li, C; Yan, Y P; Shieh, B; Lee, C M; Lin, R Y; Chen, Y M

    1997-12-01

    A specific 32-nucleotide deletion mutant of the CCR5 gene (Accr5), the coreceptor gene for human immunodeficiency virus type 1 (HIV-1), can effectively suppress the transmission and pathogenesis of the virus. Individuals homozygous for the delta ccr5 allele resist primary macrophage-tropic HIV-1 infection, despite multiple high-risk sexual exposures. This gene deletion is relatively common among Caucasians but uncommon among Africans, Asians, and South Americans. We used polymerase chain reaction (PCR) technology to determine the frequency of the delta ccr5 allele in a Taiwanese population with diverse health status and social backgrounds. Subjects included 24 HIV-1-infected persons in the northern and southern parts of Taiwan; 131 HIV-1 high-risk, licensed female sex workers in the northern part of the island (21% of whom were aborigines); and 187 unrelated, healthy, HIV-1-negative individuals in southern Taiwan. PCR with primers encompassing the entire CCR5 gene was used to explore possible deletions at regions other than the 32-nucleotide area in the female sex workers. No ccr5 deletions were detected, indicating that they are rare or absent in the Taiwanese population. This finding implies that delta ccr5 is not likely to be part of the defense against the spread of HIV-1-infection in Taiwanese.

  20. 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.

  1. Stable Allele Frequency Distribution of the Plasmodium falciparum clag Genes Encoding Components of the High Molecular Weight Rhoptry Protein Complex

    PubMed Central

    Alexandre, Jean Semé Fils; Xangsayarath, Phonepadith; Kaewthamasorn, Morakot; Yahata, Kazuhide; Sattabongkot, Jetsumon; Udomsangpetch, Rachanee; Kaneko, Osamu

    2012-01-01

    Plasmodium falciparum Clag protein is a candidate component of the plasmodial surface anion channel located on the parasite-infected erythrocyte. This protein is encoded by 5 separated clag genes and forms a RhopH complex with the other components. Previously, a signature of positive diversifying selection was detected on the hypervariable region of clag2 and clag8 by population-based analyses using P. falciparum originating from Thailand in 1988–1989. In this study, we obtained the sequence of this region of 3 clag genes (clag2, clag8, and clag9) in 2005 and evaluated the changes over time in the frequency distribution of the polymorphism of these gene products by comparison with the sequences obtained in 1988–1989. We found no difference in the frequency distribution of 18 putatively neutral loci between the 2 groups, evidence that the background of the parasite population structure has remained stable over 14 years. Although the frequency distribution of most of the polymorphic sites in the hypervariable region of Clag2, Clag8, and Clag9 was stable over 14 years, we found that a proportion of the major Clag2 group and one amino acid position of Clag8 changed significantly. This may be a response to a certain type of pressure. PMID:23264726

  2. Stable Allele Frequency Distribution of the Plasmodium falciparum clag Genes Encoding Components of the High Molecular Weight Rhoptry Protein Complex.

    PubMed

    Alexandre, Jean Semé Fils; Xangsayarath, Phonepadith; Kaewthamasorn, Morakot; Yahata, Kazuhide; Sattabongkot, Jetsumon; Udomsangpetch, Rachanee; Kaneko, Osamu

    2012-09-01

    Plasmodium falciparum Clag protein is a candidate component of the plasmodial surface anion channel located on the parasite-infected erythrocyte. This protein is encoded by 5 separated clag genes and forms a RhopH complex with the other components. Previously, a signature of positive diversifying selection was detected on the hypervariable region of clag2 and clag8 by population-based analyses using P. falciparum originating from Thailand in 1988-1989. In this study, we obtained the sequence of this region of 3 clag genes (clag2, clag8, and clag9) in 2005 and evaluated the changes over time in the frequency distribution of the polymorphism of these gene products by comparison with the sequences obtained in 1988-1989. We found no difference in the frequency distribution of 18 putatively neutral loci between the 2 groups, evidence that the background of the parasite population structure has remained stable over 14 years. Although the frequency distribution of most of the polymorphic sites in the hypervariable region of Clag2, Clag8, and Clag9 was stable over 14 years, we found that a proportion of the major Clag2 group and one amino acid position of Clag8 changed significantly. This may be a response to a certain type of pressure.

  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 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

  5. 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.

  6. 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

  7. 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

  8. Allele-dependent recombination frequency: homology requirement in meiotic recombination at the hot spot in the mouse major histocompatibility complex.

    PubMed

    Yoshino, M; Sagai, T; Lindahl, K F; Toyoda, Y; Moriwaki, K; Shiroishi, T

    1995-05-20

    Meiotic recombination break joints in the mouse major histocompatibility complex (MHC) are clustered within short segments known as hot spots. We systematically investigated the requirement for sequence homology between two chromosomes for recombination activity at the hot spot next to the Lmp2 gene. The results indicated that a high rate of recombination required a high degree of similarity of overall genome structure at the hot spot. In particular, the same copy number of repetitive sequences within the hot spot was essential for a high frequency of recombination, suggesting that recombination in mouse meiosis is more sensitive to heterozygous deletion or insertion of DNA than to mismatches of single-base substitutions.

  9. 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.

  10. 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.

  11. Observations and modeling of dynamically triggered high frequency burst events

    NASA Astrophysics Data System (ADS)

    Fischer, Adam David

    2008-10-01

    A series of high-frequency (>20Hz) bursts of energy are observed on strong motion records during the 1999 Chi-Chi, Taiwan Earthquake Mw7.6. We hypothesized that these bursts originated near the individual stations as small, shallow events that were dynamically triggered by the P- and S-waves generated by the Chi-Chi mainshock. These bursts were originally interpreted as a mainshock source signal by Chen et al., [2006] but our observations of events on strong motion records recorded at stations up to 170 km from the mainshock epicenter is consistent with the local triggering hypothesis. If the bursts originated on the Chi-Chi fault plane, as hypothesized by Chen et al. [2006] based on their analysis of recordings within 20Km from the Chelungpu fault, then they should not be observable at this distance assuming any reasonable value of crustal attenuation. The bursts on all strong motion stations in the Taiwan Central Weather Bureau network (TWCB) were identified using a numerical algorithm approach. This data set was analyzed in the context of local dynamic triggering which resulted in a stress threshold for triggering in the range 0.03 to 0.05 MPa for S-wave triggering and 0.0013 to 0.0033 MPa for P-wave triggering, consistent with prior observations of surface wave triggering. In an attempt to better characterize the nature of high frequency bursts, similar analysis of strong motion records was performed on the records of the 2004 Parkfield, CA earthquake (Mw6) at the USGS UPSAR array. The average array spacing was relatively small compared to the instruments in Taiwan so that further constraint of the location of bursts was possible. Bursts were found to be incoherent even for stations spaced 40m apart, suggesting that they occur in a region approximately 20m from the stations. The triggering threshold was found to be ~0.02Mpa, consistent with the observations from Taiwan. To test the possibility of nucleating unstable slip events in the very shallow crust we

  12. 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.

  13. Handling the satellite inter-frequency biases in triple-frequency observations

    NASA Astrophysics Data System (ADS)

    Zhao, Lewen; Ye, Shirong; Song, Jia

    2017-04-01

    The new generation of GNSS satellites, including BDS, Galileo, modernized GPS, and GLONASS, transmit navigation sdata at more frequencies. Multi-frequency signals open new prospects for precise positioning, but satellite code and phase inter-frequency biases (IFB) induced by the third frequency need to be handled. Satellite code IFB can be corrected using products estimated by different strategies, the theoretical and numerical compatibility of these methods need to be proved. Furthermore, a new type of phase IFB, which changes with the relative sun-spacecraft-earth geometry, has been observed. It is necessary to investigate the cause and possible impacts of phase Time-variant IFB (TIFB). Therefore, we present systematic analysis to illustrate the relevancy between satellite clocks and phase TIFB, and compare the handling strategies of the code and phase IFB in triple-frequency positioning. First, the un-differenced L1/L2 satellite clock corrections considering the hardware delays are derived. And IFB induced by the dual-frequency satellite clocks to triple-frequency PPP model is detailed. The analysis shows that estimated satellite clocks actually contain the time-variant phase hardware delays, which can be compensated in L1/L2 ionosphere-free combinations. However, the time-variant hardware delays will lead to TIFB if the third frequency is used. Then, the methods used to correct the code and phase IFB are discussed. Standard point positioning (SPP) and precise point positioning (PPP) using BDS observations are carried out to validate the improvement of different IFB correction strategies. Experiments show that code IFB derived from DCB or geometry-free and ionosphere-free combination show an agreement of 0.3 ns for all satellites. Positioning results and error distribution with two different code IFB correcting strategies achieve similar tendency, which shows their substitutability. The original and wavelet filtered phase TIFB long-term series show significant

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

    PubMed

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

    2013-01-01

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

  15. High Sensitive Scintillation Observations At Very Low Frequencies

    NASA Astrophysics Data System (ADS)

    Konovalenko, A. A.; Falkovich, I. S.; Kalinichenko, N. N.; Olyak, M. R.; Lecacheux, A.; Rosolen, C.; Bougeret, J.-L.; Rucker, H. O.; Tokarev, Yu.

    The observation of interplanetary scintillations of compact radio sources is powerful method of solar wind diagnostics. This method is developed mainly at decimeter- meter wavelengths. New possibilities are opened at extremely low frequencies (decameter waves) especially at large elongations. Now this approach is being actively developed using high effective decameter antennas UTR-2, URAN and Nancay Decameter Array. New class of back-end facility like high dynamic range, high resolution digital spectral processors, as well as dynamic spectra determination ideology give us new opportunities for distinguishing of the ionospheric and interplanetary scintillations and for observations of large number of radio sources, whith different angular sizes and elongations, even for the cases of rather weak objects.

  16. Optimization of short tandem repeats (STR) typing method and allele frequency of 8 STR markers in referring to forensic medicine of Semnan Province.

    PubMed

    Eskandarion, M; Najafi, M; Akbari Eidgahi, M; Alipour Tabrizi, A; Golmohamadi, T

    2015-01-01

    Background and Objective: Short Tandem Repeats (STR) show considerable differences among individuals in the population from which they used for identification. There are various methods for analysis of these STR loci, and capillary electrophoresis method already used as an international standard. Due to the high costs of this process, this study aimed to set up a Multiplex PCR method in some standard STR loci so that we can use its PCR product in STR analysis with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Materials and Methods: 8 typical STR loci in the identification selected according to their size in the two groups of four (CSF1PO, VWA, D18S51, PentaD and TPOX, Amelogenin, FGA, SE33) from NIST (National Institute of Standards and Technology). The above SSR primers prepared from Genbank and Monoplex PCR was designed based on their size. Then, with the changes in temperature conditions, magnesium ion, primers concentration, and setting-up, Hot Start Multiplex PCR of four markers was carried out. PCR product investigated on the agarose gel electrophoresis (3%) and the results of genotyping analyzed by Genetic Analyzer. Results: The Results showed that all STR loci under study are detectable as Monoplex PCR at a temperature of 62°-66° and 1.5 mM magnesium ion. Moreover, Multiplex PCR results showed that when the concentration of primer and temperature measured by the fixed concentration of magnesium, CSF1PO, and D18S51 loci bands are weaker than desired. Using a standard buffer and set Magnesium conditions against changes in the primer concentration and temperature, when Taq polymerase enzyme is added to test tubes at a temperature of 94°, Multiplex PCR bands are visible desirably. Capillary electrophoresis genotyping results obtained in all eight loci and the Locus FGA had the most allelic diversity and the loci TPOX and CSF1PO had the lowest allelic diversity. TPOX and CSF1PO loci had the lowest allelic frequencies, and FGA locus had

  17. Optimization of short tandem repeats (STR) typing method and allele frequency of 8 STR markers in referring to forensic medicine of Semnan Province

    PubMed Central

    Eskandarion, M; Najafi, M; Akbari Eidgahi, M; Alipour Tabrizi, A; Golmohamadi, T

    2015-01-01

    Background and Objective: Short Tandem Repeats (STR) show considerable differences among individuals in the population from which they used for identification. There are various methods for analysis of these STR loci, and capillary electrophoresis method already used as an international standard. Due to the high costs of this process, this study aimed to set up a Multiplex PCR method in some standard STR loci so that we can use its PCR product in STR analysis with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Materials and Methods: 8 typical STR loci in the identification selected according to their size in the two groups of four (CSF1PO, VWA, D18S51, PentaD and TPOX, Amelogenin, FGA, SE33) from NIST (National Institute of Standards and Technology). The above SSR primers prepared from Genbank and Monoplex PCR was designed based on their size. Then, with the changes in temperature conditions, magnesium ion, primers concentration, and setting-up, Hot Start Multiplex PCR of four markers was carried out. PCR product investigated on the agarose gel electrophoresis (3%) and the results of genotyping analyzed by Genetic Analyzer. Results: The Results showed that all STR loci under study are detectable as Monoplex PCR at a temperature of 62°-66° and 1.5 mM magnesium ion. Moreover, Multiplex PCR results showed that when the concentration of primer and temperature measured by the fixed concentration of magnesium, CSF1PO, and D18S51 loci bands are weaker than desired. Using a standard buffer and set Magnesium conditions against changes in the primer concentration and temperature, when Taq polymerase enzyme is added to test tubes at a temperature of 94°, Multiplex PCR bands are visible desirably. Capillary electrophoresis genotyping results obtained in all eight loci and the Locus FGA had the most allelic diversity and the loci TPOX and CSF1PO had the lowest allelic diversity. TPOX and CSF1PO loci had the lowest allelic frequencies, and FGA locus had

  18. Allelic frequencies of PRKAG3 in several pig breeds and its technological consequences on a Duroc × Landrace-Large White cross.

    PubMed

    Galve, A; Burgos, C; Varona, L; Carrodeguas, J A; Cánovas, Á; López-Buesa, P

    2013-10-01

    The allelic frequencies of PRKAG3 gene (the RN gene) have been investigated in several pig breeds. R200Q mutation appear only in Hampshire pigs, whereas V199I mutation is most abundant in Iberian, Porco Celta or Bizaro, and less in breeds selected for muscularity as Duroc, Landrace and Pietrain. A thorough study of phenotypic effects of V1991 has been performed in a Duroc × Landrace-Large White cross. 199I homozygous pigs show increased pH24 values in ham homogenates and loin (0.14 and 0.16 pH units, respectively) compared to 199V homozygous ones. Meat of 199I homozygous pigs exudates 42.6% less fluid and is darker (2.46 'L'-value units). 199I homozygous pigs are fatter (4.2 mm more backfat thickness) and contain less muscle mass in ham (1.0 percentage points) and shoulder (2.7 percentage points), than 199V homozygous ones. 199I homozygous pigs contain 7.3% less protein in the belly and 8.5% more fat in shoulder muscle mass than 199V homozygous pigs. 199I homozygous pigs have also superior functional properties: better gelling (22.8% larger G' value) and emulsion capacities (14 percentage points less of total exuded fluid), and higher curing yield in the belly (6 percentage points more). These data support the adipogenic character of the V199I mutation. The advantages and disadvantages of selecting any of the two PRKAG3 alleles for position 199 are discussed.

  19. Dual Cry2Ab and Vip3A resistant strains of Helicoverpa armigera and Helicoverpa punctigera (Lepidoptera: Noctuidae); testing linkage between loci and monitoring of allele frequencies.

    PubMed

    Walsh, T K; Downes, S J; Gascoyne, J; James, W; Parker, T; Armstrong, J; Mahon, R J

    2014-08-01

    Considerable attention has been given to delaying the evolution of insect resistance to toxins produced by transgenic crops. The major pests of cotton in Australia are the Lepidoptera Helicoverpa armigera (Hubner, 1805) and Helicoverpa punctigera (Wallengren), and the toxins deployed in current and imminent transgenic cotton varieties are Cry1Ac, Cry2Ab and Vip3A from Bacillus thuringiensis. In this study, lines that carry alleles conferring resistance to Cry2Ab and Vip3A were isolated using F2 tests. Extensive work on the Cry2Ab resistant lines, and preliminary work on the Vip3A resistant lines, suggested a single common resistance to each toxin in both species thereby justifying the use of more efficient F1 tests as the primary means for monitoring changes over time. A potential further efficiency could be gained by developing a single resistant line that carries both types of Bt resistance. Herein we report on work with both H. armigera and H. punctigera that tests whether dual Cry2Ab-Vip3A resistant lines can be developed and, if so, whether they can be used to effectively monitor resistance frequencies. Furthermore, the creation of dual resistant lines allowed linkage between the Cry2Ab and Vip3A resistances to be investigated for H. punctigera. We show that dual resistant lines can be used to increase the efficiency of the F1 screen for recessive alleles, and that in H. punctigera there is no linkage between Cry2Ab and Vip3A resistance.

  20. New observations of the low frequency interplanetary radio emissions

    NASA Technical Reports Server (NTRS)

    Kurth, W. S.; Gurnett, D. A.

    1991-01-01

    Recent Voyager 1 observations reveal reoccurrences of the low frequency interplanetary radio emissions. Three of the new events are weak transient events which rise in frequency from the range of 2-2.5 kHz to about 3 kHz with drift rates of approximately 1.5 kHz/year. The first of the transient events begins in mid-1989 and the more recent pair of events both were first detected in late 1991. In addition, there is an apparent onset of a 2-kHz component of the emission beginning near day 70 of 1991. The new transient emissions are barely detectable on Voyager 1 and are below the threshold of detectability on Voyager 2, which is less sensitive than Voyager 1. The new activity provides new opportunities to test various theories of the triggering, generation, and propagation of the outer heliospheric radio emissions and may signal a response of the source of the radio emissions to the increased solar activity associated with the recent peak in the solar cycle.

  1. 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.

  2. 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.

  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. Analysis of the CCR5 gene coding region diversity in five South American populations reveals two new non-synonymous alleles in Amerindians and high CCR5*D32 frequency in Euro-Brazilians

    PubMed Central

    2009-01-01

    The CC chemokine receptor 5 (CCR5) molecule is an important co-receptor for HIV. The effect of the CCR5*D32 allele in susceptibility to HIV infection and AIDS disease is well known. Other alleles than CCR5*D32 have not been analysed before, neither in Amerindians nor in the majority of the populations all over the world. We investigated the distribution of the CCR5 coding region alleles in South Brazil and noticed a high CCR5*D32 frequency in the Euro-Brazilian population of the Paraná State (9.3%), which is the highest thus far reported for Latin America. The D32 frequency is even higher among the Euro-Brazilian Mennonites (14.2%). This allele is uncommon in Afro-Brazilians (2.0%), rare in the Guarani Amerindians (0.4%) and absent in the Kaingang Amerindians and the Oriental-Brazilians. R223Q is common in the Oriental-Brazilians (7.7%) and R60S in the Afro-Brazilians (5.0%). A29S and L55Q present an impaired response to β-chemokines and occurred in Afro- and Euro-Brazilians with cumulative frequencies of 4.4% and 2.7%, respectively. Two new non-synonymous alleles were found in Amerindians: C323F (g.3729G > T) in Guarani (1.4%) and Y68C (g.2964A > G) in Kaingang (10.3%). The functional characteristics of these alleles should be defined and considered in epidemiological investigations about HIV-1 infection and AIDS incidence in Amerindian populations. PMID:21637640

  5. Frequency of alleles conferring resistance to the Bacillus thuringiensis toxins Cry1Ac and Cry2Ab in Australian populations of Helicoverpa punctigera (Lepidoptera: Noctuidae) from 2002 to 2006.

    PubMed

    Downes, S; Parker, T L; Mahon, R J

    2009-04-01

    Helicoverpa punctigera and Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) are important pests of field and horticultural crops in Australia. The former is endemic to the continent, whereas the latter is also distributed in Africa and Asia. Although H. armigera rapidly developed resistance to virtually every group of insecticide used against it, there is only one report of resistance to an insecticide in H. punctigera. In 1996 the Australian cotton industry adopted Ingard, which expresses the Bacillus thuringiensis (Bt) toxin gene cry1Ac. In 2004/2005, Bollgard II (which expresses Cry1Ac and Cry2Ab) replaced Ingard and has subsequently been grown on 80% of the area planted to cotton, Gossypium hirsutum L. From 2002/2003 to 2006/2007, F2 screens were used to detect resistance to Cry1Ac or Cry2Ab. We detected no alleles conferring resistance to Cry1Ac; the frequency was < 0.0005 (n = 2,180 alleles), with a 95% credibility interval between 0 and 0.0014. However, during the same period, we detected alleles that confer resistance to Cry2Ab at a frequency of 0.0018 (n = 2,192 alleles), with a 95% credibility interval between 0.0005 and 0.0040. For both toxins, the experiment-wise detection probability was 94%, i.e., if there actually was a resistance allele in any tested lines, we would have detected it 94% of the time. The first isolation of Cry2Ab resistance in H. punctigera was before the widespread deployment of Bollgard II. This finding supports our published notion for H. armigera that alleles conferring resistance to Cry2Ab may be present at detectable frequencies in populations before selection by transgenic crops.

  6. [The normotensive carriers of the MTHFR 677T allele, displaying the increased risk of development of the abdominal aortic aneurysm (AAA), occur at the highest frequency among the smoking patients].

    PubMed

    Strauss, Ewa; Waliszewski, Krzysztof; Pawlak, Andrzej L

    2004-01-01

    Abdominal aortic aneurysm (AAA) presents itself as a progressive dilation of the abdominal aorta, leading--if untreated--to rupture. It is a common disease of the elderly, with a complex etiology. Smoking, hypertension and several genetic factors are recognized as relevant for the pathogenesis of AAA. We studied association between the polymorphism of the MTHFR (methylenetetrahydrofolate reductase) gene within the fourth exon (677C>T) and the occurrence of hypertension and smoking status in the group of 74 male patients with AAA. In the patients group, the smoking hypertensive persons represented the largest subgroup (43%). We determined the the MTHFR 677C>T polymorphism in AAA patients and compared it to that in 71 healthy normotensive males. The frequencies of the 677T allele and MTHFR 677C>T genotypes were similar in both groups, but the subgroup of normotensive AAA patients (n=29) displayed significantly increased frequencies of 677T allele (0.4) and of 677CT and TT genotypes (69%), as compared to those in the control group (0.28 and 46%, respectively). This corresponds to the 3.3-fold greater risk of AAA in normotensive subjects with the 677T allele of MTHFR, as compared to the homo-zygotes 677CC (p<0.03; 95% CI=1.2-9.2). The highest frequencies of MTHFR 677T allele (0.43) and 677CT and TT genotypes (73%) were found in the subgroup of normotensive smoking patients (n=22).

  7. 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.

  8. A non-synonymous SNP with the allele frequency correlated with the altitude may contribute to the hypoxia adaptation of Tibetan chicken

    PubMed Central

    Wang, Yan; Yin, Huadong; Zhou, Lanyun; Zhong, Chengling

    2017-01-01

    The hypoxia adaptation to high altitudes is of considerable interest in the biological sciences. As a breed with adaptability to highland environments, the Tibetan chicken (Gallus gallus domestics), provides a biological model to search for genetic differences between high and lowland chickens. To address mechanisms of hypoxia adaptability at high altitudes for the Tibetan chicken, we focused on the Endothelial PAS domain protein 1 (EPAS1), a key regulatory factor in hypoxia responses. Detected were polymorphisms of EPAS1 exons in 157 Tibetan chickens from 8 populations and 139 lowland chickens from 7 breeds. We then designed 15 pairs of primers to amplify exon sequences by Sanger sequencing methods. Six single nucleotide polymorphisms (SNPs) were detected, including 2 missense mutations (SNP3 rs316126786 and SNP5 rs740389732) and 4 synonymous mutations (SNP1 rs315040213, SNP4 rs739281102, SNP6 rs739010166, and SNP2 rs14330062). There were negative correlations between altitude and mutant allele frequencies for both SNP6 (rs739010166, r = 0.758, p<0.001) and SNP3 (rs316126786, r = 0.844, P<0.001). We also aligned the EPAS1 protein with ortholog proteins from diverse vertebrates and focused that SNP3 (Y333C) was a conserved site among species. Also, SNP3 (Y333C) occurred in a well-defined protein domain Per-AhR-Arnt-Sim (PAS domain). These results imply that SNP3 (Y333C) is the most likely casual mutation for the high-altitude adaption in Tibetan chicken. These variations of EPAS1 provide new insights into the gene’s function. PMID:28222154

  9. Mutations of the GLA gene in Korean patients with Fabry disease and frequency of the E66Q allele as a functional variant in Korean newborns.

    PubMed

    Lee, Beom Hee; Heo, Sun Hee; Kim, Gu-Hwan; Park, Jung-Young; Kim, Woo-Shik; Kang, Duk-Hee; Choe, Kyung Hoon; Kim, Won-Ho; Yang, Song Hyun; Yoo, Han-Wook

    2010-08-01

    Fabry disease is caused by an alpha-galactosidase A (GLA) deficiency. In this study, we identified 28 unrelated Korean families with Fabry disease with 25 distinct mutations in the GLA gene including six novel mutations (p.W47X, p.C90X, p.D61EfsX32, IVS4(-11)T>A, p.D322E and p.W349). Notably, five subjects from four unrelated families carried the p.E66Q variant, previously known as a pathogenic mutation in atypical Fabry disease. Among these patients, only one had proteinuria and two had hypertrophic cardiomyopathy without any other systemic manifestation of Fabry disease. Substantial residual GLA activity was shown both in the leukocytes of p.E66Q patients (19.0-30.3% of normal activity) and in transiently overexpressed COS-7 cells (43.8 + or - 3.03% of normal activity). Although GLA harboring p.E66Q is unstable at neutral pH, the enzyme is efficiently expressed in the lysosomes of COS-7 cells. The location of p.E66 is distant from both the active site and the dimer interface, and has a more accessible surface area than have other mutations of atypical Fabry disease. In addition, the allele frequency of p.E66Q determined in 833 unrelated Korean individuals was remarkably high at 1.046% (95% confidence interval, 0.458-1.634%). These results indicate that p.E66Q is a functional polymorphism rather than a pathogenic mutation.

  10. Serotonin transporter protein (SLC6A4) allele and haplotype frequencies and linkage disequilibria in African- and European-American and Japanese populations and in alcohol-dependent subjects.

    PubMed

    Gelernter, J; Kranzler, H; Cubells, J F

    1997-12-01

    The SLC6A4 locus encodes the serotonin transporter, which in turn mediates the synaptic inactivation of the neurotransmitter serotonin. Two PCR-formatted polymorphisms at this locus have been described, the first of which is a variable number tandem repeat located in exon 2, and the second a repeat sequence polymorphism located in the promoter region. The latter polymorphism alters transcriptional activity of SLC6A4, and has been reported to be associated with anxiety and depression-related traits. We studied allele frequencies, and computed haplotype frequencies and linkage disequilibrium measures, for these two polymorphisms in European-American, African-American, and Japanese populations, and in a set of alcohol-dependent European-American subjects. Allele frequencies for both systems showed variation, with significant differences overall for each system, and significant differences between each pair of populations for both systems. Linkage disequilibrium also varied among the populations. There were no significant differences in allele or haplotype frequencies between the European-American population samples and alcohol-dependent subjects. The population differences demonstrate a potential for population stratification in association studies of either of these SLC6A4 polymorphisms. If genetic variation at this locus really is associated with behavioral variation, these results could reflect either different behavioral adaptations in different populations, or random genetic drift of a behaviorally important but selectively neutral polymorphism.

  11. [Differences in allele frequency at the BAIB locus, determining the level of expression of beta-aminoisobutyric acid, in healthy donors and coronary artery atherosclerosis patients from Buryat and Lithuanian populations].

    PubMed

    Spitsyn, V A; Afanas'eva, I S

    2001-12-01

    Phenotype and allele frequencies of the genetically dimorphic system determining urinary excretion of beta-aminoisobutyric acid (BAIB) were studied in population samples of Buryats from the Aginskii Buryat Autonomous District and Lithuanians from Vilnius and in patients with coronary atherosclerosis (CA) from both populations. Frequency of allele BAIB*b, which determines high BAIB excretion, proved to be more than twice higher in Buryats compared with the population sample of Lithuanians (0.620 versus 0.289, respectively). The proportion of individuals with high BAIB excretion in CA patients of either ethnic sample was twice higher than in the corresponding control sample. Frequency of allele BAIB*b in CA patients and healthy individuals was 0.348 and 0.242, respectively, in the Lithuanian population and 0.775 and 0.557, respectively, in the Buryat population. Thus, assessment of urinary excretion of BAIB proved to be prognostically valuable. The method used to detect a variation in BAIB excretion is relatively inexpensive, simple, and suitable for mass screening of patients and healthy individuals (population control). After additional testing with representative samples, the method can be used as an accessory diagnostic test in patients with cardiovascular disorders.

  12. 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.

  13. Allele frequencies and genetic diversity in two groups of wild tufted capuchin monkeys (Cebus apella nigritus) living in an urban forest fragment.

    PubMed

    Amaral, Jeanne Margareth Jimenes; Simões, Aguinaldo Luiz; De Jong, David

    2005-12-30

    There have been numerous studies genetically characterizing Old World Primates using microsatellites. However, few studies have been made of New World species and none on free-ranging Cebus apella, even though it is probably the most widely distributed species of monkey in the New World. The paucity of studies is due, in part, to the lack of polymorphisms described for this species. We studied two groups of wild tufted capuchins, Cebus apella nigritus, which inhabit Mata Santa Teresa, the Ecological Reserve of Ribeirão Preto, a 158-ha forest fragment in a semi-urban zone of Ribeirão Preto, SP, Brazil. Group 1 had about 60 animals, 35 of which were sampled, and group 2 had about 40 animals, 20 of which were sampled. These group sizes are much larger than the published reports of 6-30 for this species, despite, or perhaps due to the isolation and the size of the forest fragment. Allele PEPC59*1 was the most frequent of all alleles at all loci in both groups (55.7 and 55%), allele PEPC8*1 was the most common allele in group 2 (46.9%) and PEPC8*4 in group 1 (41.1%), allele PEPC3*2 was the most common in group 1 (35.7%) and allele PEPC3*4 in group 2 (31.6%). The genetic diversity, considering each locus in each group, varied from 61.9% at locus PEPC59 to 78.6% at locus PEPC3, both in group 1. The mean genetic diversity (H(S)), considering both groups for all of the loci, was 71.1%. The inter-group diversity (F(ST)) was 1.9%, indicating that these groups belong to the same population. These groups apparently have a high genetic diversity, despite their isolation in a limited forest fragment, although more data are needed to adequately characterize this population.

  14. 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.

  15. Allele Frequencies of the Epidermal Growth Factor Receptors Polymorphism R521K in Colorectal Cancer Patients and Healthy Subjects Indicate a Risk-Reducing Effect of K521 in Syrian Population

    PubMed Central

    Mustafa, Ola Haj; Hamzeh, Abdul Rezzak; Ghabreau, Lina; Akil, Nizar; Almoustafa, Ala-Eddin; Alachkar, Amal

    2013-01-01

    Background: Colorectal cancer contributes heavily to cancer morbidity and mortality worldwide. Numerous therapies are currently in use, including monoclonal antibodies against cellular components involved in tumorigenesis such as epidermal growth factor receptors (EGFRs). Studies showed the polymorphism [R521K] GàA in the EGFR gene to be involved in both colorectal cancer susceptibility and clinical response to therapeutics (e.g., Cetuximab). Aim: We aimed at uncovering allele frequencies of this polymorphism among Syrian colorectal cancer patients and healthy individuals. Materials and Methods: Forty-seven patients with colorectal cancer were included in a case-control study along with 48 healthy subjects, all native Syrians. Individuals were genotyped using PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) and results were statistically analyzed to elucidate significant differences between the two groups. Results: Allele frequencies were 40.4% (G/G), 57.4% (G/A) and 2.1% (A/A) in colorectal cancer patients and 41.6% (G/G), 43.7% (G/A) and 14.5% (A/A) in healthy subjects. The A/A genotype was significantly lower in colorectal cancer patients than in the control group. Conclusions: Homozygosity for the A allele is linked to reducing the risk of developing colorectal cancer in Syrian patients. The lower prevalence of (A/A) locally may predict sub-optimal rates of clinical response to Cetuximab compared with populations with higher frequencies of the A allele. Larger scale investigations are needed for a stronger conclusion. PMID:23626956

  16. 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.

  17. 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.

  18. Frequency of the HLA-B*1502 allele contributing to carbamazepine-induced hypersensitivity reactions in a cohort of Malaysian epilepsy patients.

    PubMed

    Then, Sue-Mian; Rani, Zam Zureena Mohd; Raymond, Azman Ali; Ratnaningrum, Safrina; Jamal, Rahman

    2011-09-01

    We describe the association of the HLA-B*1502 allele in 27 epilepsy patients (19 Malays, 8 Chinese) treated with carbamazepine (CBZ) at the UKM Medical Center (UKMMC), 6 with CBZ-Steven Johnson Syndrome (CBZ-SJS), 11 with CBZ-induced rash, 2 with suspected phenytoin-induced rash and 8 negative controls. Our study showed that 10 (6 Malay, 4 Chinese) patients were positive for HLA-B*1502. Out of the 10 patients, six were confirmed to have CBZ-SJS (p = 0.0006), while four patients developed a skin rash. However there were 6 Malay patients and 1 Chinese patient that developed a skin rash after CBZ administration who were not positive for the allele, indicating that there might be more that one allele associated with CBZ-induced hypersensitivity. Another 2 patients were suspected of having phenytoin-induced rash, instead of CBZ, and these patients did not have HLA-B*1502. In conclusion, this study confirmed the association of HLA-B*1502 with CBZ-SJS among Malaysian epilepsy patients, however there might be other genes that could be responsible for the CBZ-induced rash.

  19. A resonance phenomenon observed in a swept frequency experiment on a mother-daughter ionospheric rocket

    NASA Technical Reports Server (NTRS)

    Folkestad, K.; Troim, J.

    1974-01-01

    The report presents observations obtained in a swept frequency experiment conducted in a mother-daughter rocket flight at auroral latitudes. The discussion is essentially restricted to the possible interpretation of the experimental signal structures noted at and in the vicinity of a resonance frequency where signal components apparently are generated by nonlinear mechanisms. Various resonance frequencies have been considered in attempts to identify this multichannel response frequency. It is concluded that of all the possibilities invoked, the best consistency is provided by identifying the frequency concerned with the cone resonance frequency demonstrated experimentally in the case of a laboratory plasma by Fisher and Gould (1971).

  20. Radio frequency observations of lightning discharges by the forte satellite.

    SciTech Connect

    Shao, X.; Jacobson, A. R.; Light, T.; Suszcynsky, D. M.

    2002-01-01

    FORTE-observed VHF signatures for different lightning discharges are presented. For in-cloud discharges, a pulse pair is typically recorded and is named a 'transionospheric pulse pair' (TIPP). Many intense TIPPs are coherent and polarized, whereas initial and dart leaders do not show a recognizable degree of polarization. TIPPs are optically weaker than cloud-to-ground (CG) strokes, and stronger VHF TIPPs are optically darker. About 10% of CG strokes, mostly over seawater, produce extremely narrow, powerful VHF pulses at the very beginning of the return strokes. These narrow pulses are found to form an upward beam pattern.

  1. 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.

  2. Coordinated observations using the world largest low-frequency radio telescopes and space misiions

    NASA Astrophysics Data System (ADS)

    Konovalenko, A. A.; Zarka, Ph.; Kolyadin, V. L.; Zakharenko, V. V.; Stepkin, S. V.; Panchenko, M.; Lecacheux, A.; Rucker, H. O.; Fischer, G.; Ulyanov, O. M.; Melnik, V. N.; Litvinenko, G. V.; Sidorchuk, M. A.; Bubnov, I. N.; Vasilyeva, Ya. Yu.; Bojko, A. I.; Shaposhnikov, V.; Mann, G.; Kalinichenko, N. N.; Falkovich, I. S.; Koval, A. A.; Mylostna, K.; Pylaev, O. S.; Shepelev, V. A.; Reznik, A. P.

    2013-09-01

    The positive possibilities of astrophysical objects studies(including the Solar system investigations) using coordinated observations with the largest existing and coming low frequency radio telescopes are shown. The observations of the Sun, Jupiter, Saturn, ant others with UTR-2, URAN, NDA radio telescopes, and WIND, Cassini and STEREO space missions at frequencies lower than 40 MHz have been carried out.

  3. 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...

  4. The influence of human leukocyte antigen class I alleles and their population frequencies on human immunodeficiency virus type 1 control among African Americans.

    PubMed

    Lazaryan, Aleksandr; Song, Wei; Lobashevsky, Elena; Tang, Jianming; Shrestha, Sadeep; Zhang, Kui; McNicholl, Janet M; Gardner, Lytt I; Wilson, Craig M; Klein, Robert S; Rompalo, Anne; Mayer, Kenneth; Sobel, Jack; Kaslow, Richard A

    2011-04-01

    Populations of African ancestry continue to account for a disproportionate burden of the human immunodeficiency virus type 1 (HIV-1) epidemic in the United States. We investigated the effects of human leukocyte antigen (HLA) class I markers in association with virologic and immunologic control of HIV-1 infection among 338 HIV-1 subtype B-infected African Americans in 2 cohorts: Reaching for Excellence in Adolescent Care and Health (REACH) and HIV Epidemiology Research Study (HERS). One-year treatment-free interval measurements of HIV-1 RNA viral loads and CD4(+) T cells were examined both separately and combined to represent 3 categories of HIV-1 disease control (76 controllers, 169 intermediates, and 93 noncontrollers). Certain previously or newly implicated HLA class I alleles (A*32, A*36, A*74, B*14, B*1510, B*3501, B*45, B*53, B*57, Cw*04, Cw*08, Cw*12, and Cw*18) were associated with 1 or more of the endpoints in univariate analyses. After multivariable adjustments for other genetic and nongenetic risk factors of HIV-1 progression, the subset of alleles more strongly or consistently associated with HIV-1 disease control included A*32, A*74, B*14, B*45, B*53, B*57, and Cw*08. Carriage of infrequent HLA-B but not HLA-A alleles was associated with more favorable disease outcomes. Certain HLA class I associations with control of HIV-1 infection cross the boundaries of race and viral subtype, whereas others appear confined within one or the other of those boundaries.

  5. Ethnic variation of the HLA-G*0105N allele in two Chinese populations.

    PubMed

    Lin, A; Li, M; Xu, D-P; Zhang, W-G; Yan, W-H

    2009-03-01

    Unlike high polymorphic classical human leukocyte antigen (HLA) class I molecules, the genetic polymorphism of HLA-G is very limited. However, the prevalence of HLA-G alleles among different ethnic populations varied dramatically. The HLA-G null allele (HLA-G*0105N) is defined by a cytosine deletion (Delta C) at position 1597 in exon 3, which disrupts the reading frame and alters the expression of HLA-G proteins. The HLA-G*0105N allelic frequency was investigated in previous studies and possible roles were addressed. In the current study, a total of 310 Chinese Han and 260 Chinese She ethnic minority population had been genotyped for the G*0105N polymorphism. Marked difference was observed that the G*0105N allelic frequency in Chinese Han was 1.61%, while no copy of the null allele was observed in the Chinese She minority population (P(c) = 0.0073). Data also revealed that no homozygote of HLA-G*0105N allele exists in this Chinese Han population. Furthermore, significant difference was found for the frequencies of HLA-G*0105N both in Chinese Han and in Chinese She populations when compared with other ethnic populations. Taken together, our results indicated that ethnic variation of the HLA-G*0105N polymorphism among different ethnic populations is possibly the result of evolution. However, the advantages of the selection of this allele are necessary to be further investigated.

  6. OEDIPUS-C observations of electrons accelerated by radio frequency fields at whistler-mode frequencies

    NASA Astrophysics Data System (ADS)

    James, H. G.; Sotnikov, V. I.; Burke, W. J.; Huang, C. Y.

    1999-10-01

    Simultaneous measurements of transmitted 500 kHz electric fields and of electron fluxes nonlinearly energized by those fields were made during the ionospheric flight of the rocket double payload OEDIPUS C. Given the local plasma parameters, 500 kHz corresponded to the whistler mode of cold-plasma propagation. As the separation between each payload end increased from 153 to 537 m, enhanced electron fluxes were detected at energies up to 20 keV, at the receiver end of the tether. Rf (radio frequency) electric fields created by the OEDIPUS-C transmitter have been computed for positions close to the whistler-mode group resonance cone and also for locations very close to the active dipoles. Test-particle trajectory tracings show that linear acceleration can account for the energy increases of electrons with starting energies up to about 100 eV. Neither resonant field-particle interactions of background energetic electrons nor strong turbulence of the background thermal particles explain the creation of sounder-accelerated electrons at 1-10 keV. The calculated magnitudes of the very near potentials, up to 550 V, point to acceleration by intense fields in the rf sheath region.

  7. μ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype and allele frequencies.

    PubMed

    Tait, R G; Shackelford, S D; Wheeler, T L; King, D A; Casas, E; Thallman, R M; Smith, T P L; Bennett, G L

    2014-02-01

    Genetic marker effects and interactions are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to increase divergent haplotype and minor marker allele frequencies to 1) estimate effect size and mode of inheritance for previously reported SNP on targeted beef carcass quality traits; 2) estimate effects of previously reported SNP on nontarget performance traits; and 3) evaluate tenderness SNP specific residual variance models compared to a single residual variance model for tenderness. Divergent haplotypes within µ-calpain (CAPN1), and SNP within calpastatin (CAST) and growth hormone receptor (GHR) were successfully selected to increase their frequencies. Traits evaluated were birth BW, weaning BW, final BW, fat thickness, LM area, USDA marbling score, yield grade, slice shear force (SSF), and visible and near infrared predicted slice shear force. Both CAPN1 and CAST exhibited additive (P < 0.001) modes of inheritance for SSF and neither exhibited dominance (P ≥ 0.19). Furthermore, the interaction between CAPN1 and CAST for SSF was not significant (P = 0.55). Estimated additive effects of CAPN1 (1.049 kg) and CAST (1.257 kg) on SSF were large in this study. Animals homozygous for tender alleles at both CAPN1 and CAST would have 4.61 kg lower SSF (38.6% of the mean) than animals homozygous tough for both markers. There was also an effect of CAST on yield grade (P < 0.02). The tender CAST allele was associated with more red meat yield and less trimmable fat. There were no significant effects (P ≥ 0.23) for GHR on any of the traits evaluated in this study. Furthermore, CAST specific residual variance models were found to fit significantly better (P < 0.001) than single residual variance models for SSF, with the tougher genotypes having larger residual variance. Thus, the risk of a tough steak from the undesired CAST genotype is increased through both an

  8. Plasma rest frame frequencies and polarizations of the low-frequency upstream waves - ISEE 1 and 2 observations

    NASA Technical Reports Server (NTRS)

    Hoppe, M. M.; Russell, C. T.

    1983-01-01

    The plasma rest frame frequencies and polarizations of the large amplitude low frequency (0.03 Hz) upstream waves are investigated using magnetic field data from the dual ISEE 1 and 2 spacecraft. The monochromatic sinusoidal waves associated with intermediate ion fluxes are propagating in both the Alfven and magnetosonic modes, in both cases with typical frequencies approximately 0.1 times the local proton gyrofrequency and wavelengths of approximately 1 R(E). It is shown that the generation of the magnetosonic mode can be explained by the cyclotron resonance mechanism driven by narrow reflected ion beams, but the concurrent observation of Alfven mode waves appears to require wave generation by the more isotropic diffuse ion distributions as well.

  9. 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

  10. Theory and Observations of High Frequency Alfven Eigenmodes in Low Aspect Ratio Plasma

    SciTech Connect

    N.N. Gorelenkov; E. Fredrickson; E. Belova; C.Z. Cheng; D. Gates; S. Kaye; R. White

    2003-06-27

    New observations of sub-cyclotron frequency instability in low aspect ratio plasma in National Spherical Torus Experiments (NSTX) are reported. The frequencies of observed instabilities correlate with the characteristic Alfven velocity of the plasma. A theory of localized Compressional Alfven Eigenmodes (CAE) and Global shear Alfven Eigenmodes (GAE) in low aspect ratio plasma is presented to explain the observed high frequency instabilities. CAE's/GAE's are driven by the velocity space gradient of energetic super-Alfvenic beam ions via Doppler shifted cyclotron resonances. One of the main damping mechanisms of GAE's, the continuum damping, is treated perturbatively within the framework of ideal MHD. Properties of these cyclotron instabilities ions are presented.

  11. 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].

  12. Frequency Calibration of Spectral Observation System of the TM65m Radio Telescope

    NASA Astrophysics Data System (ADS)

    Juan, Li; Ya-jun, Wu; Hai-hua, Qiao; Jun-zhi, Wang; Xiu-ting, Zuo

    2016-10-01

    In order to carry out the spectral observation with the TM65m radio telescope, the frequency calibration and test of DIBAS (Digital Backend System) are performed, it is found that it has a good performance. First, by injecting the PCAL signals, the frequency resolution, frequency drift and the stability of frequency interval between two spectral lines of the DIBAS backend are measured. It is found that in one hour, the maximum frequency drift of a single spike is 0.03 channel, the maximum fluctuation of spike interval is 0.05 channel. Then, by the observations on the H2CO maser and absorbtion lines of massive star formation regions, and the comparison with the results observed by the GBT (Robert C. Byrd Green Bank Telescope), it is shown that the results of frequency calibration are correct. Finally, by the OH maser observations in more than one hour toward W3(OH), and the methanol maser observations in more than 5 hours, it is found that the spectral profiles keep consistent, and the observational noise is consistent with the theoretical value, indicating the stability and reliability of the frequency calibration program.

  13. 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.

  14. Low-frequency Observations of the Moon with the Murchison Widefield Array

    NASA Astrophysics Data System (ADS)

    McKinley, B.; Briggs, F.; Kaplan, D. L.; Greenhill, L. J.; Bernardi, G.; Bowman, J. D.; de Oliveira-Costa, A.; Tingay, S. J.; Gaensler, B. M.; Oberoi, D.; Johnston-Hollitt, M.; Arcus, W.; Barnes, D.; Bunton, J. D.; Cappallo, R. J.; Corey, B. E.; Deshpande, A.; deSouza, L.; Emrich, D.; Goeke, R.; Hazelton, B. J.; Herne, D.; Hewitt, J. N.; Kasper, J. C.; Kincaid, B. B.; Koenig, R.; Kratzenberg, E.; Lonsdale, C. J.; Lynch, M. J.; McWhirter, S. R.; Mitchell, D. A.; Morales, M. F.; Morgan, E.; Ord, S. M.; Pathikulangara, J.; Prabu, T.; Remillard, R. A.; Rogers, A. E. E.; Roshi, A.; Salah, J. E.; Sault, R. J.; Udaya Shankar, N.; Srivani, K. S.; Stevens, J.; Subrahmanyan, R.; Wayth, R. B.; Waterson, M.; Webster, R. L.; Whitney, A. R.; Williams, A.; Williams, C. L.; Wyithe, J. S. B.

    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.

  15. BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes.

    PubMed

    de Santiago, Ines; Liu, Wei; Yuan, Ke; O'Reilly, Martin; Chilamakuri, Chandra Sekhar Reddy; Ponder, Bruce A J; Meyer, Kerstin B; Markowetz, Florian

    2017-02-24

    Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most methods of detecting an allelic imbalance assume diploid genomes. This assumption severely limits their applicability to cancer samples with frequent DNA copy-number changes. Here we present a Bayesian statistical approach called BaalChIP to correct for the effect of background allele frequency on the observed ChIP-seq read counts. BaalChIP allows the joint analysis of multiple ChIP-seq samples across a single variant and outperforms competing approaches in simulations. Using 548 ENCODE ChIP-seq and six targeted FAIRE-seq samples, we show that BaalChIP effectively corrects allele-specific analysis for copy-number variation and increases the power to detect putative cis-acting regulatory variants in cancer genomes.

  16. Allelic diversity of metallothionein in Orchesella cincta (L.): traces of natural selection by environmental pollution.

    PubMed

    Timmermans, M J T N; Ellers, J; Van Straalen, N M

    2007-05-01

    The advances made in statistical methods to detect selection from DNA sequence variation has resulted in an enormous increase in the number of studies reporting positive selection. However, a disadvantage of such statistical tests is that often no insight into the actual source of selection is obtained. Finer understanding of evolution can be obtained when those statistical tests are combined with field observations on allele frequencies. We assessed whether the metallothionein (mt) gene of Orchesella cincta (Collembola), which codes for a metal-binding protein, is subject to selection, by investigating alleles and allele frequencies among European metal-stressed and reference populations. Eight highly divergent alleles were resolved in Northwest Europe. At the nucleotide level, a total of 51 polymorphic sites (five of them implying amino-acid changes) were observed. Although statistical tests applied to the sequences alone showed no indication of selection, a G-test rejected the null hypothesis that alleles are homogeneously distributed over metal-stressed and reference populations. Analysis of molecular variance assigned a small, but significant amount of the total variance to differences between metal-stressed and non-stressed populations. In addition, it was shown that metal-stressed populations tend to be more genetically diversified at this locus than non-stressed ones. These results suggest that the mt gene and its surrounding DNA region are affected by environmental metal contamination. This study illustrates that, in addition to statistical tests, field observations on allele frequencies are needed to gain understanding of selection and adaptive evolution.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. USA and RXTE Observations of a Variable Low-Frequency QPO in XTEJ1118+480

    SciTech Connect

    Bloom, Elliott

    2000-06-29

    The USA experiment on ARGOS and RXTE have extensively observed the X-ray transient XTEJ1118+480 during its recent outburst in 2000 April--June. The authors present detailed monitoring of the evolution of a low frequency QPO which drifts from 0.07 Hz to 0.15 Hz during the outburst. They examine possible correlations of the QPO frequency with the flux and spectral characteristics of the source, and compare this QPO to low frequency QPOs observed in other black hole candidates.

  2. High frequency of SLC22A12 variants causing renal hypouricemia 1 in the Czech and Slovak Roma population; simple and rapid detection method by allele-specific polymerase chain reaction.

    PubMed

    Gabrikova, Dana; Bernasovska, Jarmila; Sokolova, Jitka; Stiburkova, Blanka

    2015-10-01

    Renal hypouricemia is a rare heterogeneous inherited disorder characterized by impaired tubular uric acid transport with severe complications, such as acute kidney injury. Type 1 and 2 are caused by loss-of-function mutations in the SLC22A12 and SLC2A9 gene, respectively. A cohort of 881 randomly chosen ethnic Roma from two regions in Eastern Slovakia and two regions in the Czech Republic participated. Genomic DNA was isolated from buccal swabs and/or from blood samples. The c.1245_1253del and c.1400C>T genotypes were determined using polymerase chain reaction with allele-specific primers in a multiplex arrangement and/or direct sequencing of exon 7 and 9. Allele frequencies and genotypes were tested for Hardy-Weinberg equilibrium using the Chi-square test. 25 subjects were heterozygous and three were homozygous for the c.1245_1253del, while 92 subjects were heterozygous and two were homozygous for the c.1400C>T. Moreover, two participants were compound heterozygotes. Frequencies of the c.1245_1253del and c.1400C>T variants were 1.87 and 5.56 %, respectively. Our finding confirms an uneven geographical and ethnic distribution of SLC22A12 mutant variants. We found that the c.1245_1253del and c.1400C>T variants were present in the Czech and Slovak Roma population at unexpectedly high frequencies. Renal hypouricemia should be kept in mind during differential diagnostic on Roma patients with low serum uric acid concentrations.

  3. Theoretical interpretation of frequency sweeping observations in the Mega-Amp Spherical Tokamak

    NASA Astrophysics Data System (ADS)

    Vann, R. G. L.; Dendy, R. O.; Gryaznevich, M. P.

    2005-03-01

    Frequency sweeping (chirping) of high frequency magnetohydrodynamic modes is widely observed in tokamak plasmas. In this paper observations of chirping in neutral-beam-heated plasmas in the Mega-Amp Spherical Tokamak (MAST) [A. Sykes, R. J. Akers, L. C. Appel et al., Nucl. Fusion 41, 1423 (2001)] are considered, and it is shown that these may be interpreted using the Berk-Breizman augmentation of the Vlasov-Maxwell equations. This model includes an energetic particle source: it leads not only to a single chirp but also to a series of bursting events. This repetitious behavior is characteristic of the chirping seen in experiments such as MAST. The similarity between features in velocity space and features in frequency space reinforces the theory that hole-clump pair formation is responsible for the observed frequency sweeping.

  4. High-frequency internal waves near the Luzon Strait observed by underwater gliders

    NASA Astrophysics Data System (ADS)

    Rudnick, Daniel L.; Johnston, T. M. Shaun; Sherman, Jeffrey T.

    2013-02-01

    flow through the Luzon Strait produces large internal waves that propagate westward into the South China Sea and eastward into the Pacific. Underwater gliders gathered sustained observations of internal waves during seven overlapping missions from April 2007 through July 2008. A particular focus is the high-frequency internal waves, where the operational definition of high involves periods shorter than a glider profile taking 3-6 h. Internal wave vertical velocity is estimated from measurements of pressure and glider orientation through two methods: (1) use of a model of glider flight balancing buoyancy and drag along the glider path and (2) high-pass filtering of the observed glider vertical velocity. By combining high-frequency vertical velocities from glider flight with low-frequency estimates from isopycnal depth variations between dives, a spectrum covering five decades of frequency is constructed. A map of the standard deviation of vertical velocity over the survey area shows a decay from the Luzon Strait into the Pacific. The growth of high-frequency vertical velocity with propagation into the South China Sea is observed through two 2-week time series stations. The largest observed vertical velocities are greater than 0.2 m s-1 and are associated with displacements approaching 200 m. The high-frequency waves are observed at regular intervals of 1 day as they ride on diurnal tidal internal waves generated in the Strait.

  5. A novel allelic variant of the human TSG-6 gene encoding an amino acid difference in the CUB module. Chromosomal localization, frequency analysis, modeling, and expression.

    PubMed

    Nentwich, Hilke A; Mustafa, Zehra; Rugg, Marilyn S; Marsden, Brian D; Cordell, Martin R; Mahoney, David J; Jenkins, Suzanne C; Dowling, Barbara; Fries, Erik; Milner, Caroline M; Loughlin, John; Day, Anthony J

    2002-05-03

    Tumor necrosis factor-stimulated gene-6 (TSG-6) encodes a 35-kDa protein, which is comprised of contiguous Link and CUB modules. TSG-6 protein has been detected in the articular joints of osteoarthritis (OA) patients, with little or no constitutive expression in normal adult tissues. It interacts with components of cartilage matrix (e.g. hyaluronan and aggrecan) and thus may be involved in extracellular remodeling during joint disease. In addition, TSG-6 has been found to have anti-inflammatory properties in models of acute and chronic inflammation. Here we have mapped the human TSG-6 gene to 2q23.3, a region of chromosome 2 linked with OA. A single nucleotide polymorphism was identified that involves a non-synonymous G --> A transition at nucleotide 431 of the TSG-6 coding sequence, resulting in an Arg to Gln alteration in the CUB module (at residue 144 in the preprotein). Molecular modeling of the CUB domain indicated that this amino acid change might lead to functional differences. Typing of 400 OA cases and 400 controls revealed that the A(431) variant identified here is the major TSG-6 allele in Caucasians (with over 75% being A(431) homozygotes) but that this polymorphism is not a marker for OA susceptibility in the patients we have studied. Expression of the Arg(144) and Gln(144) allotypes in Drosophila Schneider 2 cells, and functional characterization, showed that there were no significant differences in the ability of these full-length proteins to bind hyaluronan or form a stable complex with inter-alpha-inhibitor.

  6. Estimating Relatedness in the Presence of Null Alleles

    PubMed Central

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

    2016-01-01

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

  7. 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.

  8. 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

  9. Low-cost precise measurement of oscillator frequency instability based on GNSS carrier observation

    NASA Astrophysics Data System (ADS)

    Kou, Yanhong; Jiao, Yue; Xu, Dongyang; Zhang, Meng; Liu, Ya; Li, Xiaohui

    2013-03-01

    Global navigation satellite systems (GNSS) receivers can be used in time and frequency metrology by exploiting stable GNSS time scales. This paper proposes a low-cost method for precise measurement of oscillator frequency instability using a single-frequency software GNSS receiver. The only required hardware is a common radio frequency (RF) data collection device driven by the oscillator under test (OUT). The receiver solves the oscillator frequency error in high time resolution using the carrier Doppler observation and the broadcast ephemeris from one of the available satellites employing the onboard reference atomic frequency standard that is more stable than the OUT. Considering the non-stable and non-Gaussian properties of the frequency error measurement, an unbiased finite impulse response (FIR) filter is employed to obtain robust estimation and filter out measurement noise. The effects of different filter orders and convolution lengths are further discussed. The frequency error of an oven controlled oscillator (OCXO) is measured using live Beidou-2/Compass signals. The results are compared with the synchronous measurement using a specialized phase comparator with the standard coordinated universal time (UTC) signal from the master clock H226 in the national time service center (NTSC) of China as its reference. The Allan deviation (ADEV) estimates using the two methods have a 99.9% correlation coefficient and a 0.6% mean relative difference over 1-1000 s intervals. The experiment demonstrates the effectiveness and high precision of the software receiver method.

  10. 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.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-12-07

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

  13. Protective effect of CCR5 Delta-32 allele against HIV-1 in Mexican women.

    PubMed

    Estrada-Aguirre, Jesús A; Cázarez-Salazar, Silvestre G; Ochoa-Ramírez, Luis A; Acosta-Cota, Selene de J; Zamora-Gómez, Román; Najar-Reyes, Guilermi M; Villarreal-Escamilla, Perla; Osuna-Ramírez, Ignacio; Díaz-Camacho, Sylvia P; Sánchez-Zazueta, Jorge G; Ríos-Tostado, Juan J; Velarde-Félix, Jesús S

    2013-09-01

    C-C chemokine receptor type 5 (CCR5) is known for its role as a co-receptor for HIV-1 infection. Some individuals possess a 32 bp deletion, known as Delta-32 allele which has been reported to confer resistance to HIV-1 infection. In order to estimate the distribution of Delta-32 allele of CCR5 gene, 1034 mestizo individuals from the Northwest of Mexico, including 385 HIV-1-infected individuals, 472 healthy controls and 177 uninfected female sex workers; were examined by allele-specific PCR. There was no statistically significant difference in the frequency of Delta-32 allele between HIV-1 positive and healthy individuals (OR= 1.1, p= 0.6). However, we found a significantly reduced prevalence of CCR5 Delta-32 heterozygous genotype in female patients (OR= 0.084, 95% CI= 0.011 - 0.630, p= 0.002), as well as in allele frequency, compared to male patients. Furthermore, we observed an inverse relationship between allele frequency and the risk of HIV-1 transmission and AIDS progression among female healthy controls, sex workers and HIV-1 infected groups. Our findings support previous data showing Delta-32 as a genetic protective factor against HIV-1 infection in Mexican women, as well as in women from other populations.

  14. 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.

  15. Distribution of the mutated delta 32 allele of the CCR5 gene in a Sicilian population.

    PubMed

    Sidoti, A; D'Angelo, R; Rinaldi, C; De Luca, G; Pino, F; Salpietro, C; Giunta, D E; Saltalamacchia, F; Amato, A

    2005-06-01

    The CCR5 gene encodes a cell-surface chemokine receptor molecule that serves as a co-receptor for macrophage-tropic strains of human immunodeficiency virus type 1 (HIV-1). A mutation in this gene may alter the expression or the function of the protein product, thereby altering chemokine binding and/or signalling or HIV-1 infection of cells that normally express CCR5 protein. Individuals homozygous for a 32-bp deletion allele of CCR5 (CCR5 delta32), heritable as a Mendelian trait, are relatively resistant to HIV-1 infection. The CCR5 delta32 mutation is present in the Caucasian population at different frequencies. The aim of this study was to investigate the frequency of truncated alleles of the CCR5 delta32 gene in a Sicilian population, as the interpopulation variation in CCR5 delta32 frequency may be a significant factor in the prediction of AIDS endemicity in future studies. We examined 901 healthy individuals from several Sicilian provinces. We found a mean (+/- standard deviation) delta32 allele frequency (fr) of 0.04 +/- 0.012. The highest value was observed in the province of Messina, with a mean delta32 allele frequency of 0.06 +/- 0.024, where we collected samples from a cohort of 114 HIV-1-infected individuals. The observed frequency amongst these patients was quite low (fr = 0.03 +/- 0.031) compared to the healthy population, although the difference was not statistically significant.

  16. Observation of resonant energy transfer between identical-frequency laser beams

    SciTech Connect

    Afeyan, B. B.; Cohen, B. I.; Estabrook, K. G.; Glenzer, S. H.; Joshi, C.; Kirkwood, R. K.; Moody, J. D.; Wharton, K. B.

    1998-12-09

    Enhanced transmission of a low intensity laser beam is observed when crossed with an identical-frequency beam in a plasma with a flow velocity near the ion sound speed. The time history of the enhancement and the dependence on the flow velocity strongly suggest that this is due to energy transfer between the beams via a resonant ion wave with zero frequency in the laboratory frame. The maximum energy transfer has been observed when the beams cross in a region with Mach 1 flow. The addition of frequency modulation on the crossing beams is seen to reduce the energy transfer by a factor of two. Implications for indirect-drive fusion schemes are discussed.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Allele frequencies in the VRN-A1, VRN-B1 and VRN-D1 vernalization response and PPD-B1 and PPD-D1 photoperiod sensitivity genes, and their effects on heading in a diverse set of wheat cultivars (Triticum aestivum L.).

    PubMed

    Kiss, Tibor; Balla, Krisztina; Veisz, Ottó; Láng, László; Bedő, Zoltán; Griffiths, Simon; Isaac, Peter; Karsai, Ildikó

    2014-01-01

    Heading of cereals is determined by complex genetic and environmental factors in which genes responsible for vernalization and photoperiod sensitivity play a decisive role. Our aim was to use diagnostic molecular markers to determine the main allele types in VRN-A1, VRN-B1, VRN-D1, PPD-B1 and PPD-D1 in a worldwide wheat collection of 683 genotypes and to investigate the effect of these alleles on heading in the field. The dominant VRN-A1, VRN-B1 and VRN-D1 alleles were present at a low frequency. The PPD-D1a photoperiod-insensitive allele was carried by 57 % of the cultivars and was most frequent in Asian and European cultivars. The PPD-B1 photoperiod-insensitive allele was carried by 22 % of the genotypes from Asia, America and Europe. Nine versions of the PPD-B1-insensitive allele were identified based on gene copy number and intercopy structure. The allele compositions in PPD-D1, PPD-B1 and VRN-D1 significantly influenced heading and together explained 37.5 % of the phenotypic variance. The role of gene model increased to 39.1 % when PPD-B1 intercopy structure was taken into account instead of overall PPD-B1 type (sensitive vs. insensitive). As a single component, PPD-D1 had the most important role (28.0 % of the phenotypic variance), followed by PPD-B1 (12.3 % for PPD-B1_overall, and 15.1 % for PPD-B1_intercopy) and VRN-D1 (2.2 %). Significant gene interactions were identified between the marker alleles within PPD-B1 and between VRN-D1 and the two PPD1 genes. The earliest heading genotypes were those with the photoperiod-insensitive allele in PPD-D1 and PPD-B1, and with the spring allele for VRN-D1 and the winter alleles for VRN-A1 and VRN-B1. This combination could only be detected in genotypes from Southern Europe and Asia. Late-heading genotypes had the sensitivity alleles for both PPD1 genes, regardless of the allelic composition of the VRN1 genes. There was a 10-day difference in heading between the earliest and latest groups under field conditions.

  2. Frequency management and SETI: threats to SETI observations in the 1-3 GHz band

    NASA Astrophysics Data System (ADS)

    Hovde, Gloria K.

    2000-06-01

    The nature of a SETI search makes observations uniquely vulnerable to radio frequency interference because the frequency of a possible ETI signal is unknown. Sensitive radio telescopes, sophisticated software and enhanced signal detection equipment are employed to detect faint signals in the 1-3 GHz frequency range. Frequency management at SETI occurs within a policy environment of the ITU spectrum allocation process. Increased demand by commercial satellite services for access to spectrum adjacent to bandwidth allocated to radio astronomy creates severe international and domestic pressures on SETI observations. Strategies for addressing the RFI problem at the international level will be discussed that include a contingency ITU allocation plan for exclusive use of a particular frequency range by SETI in the event a signal is detected. The lunar farside is, by international agreement, a radio quiet zone for use by radio astronomers. Protected from most human-generated emissions, a SETI radio telescope array on the lunar farside would provide reliable data with minimum interference.

  3. Low-frequency GMRT observations of the magnetic Bp star HR Lup (HD 133880)

    NASA Astrophysics Data System (ADS)

    George, Samuel J.; Stevens, Ian R.

    2012-06-01

    We present radio observations of the magnetic chemically peculiar Bp star HR Lup (HD 133880) at 647 and 277 MHz with the GMRT. At both frequencies the source is not detected but we are able to determine upper limits to the emission. The 647 MHz limits are particularly useful, with a 5σ value of 0.45 mJy. Also, no large enhancements of the emission were seen. The non-detections, along with previously published higher frequency detections, provide evidence that an optically thick gyrosynchrotron model is the correct mechanism for the radio emission of HR Lup.

  4. 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.

  5. 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.

  6. Torsion-bar antenna for low-frequency gravitational-wave observations.

    PubMed

    Ando, Masaki; Ishidoshiro, Koji; Yamamoto, Kazuhiro; Yagi, Kent; Kokuyama, Wataru; Tsubono, Kimio; Takamori, Akiteru

    2010-10-15

    We propose a novel type of gravitational-wave antenna, formed by two bar-shaped test masses and laser-interferometric sensors to monitor their differential angular fluctuations. This antenna has a fundamental sensitivity to low-frequency signals below 1 Hz, even with a ground-based configuration. In addition, it is possible to expand the observation band to a lower limit determined by the observation time, by using modulation and up-conversion of gravitational-wave signals by rotation of the antenna. The potential sensitivity of this antenna is superior to those of current detectors in a 1 mHz-10 Hz frequency band and is sufficient for observations of gravitational waves radiated from in-spiral and merger events of intermediate-mass black holes.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. Low Frequency Propagation and Observed Intensity Pattern of Jovian Radio Emissions

    NASA Astrophysics Data System (ADS)

    Lecacheux, A.

    Low frequency radio emissions from Jupiter have been extensively observed by sev- eral spacecraft (Voyager, Ulysses, Galileo and, more recently, Cassini), but some of their basic properties (exact location, radiation pattern) are still in discussion or just inferred. The whole set of observations were carried out within a few degrees from the Jovian equatorial plane (with the only exception of Ulysses in its outbound trajectory). As a consequence, radio sources were usually observed after propagation through the Io plasma torus, whose maximum critical frequency (about 0.5 MHz) is comparable in magnitude to the frequency range of HOM (hectometric) and DAM (decametric) components. One can expect several kinds of propagation effects: at small scales, in- cluding diffractive scintillation linked to turbulence properties of the medium, and at large scales, due to refraction by the Io torus, which optically acts as a diverging lens. The aim of this presentation is to examine the latter kind of effects and, in particu- lar, to quantitatively assess the spatial distribution of intensity from a small radiating source at Jupiter, when observed far from the planet through the Io plasma torus. A specific ray tracing calculation in dispersive inhomogeneous plasma was developped for this purpose, allowing the computation of both ray trace and ray intensity along its path. The method permits the determination of spatial directions from where one can observe intensity reduction (shadow zone) as well as intensity amplification (focusing and caustics) of radiation from a point source. While highly depending on the accu- racy of the used Io torus electron density model, the performed calculations show that substantial intensity drops and rises are to be expected in the lower frequency range up to several MHz. This may provide an alternative explanation for the absorption band recently described in the literature as a permanent feature of the HOM emission.

  12. 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.

  13. 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.; Calistro Rivera, G.; 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.

    2016-12-01

    The Lockman Hole is a well-studied extragalactic field with extensive multi-band ancillary data covering a wide range in frequency, essential for characterizing 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 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.

  14. 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.

  15. Observation of fundamental thermal noise in optical fibers down to infrasonic frequencies

    NASA Astrophysics Data System (ADS)

    Dong, Jing; Huang, Junchao; Li, Tang; Liu, Liang

    2016-01-01

    The intrinsic thermal noise in optical fibers represents the ultimate limit for fiber-based systems. However, at infrasonic frequencies, the spectral behavior of the intrinsic thermal noise is still unclear. In this letter, we present measurements of the fundamental thermal noise in optical fibers that are obtained using a balanced fiber Michelson interferometer. When an ultra-stable laser is used as the laser source and other noise sources are carefully controlled, the 1/f spectral density of the thermal noise is observed down to infrasonic frequencies, and the measured magnitude is consistent with the results of theoretical predictions at frequencies over the range from 0.2 Hz to 20 kHz. Moreover, as observed experimentally, the level of the 1/f thermal noise can be reduced by changing the coatings of the optical fibers. This therefore indicates one possible way to reduce thermal noise in optical fibers at low Fourier frequencies. Finally, the inconsistency between the experimental data and the existing theory for thermomechanical noise is discussed.

  16. Unusually high frequency natural VLF radio emissions observed during daytime in Northern Finland

    NASA Astrophysics Data System (ADS)

    Manninen, Jyrki; Turunen, Tauno; Kleimenova, Natalia; Rycroft, Michael; Gromova, Liudmila; Sirviö, Iina

    2016-12-01

    Geomagnetic field variations and electromagnetic waves of different frequencies are ever present in the Earth’s environment in which the Earth’s fauna and flora have evolved and live. These waves are a very useful tool for studying and exploring the physics of plasma processes occurring in the magnetosphere and ionosphere. Here we present ground-based observations of natural electromagnetic emissions of magnetospheric origin at very low frequency (VLF, 3-30 kHz), which are neither heard nor seen in their spectrograms because they are hidden by strong impulsive signals (sferics) originating in lightning discharges. After filtering out the sferics, peculiar emissions are revealed in these digital recordings, made in Northern Finland, at unusually high frequencies in the VLF band. These recently revealed emissions, which are observed for several hours almost every day in winter, contain short (˜1-3 min) burst-like structures at frequencies above 4-6 kHz, even up to 15 kHz; fine structure on the 1 s time scale is also prevalent. It seems that these whistler mode emissions are generated deep inside the magnetosphere, but the detailed nature, generation region and propagation behaviour of these newly discovered high latitude VLF emissions remain unknown; however, further research on them may shed new light on wave-particle interactions occurring in the Earth’s radiation belts.

  17. HS1,2 Ig enhancer alleles association to AIDS progression in a pediatric cohort infected with a monophyletic HIV-strain.

    PubMed

    Montesano, Carla; Giambra, Vincenzo; Frezza, Domenico; Palma, Paolo; Serone, Eliseo; Gattinara, Guido Castelli; Mattei, Maurizio; Mancino, Giorgio; Colizzi, Vittorio; Amicosante, Massimo

    2014-01-01

    Alteration in the humoral immune response has been observed during HIV infection. The polymorphisms of enhancer HS1,2, member of the 3(') regulatory region of the Ig heavy chain cluster, may play a role in the variation of the humoral response leading to pathological conditions. To assess the role of the HS1,2 polymorphic variants in the progression of AIDS, the HS1,2-A allelic frequencies were investigated in a cohort of HIV infected pediatric subjects from a nosocomial outbreak with a monophyletic strain of HIV. From a total group of 418 HIV infected children in the outbreak cohort, 42 nonprogressors and 31 progressors without bias due to antiretroviral therapy were evaluated. HS1,2 allele (∗)1 has been associated with nonprogressors (allelic frequency: 51.19% versus 33.87% in progressors, OR 0.5, and P = 0.0437), while allele (∗)2 has been associated with progression (allelic frequency: 48.39% versus 30.95% in nonprogressors, OR 2.1, and P = 0.0393). Further, only subjects carrying allele (∗)2 in absence of allele (∗)1, either in homozygous condition for allele (∗)2 [nonprogressors 2/42 (4.76%), Progressors 7/31 (22.58%), OR 5.8, and P = 0.0315] or in combination with other allelic variants [nonprogressors 7/42 (16.67%), Progressors 13/31 (41.93%), OR 3.61, and P = 0.0321], have been associated with HIV progression to AIDS. In conclusion, while the HS1,2 allele (∗)1 has a protective effect on HIV progression when present, allele (∗)2 is associated with progression toward AIDS when allele (∗)1 is absent.

  18. Quasi-simultaneous five-frequency VLBA observations of PKS 0528+134

    NASA Astrophysics Data System (ADS)

    Cai, H.-B.; Shen, Z.-Q.; Chen, X.; Shang, L.-L.

    2006-11-01

    We present results of Very Long Baseline Array (VLBA) observations of PKS 0528+134 at five frequencies (2.3, 5.0, 8.4, 15.4, and 22.2 GHz). These quasi-simultaneous data enable us to study the spectral distribution of Very Long Baseline Interferometer (VLBI) components for the first time in this highly variable source, from which the central compact core is identified. Our observations indicate that there are two bendings for the jet motion at parsec scale. We provide an approximate spatial fit to the curved jet trajectory using the Steffen et al. (1995) helical model. We further investigate the proper motions of three jet components, which all show superluminal motion. At high frequencies (15.4 and 22.2 GHz) we detected a new component, which is estimated to be related to a radio burst peaking at about 2000.

  19. 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.

  20. Comparison between simultaneous GOLF and MDI observations in search of low frequency solar oscillations

    NASA Astrophysics Data System (ADS)

    Henney, Carl John

    One of the mission objectives of both the Global Oscillations at Low Frequency (GOLF) and the Michelson Doppler Imager (MDI) instruments aboard the Solar and Heliospheric Observatory (SOHO) is the detection of new low frequency globally coherent solar oscillation modes. After more than two years of nearly continuous observing by both instruments, the clear detection of modes below 1200 μHz has still proven to be elusive. The search for new modes is aided here by combining the high duty cycle of GOLF with the spatial resolution and various data products of MDI. By combining the two data sets, a signal enhancement is anticipated since both instruments provide a low noise data stream and their sources of solar and instrumental noise are expected to be different from each other. Presented here is a comparison between the observed GOLF signal and a selection of spatially masked MDI full-disk signals for a 759 day period from May 25, 1996 through June 22, 1998. The signal-to-background ratio is compared between the various signals for low degree (l <= 3) and low frequency (<2000 μHz) p-modes. It was found that signals from both MDI and GOLF are beneficial for detecting these p-modes. Cross-analysis between GOLF and MDI signals is done to enhance the ability to detect low frequency solar oscillations. Using cross-amplitude and averaged power spectra, an unique list of low degree modes is presented here, along with three new low frequency acoustic mode candidates. Finally, the effects of early main sequence cometary mass accretion with heavy-element diffusion on the solar interior are investigated. For solar models with element diffusion, the addition of mass accretion with a rate suggested by observations of other stars has a negligible effect on the predicted p-mode frequencies for the cases investigated here. The predicted g-mode frequencies exhibit a slight shift of approximately 0.1 μHz with the addition of mass accretion. Compared to previous work, the squared

  1. Relative acoustic frequency response of induced methane, carbon dioxide and air gas bubble plumes, observed laterally.

    PubMed

    Kubilius, Rokas; Pedersen, Geir

    2016-10-01

    There is an increased need to detect, identify, and monitor natural and manmade seabed gas leaks. Fisheries echosounders are well suited to monitor large volumes of water and acoustic frequency response [normalized acoustic backscatter, when a measure at one selected frequency is used as a denominator, r(f)] is commonly used to identify echoes from fish and zooplankton species. Information on gas plume r(f) would be valuable for automatic detection of subsea leaks and for separating bubble plumes from natural targets such as swimbladder-bearing fish. Controlled leaks were produced with a specially designed instrument frame suspended in mid-water in a sheltered fjord. The frame was equipped with echosounders, stereo-camera, and gas-release nozzles. The r(f) of laterally observed methane, carbon dioxide, and air plumes (0.040-29 l/min) were measured at 70, 120, 200, and 333 kHz, with bubble sizes determined optically. The observed bubble size range (1-25 mm) was comparable to that reported in the literature for natural cold seeps of methane. A negative r(f) with increasing frequency was observed, namely, r(f) of about 0.7, 0.6, and 0.5 at 120, 200, and 333 kHz when normalized to 70 kHz. Measured plume r(f) is also compared to resolved, single bubble target strength-based, and modeled r(f).

  2. 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.

  3. High Frequency Plasma Waves Associated With Solar Wind Reconnection Exhausts: WIND/WAVES Observations

    NASA Astrophysics Data System (ADS)

    Huttunen, K. E.; Bale, S. D.; Phan, T. D.; Davis, M.; Gosling, J. T.

    2006-12-01

    Observations of strong plasma wave activity near reconnection X-line regions in THE laboratory and in the Earth's magnetosphere have suggested that plasma waves may play AN important role in the reconnection process by providing anomalous resistivity through wave-particle interactions and by accelerating electrons. Recent observations of quasi-steady magnetic reconnection in the solar wind introduces an important new environment to study the role of plasma waves in a collisionless plasma associated with the reconnection process. We have used observations by the WIND spacecraft to study high frequency plasma waves associated with 28 solar wind reconnection exhausts. The TNR (Thermal Noise Receiver) experiment included in the WAVES instrument on WIND measures electric spectral density from 4 to 256 kHz and the TDS (Time Domain Sampler) experiment also included in WAVES samples electric field waveforms at rates up to 120,000 samples/s. A large fraction (79%) of the investigated events showed significant enhancements in the wave power around ~ 4 kHz, while only about one third (39%) of the exhausts were associated with intensifications around THE local electron plasma frequency (few tens of kHz). TDS waveform samples revealed three different wave modes: electron solitary waves, ion acoustic waves and Langmuir waves. The intense plasma waves were most frequently observed close to the X-line and near the exhaust boundaries, although wave emissions were commonly observed elsewhere within the exhausts as well

  4. 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

  5. The observations of Low Frequency Zonal Flow in electrode biasing experiments on J-TEXT tokamak

    NASA Astrophysics Data System (ADS)

    Shen, H. G.; Kong, D. F.; Zhao, H. L.; Wu, J.; Lan, T.; Liu, W. D.; Yu, C. X.; Sun, Y.; Liu, H.; Chen, Z. P.; Zhuang, G.; USTC Team; HUST Team

    2013-10-01

    The long-distance correlations features of potential and density fluctuations during electrode biasing (EB) have been investigated using Langmuir probe arrays in the edge of J-TEXT tokamak. During the positive edge EB, both floating potential and density fluctuations in the high frequency ambient turbulence (AT) region are suppressed and radial particle flux is decreased. But no obvious change occurs during the negative edge EB. In the positive EB cases, toroidal and poloidal long-distance correlations of floating potentials increase in the low frequency regions of f < 3 kHz and no distinct long-distance correlations is found in density fluctuations. It shows that this low frequency long-distance correlation mode is low frequency zonal flow (LFZF). In the meantime, strong Er × B shearing is observed when applying a positive EB. The results also suggests that the LFZF may be induced by AT and then regulate the AT amplitude. Supported by NNSFC (Nos. 10990210,10990211,10335060 and 10905057), CPSF (No. 20080440104), YIF (No. WK2030040019) and KIPCAS (No. kjcx-yw-n28).

  6. 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.

  7. 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

  8. 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.

  9. A theory for low-frequency waves observed at comet Giacobini-Zinner

    NASA Technical Reports Server (NTRS)

    Goldstein, M. L.; Wong, H. K.

    1987-01-01

    As the ICE spacecraft approached comet Giacobini-Zinner, low-frequency waves in two frequency ranges were observed in the magnetic field data. Under certain conditions, a gyrating beam of water group ions is capable of generating electromagnetic waves with periods near 100 s (in the spacecraft frame of reference) and shorter-period whistler branch waves with periods near 3 s. The 100-s wave can arise from either a nonresonant firehose instability or a resonant beam driven instability so long as the angle between the directions of the local magnetic field and solar wind velocity is less than 90 percent. Whenever that angle exceeds about 30 percent, the gyrating ring distribution formed by newly ionized water is also unstable to the generation of whistler waves with 3-s periods.

  10. Temporal and spatial trends in allozyme frequencies in house fly populations, Musca domestica L.

    PubMed

    Black, W C; Krafsur, E S

    1986-02-01

    Allelic and genotypic frequencies were sampled from a single age class of the common house fly, Musca domestica L., at five farms on six dates from July 6 to October 12, 1982. Allozymes at six loci were resolved with vertical polyacrylamide gel electrophoresis. No consistent departures from random mating were detected. No consistent linkage disequilibrium was observed. Allele frequencies at the farms changed in independent and unpredictable ways. Gene frequencies at the five farms were initially divergent, converged in midsummer, and then progressively diverged. The divergence occured in mid-August when fly populations were large. Variation in gene frequencies at adjacent farms accounted for a large proportion of the variance in allele frequencies among all farms. These observations are consistent with the hypothesis that allele frequencies in young adult flies reflected the habitat in which they matured as larvae.

  11. Convective weather events in high-frequency Eulerian observations and model column outputs

    NASA Astrophysics Data System (ADS)

    Mapes, B.

    2006-05-01

    Convective cloud systems produce large fractions of the Earth's rainfall. High-frequency Eulerian time-height datasets containing such convective storm passages permit clean, objective comparisons between observations and model output. Lagged regressions of these datasets vs. surface rainfall are used to depict the characteristic structure of precipitating disturbances, mainly in the wet tropics. Both observations and models have organized convective rain events with time scales of many hours, even though convection parameterizations (and arguably cumulus cells in nature) operate column by column and typically have no long-time memory. However, different models have very different characteristic structures: very different from observations (which are fairly similar from place to place), and very different from other models. Experiments with single-column versions suggest that this characteristic structure stems largely from the physical parameterizations.

  12. 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

  13. 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° .

  14. Novel microsatellite markers for the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) and effects of null alleles on population genetics analyses.

    PubMed

    Song, W; Cao, L-J; Wang, Y-Z; Li, B-Y; Wei, S-J

    2016-11-07

    The oriental fruit moth (OFM) Grapholita molesta (Lepidoptera: Tortricidae) is an important economic pest of stone and pome fruits worldwide. We sequenced the OFM genome using next-generation sequencing and characterized the microsatellite distribution. In total, 56,674 microsatellites were identified, with 11,584 loci suitable for primer design. Twenty-seven polymorphic microsatellites, including 24 loci with trinucleotide repeat and three with pentanucleotide repeat, were validated in 95 individuals from four natural populations. The allele numbers ranged from 4 to 40, with an average value of 13.7 per locus. A high frequency of null alleles was observed in most loci developed for the OFM. Three marker panels, all of the loci, nine loci with the lowest null allele frequencies, and nine loci with the highest null allele frequencies, were established for population genetics analyses. The null allele influenced estimations of genetic diversity parameters but not the OFM's genetic structure. Both a STRUCTURE analysis and a discriminant analysis of principal components, using the three marker panels, divided the four natural populations into three groups. However, more individuals were incorrectly assigned by the STRUCTURE analysis when the marker panel with the highest null allele frequency was used compared with the other two panels. Our study provides empirical research on the effects of null alleles on population genetics analyses. The microsatellites developed will be valuable markers for genetic studies of the OFM.

  15. 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.

  16. Selective observation of starch in a water plant using optical sum-frequency microscopy

    NASA Astrophysics Data System (ADS)

    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.

  17. 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.

  18. 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...

  19. 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

  20. Commensal low frequency observing on the NRAO VLA: VLITE status and future plans

    NASA Astrophysics Data System (ADS)

    Clarke, Tracy E.; Kassim, Namir E.; Brisken, Walter; Helmboldt, Joseph; Peters, Wendy; Ray, Paul S.; Polisensky, Emil; Giacintucci, Simona

    2016-08-01

    The National Radio Astronomy Observatory's 27 antenna Karl G. Jansky Very Large Array (NRAO VLA) has been successfully transitioned to a broadband system. As part of this transition, the US Naval Research Laboratory (NRL) worked with NRAO to develop, install, and commission a new commensal low frequency system on the VLA. The VLA Low-band Ionosphere and Transient Experiment (VLITE) has dedicated samplers and uses spare NRAO optical fibers to transmit the signal from 10 low band receivers on VLA antennas to a dedicated real-time DiFX correlator. For these 10 antennas, this observing mode provides simultaneous data from both the low frequency receivers through the VLITE correlator and from the VLA higher frequencies receivers (1-50 GHz) through the NRAO WIDAR correlator. During the first 1.5 years of operation, VLITE recorded data at roughly 70% wall-time, providing 64 MHz of bandwidth centered at 352 MHz with 2s sample time and 100 kHz spectral resolution. VLITE operations require no additional resources from the VLA system and greatly expand the capabilities of the VLA through value-added PI science, stand-alone astrophysics, the opening of a new window on transient searches, and serendipity. We present an overview of the VLITE program, discuss the sky coverage and depth obtained during the first 1.5 years of operation, and brie y outline a possible path forward to a full 27 antenna LOw Band Observatory (LOBO) which could run commensally with all VLA operations.

  1. Van Allen Probes observations of cross-scale coupling between electromagnetic ion cyclotron waves and higher-frequency wave modes

    NASA Astrophysics Data System (ADS)

    Colpitts, C. A.; Cattell, C. A.; Engebretson, M.; Broughton, M.; Tian, S.; Wygant, J.; Breneman, A.; Thaller, S.

    2016-11-01

    We present observations of higher-frequency ( 50-2500 Hz, 0.1-0.7 fce) wave modes modulated at the frequency of colocated lower frequency (0.5-2 Hz, on the order of fci) waves. These observations come from the Van Allen Probes Electric Field and Waves instrument's burst mode data and represent the first observations of coupling between waves in these frequency ranges. The higher-frequency wave modes, typically whistler mode hiss and chorus or magnetosonic waves, last for a few to a few tens of seconds but are in some cases observed repeatedly over several hours. The higher-frequency waves are observed to be unmodulated before and after the presence of the electromagnetic ion cyclotron (EMIC) waves, but when the EMIC waves are present, the amplitude of the higher-frequency waves drops to the instrument noise level once every EMIC wave cycle. Such modulation could significantly impact wave-particle interactions such as acceleration and pitch angle scattering, which are crucial in the formation and depletion of the radiation belts. We present one case study with broadband, high-frequency waves observed to be modulated by EMIC waves repeatedly over a 2 h time span on both spacecraft. Finally, we show two additional case studies where other high-frequency wave modes exhibit similar modulation.

  2. [Possible causes and consequences of the spread of individual allelic variants of the BoLA-DRB3 locus in groups of Holstein and Ayrshire cattle].

    PubMed

    Kovaliuk, N V; Satsuk, V F; Matviets, A V; Machul'skaia, E V

    2010-03-01

    The frequencies of polymorphic variants of the BoLA-DRB3 locus have been estimated in groups of Holstein and Ayrshire bull sires. Considerably increased frequencies of individual alleles have been found in some groups of cattle, depending on the breed and breeding value. The possible causes and consequences of the observed relationships have been analyzed.

  3. HLA DRB1 alleles and hepatitis C virus infection in chronic kidney disease patients.

    PubMed

    Shaheen, Noha Mohamed Hosni; Soliman, Amin Roshdy; El-Khashab, Sahier Omar; Hanna, Mariam Onsy Farag

    2013-01-01

    T cell responses against HCV are regulated by the host's human leukocyte antigen (HLA) alleles, which thus are ideal candidate genes to investigate for associations with HCV susceptibility. We aimed to identify associations of HLA DRB1* alleles with HCV infection in a high risk of exposure population, chronic kidney disease (CKD) patients on dialysis, and to study any possible relationships with allele zygosity. The study population comprised 110 HCV infected and 143 HCV uninfected CKD patients undergoing regular hemodialysis. HLA DRB1* alleles were determined using polymerase chain reaction followed by hybridization with sequence-specific oligonucleotide probes. We found a significant negative association between HLA DRB1*03 and HCV infection, but the association did not retain significance after adjustment for multiple comparisons. HLA DRB1*03 was found at reduced frequency in HCV antibody positive compared to HCV antibody negative CKD patients on regular dialysis (corrected p was not significant). No significant association between HCV infection and HLA DRB1* zygosity was observed. Our results suggest that there is minimal evidence for a significant role of a particular HLA DRB1* allele or allele zygosity in the susceptibility or protection to HCV in high-risk hemodialysis patients with similar exposure to infection.

  4. Glucose dehydrogenase polymorphism among ethnic groups of Singapore--with report of two additional alleles (GDH4 and GDH5).

    PubMed

    Saha, N; Bhattacharyya, S P; Yeoh, S C; Chua, S P; Ratnam, S S

    1987-02-01

    Placental glucose dehydrogenase (GDH; E.C.1.1.1.47) polymorphism was studied in 254 Chinese, 104 Malays, and 47 Indians from Singapore using isoelectric focusing. There is suggestive evidence of two additional anodal alleles (GDH4 and GDH5) in addition to the three alleles described in earlier studies. Altogether, 14 phenotypes have been observed in the present investigation, compared with six phenotypes described in earlier studies. It appears that placental GDH is controlled by five codominant autosomal alleles producing 15 possible phenotypes. The gene frequencies of GDH1, GDH2, and GDH3 in these ethnic groups are significantly different from those reported in Caucasians. There were slight differences in the gene frequencies between the three ethnic groups, with those of Indians being nearer to the frequency in Caucasians. In general, the distribution of GDH phenotypes was at Hardy-Weinberg equilibrium in all three ethnic groups studied.

  5. Observed frequency-independent torque in flagellar bacterial motors optimizes space exploration

    NASA Astrophysics Data System (ADS)

    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.

  6. 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.

  7. 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

  8. Comparison of Model Predictions and Laboratory Observations of Transgene Frequencies in Continuously-Breeding Mosquito Populations

    PubMed Central

    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

  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

    2016-09-22

    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.

  10. 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.

  11. No evidence for strong recent positive selection favoring the 7 repeat allele of VNTR in the DRD4 gene.

    PubMed

    Naka, Izumi; Nishida, Nao; Ohashi, Jun

    2011-01-01

    The human dopamine receptor D4 (DRD4) gene contains a 48-bp variable number of tandem repeat (VNTR) in exon 3, encoding the third intracellular loop of this dopamine receptor. The DRD4 7R allele, which seems to have a single origin, is commonly observed in various human populations and the nucleotide diversity of the DRD4 7R haplotype at the DRD4 locus is reduced compared to the most common DRD4 4R haplotype. Based on these observations, previous studies have hypothesized that positive selection has acted on the DRD4 7R allele. However, the degrees of linkage disequilibrium (LD) of the DRD4 7R allele with single nucleotide polymorphisms (SNPs) outside the DRD4 locus have not been evaluated. In this study, to re-examine the possibility of recent positive selection favoring the DRD4 7R allele, we genotyped HapMap subjects for DRD4 VNTR, and conducted several neutrality tests including long range haplotype test and iHS test based on the extended haplotype homozygosity. Our results indicated that LD of the DRD4 7R allele was not extended compared to SNP alleles with the similar frequency. Thus, we conclude that the DRD4 7R allele has not been subjected to strong recent positive selection.

  12. 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.

  13. Low-frequency radio observations of Seyfert galaxies: A test of the unification scheme

    NASA Astrophysics Data System (ADS)

    Singh, V.; Shastri, P.; Ishwara-Chandra, C. H.; Athreya, R.

    2013-06-01

    Aims: We present low-frequency radio imaging and spectral properties of a well-defined sample of Seyfert galaxies using GMRT 240/610 MHz dual frequency observations. Radio spectra of Seyfert galaxies over 240 MHz to 5.0 GHz are investigated using 240 MHz, 610 MHz flux densities derived from GMRT, and 1.4 GHz and 5.0 GHz flux densities mainly from published VLA data. We test the predictions of Seyfert unification scheme by comparing the radio properties of Seyfert type 1s and type 2s. Methods: We chose a sample such that the two Seyferts subtypes have matched distributions in parameters that are independent of the orientation of AGN, obscuring torus, and the host galaxy. Our sample selection criteria allowed us to assume that the two Seyfert subtypes are intrinsically similar within the framework of the unification scheme. Results: The new observations at 240/610 MHz, together with archival observations at 1.4 GHz, 5.0 GHz show that types 1s and 2s have statistically similar radio luminosity distributions at 240 MHz, 610 MHz, 1.4 GHz, and 5.0 GHz. The spectral indices at selected frequency intervals (α240 MHz610 MHz, α610 MHz1.4 GHz, and α1.4 GHz5.0 GHz), as well as index measured over 240 MHz to 5.0 GHz (αint) for the two Seyfert subtypes, have similar distributions with median spectral index (α) ~ -0.7 (Sν ∝ να), consistent with the synchrotron emission from optically thin plasma. In our snapshot 240/610 MHz GMRT observations, most of the Seyfert galaxies primarily show an unresolved central radio component, except for a few sources in which faint kpc-scale extended emission is apparent at 610 MHz. Our results on the statistical comparison of the multifrequency radio properties of our sample Seyfert galaxies agree with the predictions of the Seyfert unification scheme. Figures 2, 4 and Appendix A are available in electronic form at http://www.aanda.org

  14. Distribution of HLA-DRB1 and HLA-DQB1 alleles in Lak population of Iran.

    PubMed

    Varzi, Ali Mohammad; Shahsavar, Farhad; Tarrahi, Mohammad Javad

    2016-07-01

    Human leukocyte antigen (HLA) genes are the most polymorphic loci in the human genome and encode the highly polymorphic molecules critically involved in immune responses. Anthropological studies based on highly polymorphic HLA genes provide useful information for bone marrow donor registry, forensic medicine, disease association studies, as well as designing peptide vaccines against tumors, and infectious or autoimmune diseases. The aim of this study was to determine the HLA-DRB1 and HLA-DQB1 allele frequencies in 100 unrelated Lak individuals from Lorestan province of Iran. Finally, we compared the results with those previously described in four other Iranian populations. Commercial HLA-Type kits were used for determination of the HLA-DRB1 and HLA-DQB1 allele frequencies. Differences between populations in the distribution of HLA-DRB1 and HLA-DQB1 alleles were estimated by χ2 test with Yate's correction and Fisher's exact test. The most frequent HLA-DRB1 alleles were (*)1103=4 (23%), (*)1502 (9.5%), (*)0701 (9%), (*)0301 (8.5%), (*)1101 (7.5%) and (*)1501 (6%) while HLA-DQB1(*)0301 (40%), (*)0201 (15%), (*)0502 (10.5%), (*)0303 (10%), (*)0602=3 (9.5%), and (*)0501 (7.5%) were the most frequent alleles in Lak population. HLA-DRB1(*)0409, (*)0804, (*)1102, (*)1112, (*)1405, and HLA-DQB1(*)0503, (*)0604 were the least observed frequencies in Lak population. Our results based on HLA-DRB1 and HLA-DQB1 allele frequencies showed that the Lak population possesses the previously reported general features of the Lur and Kurd populations but still with unique, decreased or increased frequencies of several alleles. In other words, the Lak population is close to Lurs Khorramabadi and Kurd but far from Lurs Kohkiloyeh/Boyerahmad and Bakhtiari.

  15. Research Article. Improved Dual Frequency PPP Model Using GPS and BeiDou Observations

    NASA Astrophysics Data System (ADS)

    Afifi, A.; El-Rabbany, A.

    2017-02-01

    This paper introduces a new dual-frequency precise point positioning (PPP) model, which combines GPS and BeiDou observations. Combining GPS and BeiDou observations in a PPP model offers more visible satellites to the user, which is expected to enhance the satellite geometry and the overall PPP solution in comparison with GPSonly PPP solution. However, combining different GNSS constellations introduces additional biases, which require rigorous modelling, including GNSS time offset and hardware delays. In this research, ionosphere-free linear combination PPP model is developed. The additional biases, which result from combining the GPS and BeiDou observables, are lumped into a new unknown parameter identified as the inter-system bias. Natural Resources Canada's GPSPace PPP software is modified to enable a combined GPS/BeiDou PPP solution and to handle the newly introduced biases. A total of four data sets at four IGS stations are processed to verify the developed PPP model. Precise satellite orbit and clock products from the IGS-MGEX network are used to correct both of the GPS and BeiDou measurements. It is shown that a sub-decimeter positioning accuracy level and 25% reduction in the solution convergence time can be achieved with combining GPS and Bei-Dou observables in a PPP model, in comparison with the GPS-only PPP solution.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  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. 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.

  2. 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.

  3. HIGH DYNAMIC RANGE OBSERVATIONS OF SOLAR CORONAL TRANSIENTS AT LOW RADIO FREQUENCIES WITH A SPECTRO-CORRELATOR

    SciTech Connect

    Hariharan, K.; Ramesh, R.; Kathiravan, C.; Rajalingam, M.; Abhilash, H. N.

    2016-02-15

    A new antenna system with a digital spectro-correlator that provides high temporal, spectral, and amplitude resolutions has been commissioned at the Gauribidanur Observatory near Bangalore in India. Presently, it is used for observations of the solar coronal transients in the scarcely explored frequency range ≈30–15 MHz. The details of the antenna system, the associated receiver setup, and the initial observational results are reported. Some of the observed transients exhibited quasi-periodicity in their time profiles at discrete frequencies. Estimates of the associated magnetic field strength (B) indicate that B ≈ 0.06–1 G at a typical frequency such as 19.5 MHz.

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

    PubMed

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

    2011-08-02

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

  5. Observation of ion-cyclotron-frequency mode-conversion flow drive in tokamak plasmas.

    PubMed

    Lin, Y; Rice, J E; Wukitch, S J; Greenwald, M J; Hubbard, A E; Ince-Cushman, A; Lin, L; Porkolab, M; Reinke, M L; Tsujii, N

    2008-12-05

    Strong toroidal flow (Vphi) and poloidal flow (Vtheta) have been observed in D-3He plasmas with ion cyclotron range of frequencies (ICRF) mode-conversion (MC) heating on the Alcator C-Mod tokamak. The toroidal flow scales with the rf power Prf (up to 30 km/s per MW), and is significantly larger than that in ICRF minority heated plasmas at the same rf power or stored energy. The central Vphi responds to Prf faster than the outer regions, and the Vphi(r) profile is broadly peaked for r/a < or =0.5. Localized (0.3 < or = r/a < or =0.5) Vtheta appears when Prf > or =1.5 MW and increases with power (up to 0.7 km/s per MW). The experimental evidence together with numerical wave modeling suggests a local flow drive source due to the interaction between the MC ion cyclotron wave and 3He ions.

  6. Picosecond laser-induced breakdown at 5321 and 5347 A - Observation of frequency-dependent behavior

    NASA Technical Reports Server (NTRS)

    Smith, W. L.; Bechtel, J. H.; Bloembergen, N.

    1977-01-01

    A study is presented of picosecond laser-induced breakdown at 3547 and 5321 A of several materials. The thresholds obtained for breakdown at 5321 A are compared to previous results obtained at 1.064 microns using the same laser system. This comparison illustrates the transition of bulk laser-induced breakdown as it becomes increasingly frequency dependent. UV picosecond pulses are obtained by mixing 5321 A and 1.064 micron pulses in a KH2PO4 crystal. Upper and lower bounds on the 3547 A breakdown threshold are defined, although some effects of walk-off distortion and self-focusing are observed. The results are discussed with reference to models for the intrinsic processes involved in the breakdown, i.e., avalanche and multiphoton ionization.

  7. 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.

  8. 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.

  9. 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).

  10. MAVEN Observation of an Obliquely Propagating Low-Frequency Wave Upstream of Mars

    NASA Technical Reports Server (NTRS)

    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.

    2016-01-01

    We report Mars Atmosphere and Volatile EvolutioN (MAVEN) 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.

  11. EXPLORATION OF SOURCE FREQUENCY PHASE REFERENCING TECHNIQUES FOR ASTROMETRY AND OBSERVATIONS OF WEAK SOURCES WITH HIGH FREQUENCY SPACE VERY LONG BASELINE INTERFEROMETRY

    SciTech Connect

    Rioja, M.; Dodson, R.; Malarecki, J.; Asaki, Y.

    2011-11-15

    Space very long baseline interferometry (S-VLBI) observations at high frequencies hold the prospect of achieving the highest angular resolutions and astrometric accuracies, resulting from the long baselines between ground and satellite telescopes. Nevertheless, space-specific issues, such as limited accuracy in the satellite orbit reconstruction and constraints on the satellite antenna pointing operations, limit the application of conventional phase referencing. We investigate the feasibility of an alternative technique, source frequency phase referencing (SFPR), to the S-VLBI domain. With these investigations we aim to contribute to the design of the next generation of S-VLBI missions. We have used both analytical and simulation studies to characterize the performance of SFPR in S-VLBI observations, applied to astrometry and increased coherence time, and compared these to results obtained using conventional phase referencing. The observing configurations use the specifications of the ASTRO-G mission for their starting point. Our results show that the SFPR technique enables astrometry at 43 GHz, using alternating observations with 22 GHz, regardless of the orbit errors, for most weathers and under a wide variety of conditions. The same applies to the increased coherence time for the detection of weak sources. Our studies show that the capability to carry out simultaneous dual frequency observations enables application to higher frequencies, and a general improvement of the performance in all cases, hence we recommend its consideration for S-VLBI programs.

  12. 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.

  13. 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

  14. A maximum-likelihood method to correct for allelic dropout in microsatellite data with no replicate genotypes.

    PubMed

    Wang, Chaolong; Schroeder, Kari B; Rosenberg, Noah A

    2012-10-01

    Allelic dropout is a commonly observed source of missing data in microsatellite genotypes, in which one or both allelic copies at a locus fail to be amplified by the polymerase chain reaction. Especially for samples with poor DNA quality, this problem causes a downward bias in estimates of observed heterozygosity and an upward bias in estimates of inbreeding, owing to mistaken classifications of heterozygotes as homozygotes when one of the two copies drops out. One general approach for avoiding allelic dropout involves repeated genotyping of homozygous loci to minimize the effects of experimental error. Existing computational alternatives often require replicate genotyping as well. These approaches, however, are costly and are suitable only when enough DNA is available for repeated genotyping. In this study, we propose a maximum-likelihood approach together with an expectation-maximization algorithm to jointly estimate allelic dropout rates and allele frequencies when only one set of nonreplicated genotypes is available. Our method considers estimates of allelic dropout caused by both sample-specific factors and locus-specific factors, and it allows for deviation from Hardy-Weinberg equilibrium owing to inbreeding. Using the estimated parameters, we correct the bias in the estimation of observed heterozygosity through the use of multiple imputations of alleles in cases where dropout might have occurred. With simulated data, we show that our method can (1) effectively reproduce patterns of missing data and heterozygosity observed in real data; (2) correctly estimate model parameters, including sample-specific dropout rates, locus-specific dropout rates, and the inbreeding coefficient; and (3) successfully correct the downward bias in estimating the observed heterozygosity. We find that our method is fairly robust to violations of model assumptions caused by population structure and by genotyping errors from sources other than allelic dropout. Because the data sets

  15. Analysis of allelic variation of the apolipoprotein B hypervariable locus in the Bashkir and Komi populations

    SciTech Connect

    Khusnutdinova, E.K.; Khidiatova, I.M.; Rafikov, H.S.

    1995-07-01

    Allelic variation of the hypervariable apolipoprotein B gene locus (APOB) in three groups of the Bashkir population and in the Komi population was analyzed. Among 219 individuals studied, 13 allelic variants were identified with a number of repeats ranging from 28 to 52. The frequency of alleles varied from 0.01 to 0.51 with the mean heterozygosity index being 0.66 in the Bashkir population and 0.74 in the Komi one. Considerable difference in the frequency distribution of the APOB loci genotypes between the Bashkir and Komi populations was observed, and the distribution patterns for Bashkirs from Abzelilovskii and Ilishevskii raions deviated from the Hardy-Weinberg equilibrium. The genetic distance between the Bashkir and Komi populations calculated on the basis of allele frequencies at the hypervariable APOB gene locus corresponded to the expected degree similarity of the population studied. Thus, this locus can be recommended as an informative marker for studying the gene pool and genetic processes in the populations because of the high level of its polymorphism and the heterozygosity in the populations. 19 refs., 1 fig., 4 tabs.

  16. Study of MICA alleles in 201 African Americans by multiplexed single nucleotide extension (MSNE) typing.

    PubMed

    Zhang, Yanzheng; Han, Mei; Vorhaben, Robert; Giang, Chris; Lavingia, Bhavna; Stastny, Peter

    2003-01-01

    We have developed a method for major histocompatibility complex class I chain-related gene A (MICA) genotyping using multiplexed single nucleotide extension (MSNE) and flow cytometric analysis of an array of fluorescent microspheres. This technique employs a polymerase chain reaction-derived target DNA containing all the polymorphic sites of MICA, synthetic complementary primers, biotinylated dideoxynucleotide triphosphate, fluorescent reporter molecules (streptavidin-phycoerythrin), and thermophilic DNA polymerase. Genomic DNA was amplified by MICA locus-specific primers and the MSNE reactions were carried out in the presence of 30 MSNE primers used to assay polymorphisms in exons 2, 3, and 4 of the MICA genes. Thirty-two previously typed cell lines were used as reference material. The MICA gene frequencies among 201 African-American unrelated donors were determined. Of 51 previously known alleles, 18 were observed in African-Americans, compared to 16 that were found in North American Caucasians and 9 in South American Indians, suggesting a more diversified allelic distribution in African-Americans. MICA*00201 and MICA*00801 were the two most frequent alleles in African-Americans. We observed a high degree of linkage disequilibrium between certain alleles of MICA and of human leukocyte antigen-B in the African-American population. The methodology described here offers a powerful new approach to DNA typing of the MICA alleles.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Preferential transmission of the MTHFR 677 T allele to infants with Down syndrome: implications for a survival advantage.

    PubMed

    Hobbs, Charlotte A; Cleves, Mario A; Lauer, Ronald M; Burns, Trudy L; James, S Jill

    2002-11-15

    We have examined the transmission frequencies of the methylenetetrahydrofolate reductase (MTHFR) 677 T and C alleles from heterozygous parents to children with Down syndrome (trisomy 21) in 202 Caucasian families. Our results indicated that the MTHFR 677T allele was transmitted to children with Down syndrome at a significantly higher rate than would be expected based on Mendelian inheritance patterns, and the C allele was transmitted at a significantly lower rate (P < 0.009). Transmission frequencies were also examined independently for maternally and paternally transmitted alleles to assess potential parent-of-origin effects. Because the vast majority of conceptions with trisomy 21 end in pregnancy loss, we questioned whether the observed preferential transmission of the T allele to this population of liveborn infants with Down syndrome could reflect a survival advantage. A plausible biochemical interpretation of these results is presented based on a maternal-fetal MTHFR 677T allele interaction in the context of the constitutive overexpression of three copies of the cystathionine beta synthase gene in the trisomy 21 fetus. Published 2002 Wiley-Liss, Inc.

  2. 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.

  3. Estimates of the radiation-induced mutation frequencies to recessive visible, dominant cataract and enzyme-activity alleles in germ cells of AKR, BALB/c, DBA/2 and (102xC3H)F1 mice.

    PubMed

    Pretsch, W; Favor, J; Lehmacher, W; Neuhäuser-Klaus, A

    1994-07-01

    Male mice of the genotypes AKR, BALB/c, (102/ElxC3H/El)F1 or DBA/2 were exposed to 3 + 3 Gy irradiation with a 24 h fractionation interval and mated to untreated Test-stock females. The offspring were screened for activity alterations of 10 erythrocyte enzymes as well as recessive specific-locus and dominant cataract mutations. The observed mutation rates per locus per gamete x 10(-5) for treated spermatogonia were 6.8, 4.9, 2.5 and 1.3 for enzyme-activity mutations, 8.6, 24.1, 22.8 and 31.4 for specific-locus mutations, and 0.7, 0.9, 0.6 and 2.5 for cataract mutations, respectively. Some variability from strain to strain in the frequency of radiation-induced mutations was observed. However, there was no consistent effect of genotype on the frequency of induced mutations and it is concluded that no effect of genetic background exists for the four genotypes tested. There is good agreement between the observed enzyme-activity mutation rate in children of survivors of the atomic bombings and the expected mutation rate based on results with mice. Results are therefore consistent with an estimation of human radiation-induced genetic risks based upon an extrapolation of experimental results in the mouse.

  4. Characterization of allele-specific expression of the X-linked gene MAO-A in trophectoderm cells of bovine embryos produced by somatic cell nuclear transfer.

    PubMed

    Ferreira, A R; Aguiar Filho, L F C; Sousa, R V; Sartori, R; Franco, M M

    2015-10-05

    Somatic cell nuclear transfer (SCNT) may affect epigenetic mechanisms and alter the expression of genes related to embryo development and X chromosome inactivation (XCI). We characterized allele-specific expression of the X-linked gene monoamine oxidase type A (MAO-A) in the trophectoderm (TF) of embryos produced by SCNT. Total RNA was isolated from individual biopsies (N = 25), and the allele-specific expression assessed by reverse transcription-polymerase chain reaction-restriction fragment length polymorphism. Both paternal and maternal alleles were expressed in the trophectoderm. However, a higher frequency of the mono-allelic expression of a specific allele was observed (N = 17; 68%), with the remaining samples showing the presence of mRNA from both alleles (N = 8; 32%). Considering that MAO-A is subject to XCI in bovine, our results suggest that SCNT may influence XCI because neither an imprinted (mono-allelic expression in all samples) nor a random (presence of mRNA from both alleles in all samples) pattern of XCI was observed in TF. Due to the importance of XCI in mammalian embryo development and its sensitivity to in vitro conditions, X-linked genes subject to XCI are candidates for use in the development of embryo quality molecular markers for assisted reproduction.

  5. 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

  6. Regional frequency analysis of observed sub-daily rainfall maxima over eastern China

    NASA Astrophysics Data System (ADS)

    Sun, Hemin; Wang, Guojie; Li, Xiucang; Chen, Jing; Su, Buda; Jiang, Tong

    2017-02-01

    Based on hourly rainfall observational data from 442 stations during 1960-2014, a regional frequency analysis of the annual maxima (AM) sub-daily rainfall series (1-, 2-, 3-, 6-, 12-, and 24-h rainfall, using a moving window approach) for eastern China was conducted. Eastern China was divided into 13 homogeneous regions: Northeast (NE1, NE2), Central (C), Central North (CN1, CN2), Central East (CE1, CE2, CE3), Southeast (SE1, SE2, SE3, SE4), and Southwest (SW). The generalized extreme value performed best for the AM series in regions NE, C, CN2, CE1, CE2, SE2, and SW, and the generalized logistic distribution was appropriate in the other regions. Maximum return levels were in the SE4 region, with value ranges of 80-270 mm (1-h to 24-h rainfall) and 108-390 mm (1-h to 24-h rainfall) for 20- and 100 yr, respectively. Minimum return levels were in the CN1 and NE1 regions, with values of 37-104 mm and 53-140 mm for 20 and 100 yr, respectively. Comparing return levels using the optimal and commonly used Pearson-III distribution, the mean return-level differences in eastern China for 1-24-h rainfall varied from -3-4 mm to -23-11 mm (-10%-10%) for 20-yr events, reaching -6-26 mm (-10%-30%) and -10-133 mm (-10%-90%) for 100-yr events. In view of the large differences in estimated return levels, more attention should be given to frequency analysis of sub-daily rainfall over China, for improved water management and disaster reduction.

  7. 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

  8. 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.

  9. Estimation of Lunar Surface Permittivity for Low Frequency from Polarizations of Natural Waves Observed by SELENE (Kaguya)

    NASA Astrophysics Data System (ADS)

    Goto, Y.; Kimura, R.; Kasahara, Y.; Kumamoto, A.

    2015-12-01

    Lunar surface permittivity is an important parameter for understanding the Moon and has been observed by many radar experiments from spacecraft since 1960s. In these observations, frequencies of radio transmissions are generally high (HF to UHF band) because of instrumental limitations. One of the interesting topics about the lunar surface permittivity is its frequency response in lower bands. It is known that frequency response of permittivity in the low bands can be a good indicator of the moisture content. In theory, there is a considerable difference between the permittivity of dry soil and ice especially below 100 kHz.The lunar orbiter SELENE (Kaguya) carried out radar observations of the lunar subsurface structures and passive observations of natural waves with the Lunar Radar Sounder instrument (LRS). In the passive observations, an electromagnetic wave from the Earth's auroral region that is called auroral kilometric radiation (AKR) was frequently observed in low frequency (LF) band. An interesting feature of AKR observation from SELENE is that the observed AKR consists of not only waves reached directly from the Earth's auroral region but also waves reflected on the lunar surface. Since such reflections influence polarizations of the observed AKR, we can estimate the lunar surface permittivity for low frequency waves from the comparison between observed polarizations and those theoretically calculated for various parameter sets of the lunar surface. As a result, the observed polarizations are well reconstructed when the permittivity of the lunar surface is assumed to be around 4 to 8 in average. In the presentation, we show the regional distributions of the permittivity that is derived from detailed data analysis and compare them with permittivity map for high frequencies (HF band) that are derived from radar observations from SELENE.

  10. 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.

  11. 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.

  12. Limitations to Dual Frequency Ionosphere Corrections for Frequency Switched K-Q-Band Observations with the VLBA

    NASA Technical Reports Server (NTRS)

    Lanyi, Gabor; Gordon, David; Sovers, Ojars J.

    2004-01-01

    A series of VLBA experiments were carried out at K and Q bands for astrometry and imaging within the KQ VLBI Survey Collaboration. The paired K and Q observations of each source are separated by approximately 3 minutes of time. We investigate the delay effect of the ionosphere between K and Q bands involving the interscan separation. This differential delay effect is intermixed with the differential fluctuation effect of the troposphere.

  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 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

  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. 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.

  16. A genomic study on distribution of human leukocyte antigen (HLA)-A and HLA-B alleles in Lak population of Iran.

    PubMed

    Shahsavar, Farhad; Varzi, Ali-Mohammad; Ahmadi, Seyyed Amir Yasin

    2017-03-01

    Anthropological studies based on the highly polymorphic gene, human leukocyte antigen (HLA), provide useful information for bone marrow donor registry, forensic medicine, disease association studies, as well as infertility treatment, designing peptide vaccines against tumors, and infectious or autoimmune diseases. The aim of this study was to determine HLA-A and HLA-B allele frequencies in 100 unrelated Lak/lᴂk/individuals from Lorestan province of Iran. Finally, we compared the results with that previously described in Iranian population. Commercial HLA-Type kits from BAG (Lich, Germany) company were used for determination of the HLA-A and HLA-B allele frequencies in genomic DNA, based on polymerase chain reaction with sequence specific primer (PCR-SSP) assay. The differences between the populations in distribution of HLA-A and HLA-B alleles were estimated by chi-squared test with Yate's correction. The most frequent HLA-A alleles were *24 (20%), *02 (18%), *03 (12%) and *11 (10%), and the most frequent HLA-B alleles were *35 (24%), *51 (16%), *18 (6%) and *38 (6%) in Lak population. HLA-A*66 (1%), *74(1%) and HLA-B*48 (1%), *55(1%) were the least observed frequencies in Lak population. Our results based on HLA-A and HLA-B allele frequencies showed that Lak population possesses the previously reported general features of Iranians but still with unique.

  17. Angular Broadening: Effects of Nonzero, Spatially Varying Plasma Frequency Between the Source and Observer

    NASA Technical Reports Server (NTRS)

    Cairns, Iver H.

    1998-01-01

    Angular broadening of radiation due to scattering by density irregularities is usually described using geometric optics (GO) or the parabolic wave equation (PWE) with the assumptions that the radiation frequency f greatly exceeds the local plasma frequency f(sub p0) or that f(sub p0)/f is constant along the path. These assumptions are inappropriate for many solar system radio phenomena. Here the PWE and GO formalisms are extended to treat angular broadening in plasmas with nonzero, spatially varying ratios, f(sub p0)(z)/f < 1. The new PWE results show that the correlation function, scattered angular spectrum, and other quantities are modified by inclusion of a denominator factor [1 - f(sup 2, sub p0)(z prime)/f prime] inside the path integral over z prime, while the mean-square scattering angle depends on both f(sub p0)(z)/f at the observer and the foregoing factor inside the path integral. The PWE and GO predictions for are identical and involve equivalent assumptions. Previous GO and PWE results are recovered in the limits that f(sub p0)(z prime)/f is constant or zero. The new PWE and GO results will permit more accurate calculation of angular broadening for solar system and astrophysical sources. Moreover and importantly, due to the PWE and GO results for being identical, previous GO analyses of in solar system contexts are essentially correct, except for the neglect of or minor deficiencies in the treatment of nonzero, spatially varying f(sub p0)/f effects. The identical GO and PWE results for and the form of the PWE equation for the correlation function raise questions as to whether diffraction is unimportant for angular broadening (under the usual PWE conditions). Future direct comparisons of the PWE predictions with angular spectra calculated using existing GO ray-tracing codes should answer these questions. Diffraction effects are probably important when the medium and turbulence are

  18. 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.

  19. High-frequency Oscillations in Small Magnetic Elements Observed with Sunrise/SuFI

    NASA Astrophysics Data System (ADS)

    Jafarzadeh, S.; Solanki, S. K.; Stangalini, M.; Steiner, O.; Cameron, R. H.; Danilovic, S.

    2017-04-01

    We characterize waves in small magnetic elements and investigate their propagation in the lower solar atmosphere from observations at high spatial and temporal resolution. We use the wavelet transform to analyze oscillations of both horizontal displacement and intensity in magnetic bright points found in the 300 nm and the Ca ii H 396.8 nm passbands of the filter imager on board the Sunrise balloon-borne solar observatory. Phase differences between the oscillations at the two atmospheric layers corresponding to the two passbands reveal upward propagating waves at high frequencies (up to 30 mHz). Weak signatures of standing as well as downward propagating waves are also obtained. Both compressible and incompressible (kink) waves are found in the small-scale magnetic features. The two types of waves have different, though overlapping, period distributions. Two independent estimates give a height difference of approximately 450 ± 100 km between the two atmospheric layers sampled by the employed spectral bands. This value, together with the determined short travel times of the transverse and longitudinal waves provide us with phase speeds of 29 ± 2 km s‑1 and 31 ± 2 km s‑1, respectively. We speculate that these phase speeds may not reflect the true propagation speeds of the waves. Thus, effects such as the refraction of fast longitudinal waves may contribute to an overestimate of the phase speed.

  20. 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.

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

    PubMed

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

    1995-01-01

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

  2. 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.

  3. Multistation observations of the azimuth, polarization, and frequency dependence of ELF/VLF waves generated by electrojet modulation

    NASA Astrophysics Data System (ADS)

    Maxworth, A. S.; Gołkowski, M.; Cohen, M. B.; Moore, R. C.; Chorsi, H. T.; Gedney, S. D.; Jacobs, R.

    2015-10-01

    Modulated ionospheric heating experiments are performed with the High Frequency Active Auroral Research Program facility in Gakona, Alaska, for the purpose of generating extremely low frequency (ELF) and very low frequency (VLF) waves. Observations are made at three different azimuths from the heating facility and at distances from 37 km to 99 km. The polarization of the observed waves is analyzed in addition to amplitude as a function of modulation frequency and azimuth. Amplitude and eccentricity are observed to vary with both azimuth and distance from the heating facility. It is found that waves radiated at azimuths northwest of the facility are generated by a combination of modulated Hall and Pedersen currents, while waves observed at other azimuths are dominated by modulated Hall currents. We find no evidence for vertical currents contributing to ground observations of ELF/VLF waves. Observed amplitude peaks near multiples of 2 kHz are shown to result from vertical resonances in the Earth-ionosphere waveguide, and variations of the frequency of these resonances can be used to determine the D region ionosphere electron density profile in the vicinity of the HF heater.

  4. SCINTILLATION ARCS IN LOW-FREQUENCY OBSERVATIONS OF THE TIMING-ARRAY MILLISECOND PULSAR PSR J0437–4715

    SciTech Connect

    Bhat, N. D. R.; Ord, S. M.; Tremblay, S. E.; McSweeney, S. J.; Tingay, S. J.

    2016-02-10

    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 (λ{sup 2}) 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.

  5. 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

  6. 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.

  7. Microsatellite null alleles and estimation of population differentiation.

    PubMed

    Chapuis, Marie-Pierre; Estoup, Arnaud

    2007-03-01

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

  8. HLA alleles and haplotypes among the Lakota Sioux: report of the ASHI minority workshops, part III.

    PubMed

    Leffell, Mary S; Fallin, M Daniele; Hildebrand, William H; Cavett, Joshua W; Iglehart, Brian A; Zachary, Andrea A

    2004-01-01

    Human leukocyte antigen (HLA) class I and II alleles were defined for 302 Lakota Sioux American Indians as part of the American Society for Histocompatibility and Immunogenetics coordinated studies on minority populations. The study group was comprised of adult volunteers from the Cheyenne River and Ogala Sioux tribes residing, respectively, on the Cheyenne River and Pine Ridge Reservations in South Dakota. Of the participants, 263 (87%) claimed full American Indian ancestry through both maternal and paternal grandparents. The study group included 25 nuclear families that were informative for genotyping. HLA phenotypes from 202 adults with no other known first-degree relative included in the study were used for calculation of allele and haplotype frequencies by maximum likelihood estimation. HLA-A, -B, and -Cw alleles were found to be in Hardy Weinberg equilibrium. Deviation from equilibrium was observed for DRB1 alleles (p=0.01), but could be attributed to the sample size and the occurrence of some genotypes with low expected frequencies. Polymorphism among the Sioux was limited with four to seven alleles comprising >80% of those observed at each locus. Several alleles were found at high frequency (0.05-0.30) among the Sioux that are also prevalent in other Native Americans and Alaska Natives, including: A*2402, *3101, and *0206; B*3501,*3901, *5101, and *2705; Cw*0702, *0404, and *03041; DRB1*0407, *0404, *1402, and *16021; and DQB1*0301, *0302, and *0402. DRB1*0811, which has been only previously described in Navajo and Tlingit Indians, was found to occur at a frequency of 0.119 among the Sioux. Two new alleles were defined among the Sioux: Cw*0204 and DRB1*040703, which were found in two and four individuals, respectively. In the haplotype analyses, significant linkage disequilibrium (p<0.00001) was seen in all pairwise comparisons of loci and numerous two and three locus haplotypes were found to have strong, positive linkage disequilibrium values. The two most

  9. Observations of the frequencies in a sphere wake and of drag increase by acoustic excitation

    NASA Technical Reports Server (NTRS)

    Kim, H. J.; Durbin, P. A.

    1988-01-01

    Vortex shedding and instability wave frequencies have been measured in the wakes of spheres in the Reynolds number range 500 less than Re less than 60,000. The effect of acoustic excitation was examined and an interaction between the two frequency modes was found at the lower Reynolds numbers; through this interaction, external forcing at the instability frequency could change the vortex shedding frequency. The development of the mean wake was manipulated by forcing near to the dominant shear layer instability frequency. With this forcing, the separated shear layer moved closer to the surface of the sphere and the reversed flow region of the wake was shortened. Concomitantly, the base pressure decreased and drag increased.

  10. Observation of quasi-periodic frequency sweeping in electron cyclotron emission of nonequilibrium mirror-confined plasma

    NASA Astrophysics Data System (ADS)

    Viktorov, M. E.; Shalashov, A. G.; Mansfeld, D. A.; Golubev, S. V.

    2016-12-01

    Chirping frequency patterns have been observed in the electron cyclotron emission from strongly nonequilibrium plasma confined in a table-top mirror magnetic trap. Such patterns are typical for the formation of nonlinear phase-space structures in a proximity of the wave-particle resonances of a kinetically unstable plasma, also known as the “holes and clumps” mechanism. Our data provides the first experimental evidence for the acting of this mechanism in the electron cyclotron frequency domain.

  11. 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

  12. 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.

  13. 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.

  14. Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern.

    PubMed

    Trask, Amanda E; Bignal, Eric M; McCracken, Davy I; Monaghan, Pat; Piertney, Stuart B; Reid, Jane M

    2016-07-01

    Deleterious recessive alleles that are masked in outbred populations are predicted to be expressed in small, inbred populations, reducing both individual fitness and population viability. However, there are few definitive examples of phenotypic expression of lethal recessive alleles under inbreeding conditions in wild populations. Studies that demonstrate the action of such alleles, and infer their distribution and dynamics, are required to understand their potential impact on population viability and inform management responses. The Scottish population of red-billed choughs (Pyrrhocorax pyrrhocorax), which currently totals <60 breeding pairs and is of major conservation concern, has recently been affected by lethal blindness in nestlings. We used family data to show that the pattern of occurrence of blindness within and across affected families that produced blind nestlings was exactly 0·25, matching that expected given a single-locus autosomal lethal recessive allele. Furthermore, the observed distribution of blind nestlings within affected families did not differ from that expected given Mendelian inheritance of such an allele. Relatedness estimates showed that individuals from affected families were not more closely related to each other than they were to individuals from unaffected families that did not produce blind nestlings. Blind individuals tended to be less heterozygous than non-blind individuals, as expected if blindness was caused by the expression of a recessive allele under inbreeding. However, there was no difference in the variance in heterozygosity estimates, suggesting that some blind individuals were relatively outbred. These results suggest carriers of the blindness allele may be widely distributed across contemporary families rather than restricted to a single family lineage, implying that the allele has persisted across multiple generations. Blindness occurred at low frequency (affecting 1·6% of observed nestlings since 1981). However

  15. PCR/oligonucleotide probe typing of HLA class II alleles in a Filipino population reveals an unusual distribution of HLA haplotypes.

    PubMed Central

    Bugawan, T. L.; Chang, J. D.; Klitz, W.; Erlich, H. A.

    1994-01-01

    We 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' = .41) with DPB1*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 population. PMID:8304349

  16. Demodulation effect is observed in neurones by exposure to low frequency modulated microwaves

    NASA Astrophysics Data System (ADS)

    Pérez-Bruzón, R. N.; Figols, T.; Azanza, M. J.; del Moral, A.

    2010-01-01

    Neurones exposure to a microwave (carrier fc=13.6 GHz; power P simeq 5 mW; Ho simeq 0.10 Am-1 = 1.25 mOe; E0 simeq 3.5 V/m; ΔT simeq 0.01°C SAR: 3.1×10-3 - 5.8×10-3 W/Kg) EMF amplitude modulated by ELF-AC field (frequency, fm= 0-100 Hz) shows no electrophysiological effect under the carrier MF alone, but "frequency resonances: at 2, 4, 8, 12, 16, 50, 100 Hz: demodulation effect. Resonances appear when applied ELF-MF is close to a dominant characteristic frequency of the neurone impulse Fourier spectrum. This is an interesting result considering that ELF-MF modulating RF or MW in the range of human EEG could induce frequency-resonant effects on exposed human brain.

  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.

  19. 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.

  20. Two-layer observer based control for a class of uncertain systems with multi-frequency disturbances.

    PubMed

    Wen, Xinyu; Yan, Peng

    2016-07-01

    A novel disturbance estimation approach is presented for a class of uncertain systems subject to multiple-sinusoidal disturbances with unknown frequencies. Different from existing results on disturbance observer based control (DOBC), a new methodology with a two-layer observer structure is developed to effectively estimate and reject the disturbances. In the proposed control architecture, an auxiliary observer is derived to generate a disturbance representation in a parametric uncertainty form. Furthermore, the unknown parameters can be reduced to a constant vector with the dimension of the number of harmonic components in the disturbances. Then an augmented observer is designed to estimate the corresponding unknown parameters of the disturbances. As a result, the uncertain systems with disturbances constituting of multiple unknown-frequency sinusoidal components can be controlled within the DOBC framework, where asymptotic stability can be guaranteed. The proposed approach is successfully validated on a robotic manipulating example.

  1. Resonances observed on mother-daughter rocket flights in the ionosphere. [signal frequency enhancement in auroral zones

    NASA Technical Reports Server (NTRS)

    Folkestad, K.; Troeim, J.

    1973-01-01

    Resonance phenomena have been observed in swept frequency experiments carried out on two mother-daughter Nike-Tomahawk rocket flights at auroral latitudes. The experimental method is briefly described and characteristic samples of the results are presented. A possible interpretation of some main resonances is offered, involving cold plasma cone resonances.

  2. 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.

  3. Two-Way Frequency Fluctuations Observed During Coronal Radio Sounding Experiments

    NASA Astrophysics Data System (ADS)

    Efimov, A. I.; Lukanina, L. A.; Samoznaev, L. N.; Rudash, V. K.; Chashei, I. V.; Bird, M. K.; Pätzold, M.

    2014-05-01

    Coronal radio-sounding experiments were carried out using two-way coherent dual-frequency carrier signals of the ESA spacecraft Rosetta (ROS) in 2006. Frequency measurements recorded at both NASA and ESA tracking stations (sample rate: 1 Hz) are analyzed in this work. Spectral analysis of the S-band, X-band, and differential frequency records has shown that the mean frequency fluctuation of each signal can be described by a radial power-law function of the form σ i = A i ( R/R⊙)- mi , where i=x,s,sx. The ratio of the coefficients A s and A x is not the expected theoretical value A s/ A x= f s/ f x. This occurs because the X-band fluctuations underlie a two-way propagation mode while the S-band fluctuations are essentially the product of a one-way propagation experiment. Results are compared with similar, but not identical, two-way radio propagation experiments performed during the 1991 solar conjunction of the Ulysses spacecraft.

  4. Low-radio-frequency eclipses of the redback pulsar J2215+5135 observed in the image plane with LOFAR.

    PubMed

    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.

  5. Different Alleles of a Gene Encoding Leucoanthocyanidin Reductase (PaLAR3) Influence Resistance against the Fungus Heterobasidion parviporum in Picea abies.

    PubMed

    Nemesio-Gorriz, Miguel; Hammerbacher, Almuth; Ihrmark, Katarina; Källman, Thomas; Olson, Åke; Lascoux, Martin; Stenlid, Jan; Gershenzon, Jonathan; Elfstrand, Malin

    2016-08-01

    Despite the fact that fungal diseases are a growing menace for conifers in modern silviculture, only a very limited number of molecular markers for pathogen resistance have been validated in conifer species. A previous genetic study indicated that the resistance of Norway spruce (Picea abies) to Heterobasidion annosum s.l., a pathogenic basidiomycete species complex, is linked to a quantitative trait loci that associates with differences in fungal growth in sapwood (FGS) that includes a gene, PaLAR3, which encodes a leucoanthocyanidin reductase. In this study, gene sequences showed the presence of two PaLAR3 allelic lineages in P. abies. Higher resistance was associated with the novel allele, which was found in low frequency in the four P. abies populations that we studied. Norway spruce plants carrying at least one copy of the novel allele showed a significant reduction in FGS after inoculation with Heterobasidion parviporum compared to their half-siblings carrying no copies, indicating dominance of this allele. The amount of (+) catechin, the enzymatic product of PaLAR3, was significantly higher in bark of trees homozygous for the novel allele. Although we observed that the in vitro activities of the enzymes encoded by the two alleles were similar, we could show that allele-specific transcript levels were significantly higher for the novel allele, indicating that regulation of gene expression is responsible for the observed effects in resistance, possibly caused by differences in cis-acting elements that we observe in the promoter region of the two alleles.

  6. 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.

  7. High-frequency observations of signals and noise near RSON: implications for the discrimination of ripple-fired mining blasts

    SciTech Connect

    Smith, A.T.; Grose, R.D.

    1987-04-27

    Discrimination of large chemical explosions from possible clandestine nuclear tests is a significant issue for seismic verification. Unless discrimination is possible, the numerous mining blasts within the USSR would give ample opportunity for concealing a clandestine test. Evernden et al. (1986) advocate high frequencies as a means to detect these clandestine tests; however, mining blasts must still give a unique signature for their discrimination. Specific conditions are also necessary for high-frequency verification: low attenuation and quiet seismic stations are among the most important. In this study we address these problems under conditions representing a best case scenerio. During the summer of 1985, LLNL deployed a regional array and high-frequency station near RSON (Red Lake, Ontario, Canada) to study regional seismic signals at a low-noise site with excellent propagation characteristics, the continental shield. One objective was to evaluate the performance of regional seismic arrays and high-frequency stations in this geological environment. Using high-frequency data from mining blasts within the Masabi Iron Range in northern Minnesota (distance of 400 km), we observed the high-frequency P/sub n/ phase of ripple-fired blasts, modelled their source properties, and evaluated a possible discriminant for chemical explosions. This study suggests the existence of a distinctive signature for large chemical explosions: strong, high-frequency spectral peaks in the P spectra introduced by delay shooting or ripple-firing. Its application depends, however, on a frequency band extending to at least 35 Hz at regional distances and predictably quiet seismic sites.

  8. Normal vibrational modes of phospholipid bilayers observed by low-frequency Raman scattering

    NASA Astrophysics Data System (ADS)

    Surovtsev, N. V.; Dmitriev, A. A.; Dzuba, S. A.

    2017-03-01

    Low-frequency Raman spectra of multilamellar vesicles made either of 1-palmitoyl-2-oleoyl-s n -glycero-3-phosphocholine (POPC) or 1,2-dipalmitoyl-s n -glycero-3-phosphocholine (DPPC) have been studied in a wide temperature range. Below 0 ∘C two peaks are found at frequencies around 8-9 and 14 -17 c m -1 and attributed to the normal vibrational modes of the phospholipid bilayer, which are determined by the bilayer thickness and stiffness (elastic modulus). The spectral positions of the peaks depend on the temperature and the bilayer composition. It is suggested that the ratio of the intensities of the first and second peaks can serve as a measure of the interleaflet elastic coupling. The addition of cholesterol to the phospholipid bilayer leads to peak shift and broadening, which may be assigned to the composition heterogeneities commonly attributed to the lipid raft formation.

  9. Low Frequency Radar Sensor Observations of Tropical Forests in the Panama Canal Area

    NASA Technical Reports Server (NTRS)

    Imhoff, M. L.; Lawrence, W.; Condit, R.; Wright, J.; Johnson, P.; Hyer, J.; May, L.; Carson, S.; Smith, David E. (Technical Monitor)

    2000-01-01

    A synthetic aperture radar sensor operating in 5 bands between 80 and 120 MHz was flown over forested areas in the canal zone of the Republic of Panama in an experiment to measure biomass in heavy tropical forests. The sensor is a pulse coherent SAR flown on a small aircraft and oriented straight down. The doppler history is processed to collect data on the ground in rectangular cells of varying size over a range of incidence angles fore and aft of nadir (+45 to - 45 degrees). Sensor data consists of 5 frequency bands with 20 incidence angles per band. Sensor data for over 12+ sites were collected with forest stands having biomass densities ranging from 50 to 300 tons/ha dry above ground biomass. Results are shown exploring the biomass saturation thresholds using these frequencies, the system design is explained, and preliminary attempts at data visualization using this unique sensor design are described.

  10. 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.

  11. Experimental observation of three-frequency quasiperiodic solution in a ring of unidirectionally coupled oscillators

    NASA Astrophysics Data System (ADS)

    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.

  12. Observation of mode instability and coherence collapse in a single-frequency polarization-maintaining fiber ring laser

    NASA Astrophysics Data System (ADS)

    Ma, Mingxiang; Hu, Zhengliang; Xu, Pan; Hu, Yongming

    2014-06-01

    Mode instability acts as a common feature in single-frequency fiber ring lasers. The mechanism of coherence collapse by mode instability is theoretically analyzed and demonstrated with an unbalanced fiber Michelson interferometer utilizing phase modulation, which is illuminated by a single-frequency erbium-doped fiber ring laser. Multiform mode instability phenomena accompanied with coherence collapse are observed and discussed in detail by tracing the dynamics of the interference fringe visibility. The results show that mode instability would introduce extra phase noises like a false alarm to interferometric fiber optic sensing systems.

  13. First Observation of a (1,0) Mode Frequency Shift of an Electron Plasma at Antiproton Beam Injection

    NASA Astrophysics Data System (ADS)

    Kuroda, N.; Mohri, A.; Torii, H. A.; Nagata, Y.; Shibata, M.

    2014-07-01

    The frequency shift of the center-of-mass oscillation, known as the (1,0) mode, of a trapped electron plasma and, furthermore, its time evolution were observed during the cooling of an injected antiproton beam for the first time. Here, antiprotons mixed with the electrons did not follow faster electron oscillations but contributed to the modification of the effective potential. The time evolution of the plasma temperature, deduced from the frequency shift of the excited (3,0) mode, suggested that there was an abnormal energy deposition of the antiproton beam in the electron plasma before thermalization.

  14. Space borne GPM dual-frequency radar simulation from high resolution ground radar observations.

    SciTech Connect

    Rose, C. R.; Chandrasekar, V.

    2004-01-01

    The Global Precipitation Measurement (GPM) mission is dedicated to improving the understanding of the global water cycle by measuring and mapping precipitation throughout the globe. The core GPM satellite will incorporate two separate precipitation radars: one operating at Ku-band (13.6 GHz) and the other at Ka band (35.6 GHz). Each radar beam will be steered such that they both point to the same location in the atmosphere. The main purpose of the dual-frequency radar system is to resolve the DSD in precipitation as well as discriminate between rain and ice. With the two beams collocated on the same precipitation volume, new algorithms are being developed to reliably es timate attenuation and rain rate. Any algorithm is based on models of precipitation. In addition, the GPM system assumes collocated beams and matched resolu tion volumes. Electromagnetic and microphysical models have been developed based on ground-based dual-frequency radar data at S-band to simulate Ku- and Ka-band results for comparison with the new GPM algorithms. This paper evaluates the dual-frequency inversion algorithm with synthesized S-band and known perfect data and presents results. Results show the expected performance of the new dual-precipitation radar algorithms with the potential for guiding algorithm and system improvements.

  15. Observation of a different birefringence order at optical and THz frequencies in LBO crystal

    NASA Astrophysics Data System (ADS)

    Andreev, Yu. M.; Kokh, A. E.; Kokh, K. A.; Lanskii, G. V.; Litvinenko, K.; Mamrashev, A. A.; Molloy, J. F.; Murdin, B.; Naftaly, M.; Nikolaev, N. A.; Svetlichnyi, V. A.

    2017-04-01

    THz optical properties of lithium borate (LBO) crystals were measured using time-domain spectroscopy (TDS). The LBO crystal samples were of high optical quality and were cut and polished along the <100>, <010> and <001> axes. Two independent measurements were performed in order to confirm the reproducibility and consistency of results. The contradictions in the previously published data on the THz optical properties of LBO were clarified. It was shown that the birefringence order at THz frequencies is nz frequencies it is known to be nx frequencies up to 0.5 THz for a wave polarized parallel to the Z-axis. A set of new dispersion equations was designed for the entire transparency range.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Can simple population genetic models reconcile partial match frequencies observed in large forensic databases?

    PubMed

    Mueller, Laurence D

    2008-08-01

    A recent study of partial matches in the Arizona offender database of DNA profiles has revealed a large number of nine and ten locus matches. I use simple models that incorporate the product rule, population substructure, and relatedness to predict the expected number of matches in large databases. I find that there is a relatively narrow window of parameter values that can plausibly describe the Arizona results. Further research could help determine if the Arizona samples are congruent with some of the models presented here or whether fundamental assumptions for predicting these match frequencies requires adjustments.

  1. 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.

  2. [Frequency of recurrent convulsions after a first febrile seizure: two-year observation results].

    PubMed

    Mustafić, Nevzeta; Tahirović, Husref; Trnovcević, Jasmina

    2010-01-01

    Febrile convulsions are the most frequent neurological disorder of early childhood. One third of children with febrile convulsions will have a recurrence, and only a small number will develop afebrile convulsions with epilepsy variation. The aim of the work was to establish the frequency of convulsion recurrence through the retrospective study with regard to age, type of recurrence, and applied prophylaxis in children in Tuzla Canton in a two-year period after the first febrile convulsion. Amongst 716 patients, 21.9% had a recurrence. Recurrence of simple febrile convulsions occurred in 124 (78.9%), complex in 18 (11.5%), and 14 (9.8%) patients had afebrile convulsions. There was no statistically significant difference in recurrence appearance between patients who received continuous and intermittent prophylaxis or different type of continuous prophylaxis. Knowledge of recurrence frequency according to age groups opens the possibility of recurrence prevention with adequate therapeutic measures, especially in home care conditions. Good parent education would represent the first step in recurrence prevention.

  3. Frequency-Dependent Scattering Observed in P- and Surface-Wave Arrivals From South India

    NASA Astrophysics Data System (ADS)

    Rai, A. K.

    2016-12-01

    Anomalies in polarization angles of teleseismic waves have been used to understand effect of scattered arrivals from subsurface heterogeneities. Seismological data recorded in southern India show polarization anomalies up to 5° for several stations. These anomalies are most pronounced for earthquakes from western and southern azimuths. Furthermore, stations located near the boundary of Dharwar craton and southern Granulites are more affected by scattered waves. Considering that many of the nearby stations show similar patterns of polarization anomalies, it is likely that the source of scattered energy is located at shallower depths. The non-stationary nature of seismic arrivals warrants determination of frequency-dependent polarization. Result obtained using multi-taper spectral analysis method indicates that data are contaminated at frequencies greater than 2 Hz for most of the stations. Furthermore, surface-wave records also indicate off-azimuth arrivals, and quasi-Love waves indicating heterogeneities or anisotropy in the subsurface. These small-scale heterogeneities that may be located in crust may be important for studies using converted phases and ground motion prediction studies.

  4. Observations of enhanced ion line frequency spectrum during Arecibo ionospheric modification experiment

    NASA Technical Reports Server (NTRS)

    Hagfors, T.; Zamlutti, C. J.

    1974-01-01

    The Arecibo 430 MHz incoherent scatter radar (ISR) was used to monitor the effects of modifying the ionosphere by a high power HF transmitter feeding the 305 m reflector antenna. When in the ordinary magnetoionic mode parametric instabilities develop in the ionosphere near the reflection level. Manifestations of these instabilities are the strong enhancement of Langmuir oscillations in the direction of the ISR beam at a wavelength of 35 cm and the simultaneous much weaker enhancement of ion oscillations in that direction. The spectral analysis of the enhanced peak with a height resolution of 2.4 km shows that the ionic mode enhancement most often has a double humped frequency spectrum corresponding to up- and down-going ion acoustic waves. The shape of the frequency spectrum is interpreted in terms of a stable oscillation which is driven by a secondary electrostatic field caused by nonlinear interaction of Langmuir waves within a cone centered on the magnetic field and by the scattering of the pump field on stable Langmuir waves travelling along the direction of the ISR.

  5. Frequency-Dependent Scattering Observed in P- and Surface-Wave Arrivals From South India

    NASA Astrophysics Data System (ADS)

    Rai, A. K.

    2017-03-01

    Anomalies in polarization angles of teleseismic waves have been used to understand effect of scattered arrivals from subsurface heterogeneities. Seismological data recorded in southern India show polarization anomalies up to 5° for several stations. These anomalies are most pronounced for earthquakes from western and southern azimuths. Furthermore, stations located near the boundary of Dharwar craton and southern Granulites are more affected by scattered waves. Considering that many of the nearby stations show similar patterns of polarization anomalies, it is likely that the source of scattered energy is located at shallower depths. The non-stationary nature of seismic arrivals warrants determination of frequency-dependent polarization. Result obtained using multi-taper spectral analysis method indicates that data are contaminated at frequencies greater than 2 Hz for most of the stations. Furthermore, surface-wave records also indicate off-azimuth arrivals, and quasi-Love waves indicating heterogeneities or anisotropy in the subsurface. These small-scale heterogeneities that may be located in crust may be important for studies using converted phases and ground motion prediction studies.

  6. 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.

  7. 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.

  8. The low frequency waves observed by Cluster in the polar cusp-relation to fan and horseshoe instabilities

    NASA Astrophysics Data System (ADS)

    Blecki, Jan; Parrot, Michel; Savin, Sergey; Slominska, Ewa; Wronowski, Roman

    The main goal of this presentation is discussion of the possible source of the low frequency plasma waves registered by CLUSTER in the polar cusp. These waves have been sometimes registered in the polar cusp as emissions with extremely high intensity below the electron cyclotron frequency by Interball 1. They correlate with strong fluxes of high energetic electrons often observed within the polar cusp by Interball 1 and Magion 4. Similar effects have been registered by Polar satellite. Cluster measurements give new insight of these emissions. The observations of the waves at the frequencies close to electron cyclotron frequency done by Cluster satellites associated with strong fluxes of energetic electrons will be presented. Taking into account the plasma and magnetic field parameters in the polar cusp as well as geometry of the waves propagation, one has found that these emissions can be generated by so called "fan instability", but also horse shoe instability can be discussed. Both instabilities play important role in the nonlinear wave -particle interactions leading to the isotropisation of the fluxes of the particles and heating of the plasma.

  9. Association between Age and the 7 Repeat Allele of the Dopamine D4 Receptor Gene

    PubMed Central

    Szekely, Anna; Bircher, Julianna; Vereczkei, Andrea; Balota, David A.; Sasvari-Szekely, Maria; Ronai, Zsolt

    2016-01-01

    Longevity is in part (25%) inherited, and genetic studies aim to uncover allelic variants that play an important role in prolonging life span. Results to date confirm only a few gene variants associated with longevity, while others show inconsistent results. However, GWAS studies concentrate on single nucleotide polymorphisms, and there are only a handful of studies investigating variable number of tandem repeat variations related to longevity. Recently, Grady and colleagues (2013) reported a remarkable (66%) accumulation of those carrying the 7 repeat allele of the dopamine D4 receptor gene in a large population of 90–109 years old Californian centenarians, as compared to an ancestry-matched young population. In the present study we demonstrate the same association using continuous age groups in an 18–97 years old Caucasian sample (N = 1801, p = 0.007). We found a continuous pattern of increase from 18–75, however frequency of allele 7 carriers decreased in our oldest age groups. Possible role of gene-environment interaction effects driven by historical events are discussed. In accordance with previous findings, we observed association preferentially in females (p = 0.003). Our results underlie the importance of investigating non-disease related genetic variants as inherited components of longevity, and confirm, that the 7-repeat allele of the dopamine D4 receptor gene is a longevity enabling genetic factor, accumulating in the elderly female population. PMID:27992450

  10. Dynamics of the EEG power in the frequency and spatial domains during observation and execution of manual movements.

    PubMed

    Frenkel-Toledo, Silvi; Bentin, Shlomo; Perry, Anat; Liebermann, Dario G; Soroker, Nachum

    2013-05-06

    Mu suppression is the attenuation of EEG power in the alpha frequency range (8-12 Hz) while executing or observing a motor action. Whereas typically observed at central scalp sites, there are diverging reports about the extent of the attenuation over the cortical mantle, its exact frequency range and the specificity of this phenomenon. We investigated the modulation of EEG oscillations in frequency-bands between 4 to 12 Hz at frontal, central, parietal and occipital sites during the execution of manual movements and during observation of similar actions from allocentric (i.e., facing the actor) and egocentric (i.e., seeing the actor from behind) viewpoints. Suppression was determined relative to observation of a non-biological movement. Action observation elicited greater suppression in the lower (8-10 Hz) compared to the higher mu range (10-12 Hz), and greater suppression in the entire range (4-12 Hz) at frontal and central sites compared to parietal and occipital sites. In addition, suppression tended to be greater during observation of a motor action from allocentric compared to egocentric viewpoints. During execution of movement, suppression of the EEG occurred primarily in the higher alpha range and was absent at occipital sites. In the theta range (4-8 Hz), the EEG amplitude was suppressed during action observation and execution. The results suggest a functional distinction between modulation of mu and alpha rhythms, and between the higher and lower ranges of the mu rhythms. The activity of the presumed human mirror-neuron system seems primarily evident in the lower mu range and in the theta range.

  11. 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.

  12. 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.

  13. 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.

  14. 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)

  15. Age-, tissue- and length-dependent bidirectional somatic CAG•CTG repeat instability in an allelic series of R6/2 Huntington disease mice.

    PubMed

    Larson, Eloise; Fyfe, Ian; Morton, A Jennifer; Monckton, Darren G

    2015-04-01

    The expansion of simple sequence CAG•CTG repeats is associated with a number of inherited disorders including Huntington disease (HD), myotonic dystrophy type 1 and several of the spinocerebellar ataxias. Inherited disease-associated alleles usually exceed 40 repeats and may be in excess of 1,000 repeats in some disorders. Inherited allele length is inversely proportional to age at onset, and frequent germline expansions account for the striking anticipation observed in affected families. Expanded disease associated alleles are also somatically unstable via a pathway that is age dependent and tissue specific, and also appears to be expansion biased. Somatic expansions are thought to contribute toward both tissue specificity and disease progression. Here we have examined the somatic mutational dynamics in brain and peripheral tissues from an allelic series of R6/2 HD transgenic mice inheriting from 52 to >700 CAG repeats. We found age-dependent, tissue-specific somatic instability, with particularly large expansions observed in the striatum and cortex. We also found a positive increase in somatic instability with increasing allele length. Surprisingly, however, the degree of somatic variation did not increase in a linear fashion, but leveled off with increasing allele length. Most unexpectedly, the almost exclusive bias toward the accumulation of expansions observed in mice inheriting smaller alleles was lost, and a high frequency of large somatic contractions was observed in mice inheriting very large alleles (>500 repeats). These data highlight the bidirectional nature of CAG•CTG repeat instability and the subtle balance that exists between expansion and contraction in vivo. Defining the dynamics and tissue specificity of expansion and contraction is important for understanding the role of genetic instability in pathophysiology and in particular the development of novel therapies based on suppressing expansions and/or promoting contractions.

  16. Frequency domain observations of small motions at concrete/steel interfaces

    SciTech Connect

    Bonner, B.P.

    1996-06-01

    When two rough interfaces in contact are driven in harmonic motion, the frictional resistance to shear causes the response of the driven system to be nonlinear. Displacement along the interface cannot be described by a linear predictor, one analogous to Hooke`s law for elastic response. Laboratory experiments are described here to illustrate that the resulting motion is not random, but produces measurable and characteristic output at harmonics of the driving frequency. Although the geometry of the tests is not practical for evaluating the integrity of steel/concrete interfaces in structures, the results illustrate that the principle should apply to other geometries where shearing forces can be applied to interfaces to determine the quality of bonding.

  17. 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.

  18. High-frequency and time resolution rocket observations of structured low- and medium-frequency whistler mode emissions in the auroral ionosphere

    NASA Astrophysics Data System (ADS)

    LaBelle, J.; McAdams, K. L.; Trimpi, M. L.

    High bandwidth electric field waveform measurements on a recent auroral sounding rocket reveal structured whistler mode signals at 400-800 kHz. These are observed intermittently between 300 and 500 km with spectral densities 0-10 dB above the detection threshold of 1.5×10-11V2/m2Hz. The lack of correlation with local particle measurements suggests a remote source. The signals are composed of discrete structures, in one case having bandwidths of about 10 kHz and exhibiting rapid frequency variations of the order of 200 kHz per 100 ms. In one case, emissions near the harmonic of the whistler mode signals are detected simultaneously. Current theories of auroral zone whistler mode emissions have not been applied to explain quantitatively the fine structure of these signals, which resemble auroral kilometric radiation (AKR) rather than auroral hiss.

  19. Low Frequency Oscillations in Assimilated Global Datasets Using TRMM Rainfall Observations

    NASA Technical Reports Server (NTRS)

    Tao, Li; Yang, Song; Zhang, Zhan; Hou, Arthur; Olson, William S.

    2004-01-01

    Global datasets for the period May-August 1998 from the Goddard Earth Observing System (GEOS) data assimilation system (DAS) with/without assimilated Tropical Rainfall Measuring Mission (TRMM) precipitation are analyzed against European Center for Medium-Range Weather Forecast (ECMWF) output, NOAA observed outgoing longwave radiation (OLR) data, and TRMM measured rainfall. The purpose of this study is to investigate the representation of the Madden-Julian Oscillation (MJO) in GEOS assimilated global datasets, noting the impact of TRMM observed rainfall on the MJO in GEOS data assimilations. A space-time analysis of the OLR data indicates that the observed OLR exhibits a spectral maximum for eastward-propagating wavenumber 1-3 disturbances with periods of 20-60 days in the 0deg-30degN latitude band. The assimilated OLR has a similar feature but with a smaller magnitude. However, OLR spectra from assimilations including TRMM rainfall data show better agreement with observed OLR spectra than spectra from assimilations without TRMM rainfall. Similar results are found for wavenumber 4-6 disturbances. There is a spectral peak for eastward-propagating wavenumber 4-6 disturbances with periods of 20-40 days near the equator, while for westward-moving disturbances, a spectral peak is noted for periods of 30-50 days near 25degN. To isolate the MJO, a 30-50 day band filter is selected for this study. It was found that the eastward-propagating waves from the band-filtered observed OLR between 10degs- 10degN are located in the eastern hemisphere. Similar patterns are evident in surface rainfall and the 850 hPa wind field. Assimilation of TRMM-observed rainfall reveals more distinct MJO features in the analysis than without rainfall assimilation. Similar analyses are also conducted over the Indian summer monsoon and East Asia summer monsoon regions, where the MJO is strongly related to the summer monsoon active-break patterns.

  20. Choreography of Ig allelic exclusion.

    PubMed

    Cedar, Howard; Bergman, Yehudit

    2008-06-01

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

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

    PubMed

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

    2006-11-01

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

  2. Polar mesosphere summer echo observations at HF frequencies using the HAARP Gakona Ionospheric Observatory

    NASA Astrophysics Data System (ADS)

    Kelley, Michael C.; Huaman, Mercedes; Chen, Charlie Y.; Ramos, Camilo; Djuth, Frank; Kennedy, Edward

    2002-06-01

    We present initial polar mesosphere summer echo (PMSE) observations over Alaska in the HF band. Echoes were detected near 85 km over 50% of the observation time even though it was late in the PMSE season. The signal-to-noise ratio sometimes exceeded 25 dB. We also present the effects of different transmitted powers and antenna pointing directions on PMSE strength and occurrence. There is some evidence that using 4.5 MHz electron heating occurred, even at the low duty cycle used.

  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. Detection of patients considering observation frequency of continuous and discontinuous adventitious sounds in lung sounds.

    PubMed

    Nakamura, Naoki; Yamashita, Masaru; Matsunaga, Shoichi

    2016-08-01

    We propose an improved approach for distinguishing between healthy subjects and patients with pulmonary emphysema by the use of one stochastic acoustic model for continuous adventitious sounds and another for discontinuous adventitious sounds. These models are able to represent the spectral features of the adventitious sounds for the detection of abnormal respiration. However, abnormal respiratory sounds with unclassifiable spectral features are present among the continuous and discontinuous adventitious sounds and mixing noises. These sounds cause difficulties in achieving a highly accurate classification. In this study, the difference in occurrence frequencies between two types of adventitious sounds for each considered auscultation point and inspiration/expiration was considered. This difference, in combination with the confusion tendency of the classifier, was formulated as the validity score of each respiratory sound. The conventional spectral likelihood and the newly formulated validity score were combined to perform detection of abnormal respiration and patients. In the classification of healthy subjects and patients, the proposed approach achieved a higher classification rate (87.7%) than the conventional method (85.2%), demonstrating the statistical superiority (5% level) of the former.

  6. 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 image of a galaxy at frequencies below 300 MHz so far. The integrated spectrum of total radio emission is described well by a power law, while flat spectral indices in the central region indicate thermal absorption. We observe that the disk extends out to 16 kpc and see a break in the radial profile near the optical radius of the disk. The radial scale lengths in the inner and outer disks are greater at 151 MHz, and the break is smoother at 151 MHz than those observed at 1.4 GHz. The arm-interarm contrast is lower at 151 MHz than at 1400 MHz, indicating propagation of CRE from spiral arms into interarm regions. The correlations between the images of radio emission at 151 MHz and 1400 MHz and the FIR emission at 70 μm reveal breaks on scales of 1.4 and 0.7 kpc, respectively. The total (equipartition) magnetic field strength decreases from about 28 μG in the central region to

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

    PubMed

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

    2009-08-01

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

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

    PubMed

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

    2015-07-01

    Genome-wide association studies (GWAS) have generated sufficient data to assess the role of selection in shaping