Inferring recent outcrossing rates using multilocus individual heterozygosity: application to evolving wheat populations.

PubMed Central

Enjalbert, J; David, J L

2000-01-01

Using multilocus individual heterozygosity, a method is developed to estimate the outcrossing rates of a population over a few previous generations. Considering that individuals originate either from outcrossing or from n successive selfing generations from an outbred ancestor, a maximum-likelihood (ML) estimator is described that gives estimates of past outcrossing rates in terms of proportions of individuals with different n values. Heterozygosities at several unlinked codominant loci are used to assign n values to each individual. This method also allows a test of whether populations are in inbreeding equilibrium. The estimator's reliability was checked using simulations for different mating histories. We show that this ML estimator can provide estimates of outcrossing rates for the final generation outcrossing rate (t(0)) and a mean of the preceding rates (t(p)) and can detect major temporal variation in the mating system. The method is most efficient for low to intermediate outcrossing levels. Applied to nine populations of wheat, this method gave estimates of t(0) and t(p). These estimates confirmed the absence of outcrossing t(0) = 0 in the two populations subjected to manual selfing. For free-mating wheat populations, it detected lower final generation outcrossing rates t(0) = 0-0.06 than those expected from global heterozygosity t = 0.02-0.09. This estimator appears to be a new and efficient way to describe the multilocus heterozygosity of a population, complementary to Fis and progeny analysis approaches. PMID:11102388

CHARACTERIZATION OF A LOSS OF HETEROZYGOSITY CANCER HAZARD IDENTIFICATION ASSAY.

EPA Science Inventory

Tumor development generally requires the loss of heterozygosity (LOH) at one or more loci. Thus, the ability to determine whether a chemical is capable of causing LOH is an important part of cancer hazard identification. The mouse lymphoma assay detects a broad spectrum of geneti...

Loss of Heterozygosity Drives Adaptation in Hybrid Yeast.

PubMed

Smukowski Heil, Caiti S; DeSevo, Christopher G; Pai, Dave A; Tucker, Cheryl M; Hoang, Margaret L; Dunham, Maitreya J

2017-07-01

Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we examine hybrid genome evolution using experimental evolution of de novo interspecific hybrid yeast Saccharomyces cerevisiae × Saccharomyces uvarum and their parentals. We evolved these strains in nutrient-limited conditions for hundreds of generations and sequenced the resulting cultures identifying numerous point mutations, copy number changes, and loss of heterozygosity (LOH) events, including species-biased amplification of nutrient transporters. We focused on a particularly interesting example, in which we saw repeated LOH at the high-affinity phosphate transporter gene PHO84 in both intra- and interspecific hybrids. Using allele replacement methods, we tested the fitness of different alleles in hybrid and S. cerevisiae strain backgrounds and found that the LOH is indeed the result of selection on one allele over the other in both S. cerevisiae and the hybrids. This is an example where hybrid genome resolution is driven by positive selection on existing heterozygosity and demonstrates that even infrequent outcrossing may have lasting impacts on adaptation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Acquired copy-neutral loss of heterozygosity of chromosome 1p as a molecular event associated with marrow fibrosis in MPL-mutated myeloproliferative neoplasms.

PubMed

Rumi, Elisa; Pietra, Daniela; Guglielmelli, Paola; Bordoni, Roberta; Casetti, Ilaria; Milanesi, Chiara; Sant'Antonio, Emanuela; Ferretti, Virginia; Pancrazzi, Alessandro; Rotunno, Giada; Severgnini, Marco; Pietrelli, Alessandro; Astori, Cesare; Fugazza, Elena; Pascutto, Cristiana; Boveri, Emanuela; Passamonti, Francesco; De Bellis, Gianluca; Vannucchi, Alessandro; Cazzola, Mario

2013-05-23

We studied mutations of MPL exon 10 in patients with essential thrombocythemia (ET) or primary myelofibrosis (PMF), first investigating a cohort of 892 consecutive patients. MPL mutation scanning was performed on granulocyte genomic DNA by using a high-resolution melt assay, and the mutant allele burden was evaluated by using deep sequencing. Somatic mutations of MPL, all but one involving codon W515, were detected in 26/661 (4%) patients with ET, 10/187 (5%) with PMF, and 7/44 (16%) patients with post-ET myelofibrosis. Comparison of JAK2 (V617F)-mutated and MPL-mutated patients showed only minor phenotypic differences. In an extended group of 62 MPL-mutated patients, the granulocyte mutant allele burden ranged from 1% to 95% and was significantly higher in patients with PMF or post-ET myelofibrosis compared with those with ET. Patients with higher mutation burdens had evidence of acquired copy-neutral loss of heterozygosity (CN-LOH) of chromosome 1p in granulocytes, consistent with a transition from heterozygosity to homozygosity for the MPL mutation in clonal cells. A significant association was found between MPL-mutant allele burden greater than 50% and marrow fibrosis. These observations suggest that acquired CN-LOH of chromosome 1p involving the MPL location may represent a molecular mechanism of fibrotic transformation in MPL-mutated myeloproliferative neoplasms.

Acquired copy-neutral loss of heterozygosity of chromosome 1p as a molecular event associated with marrow fibrosis in MPL-mutated myeloproliferative neoplasms

PubMed Central

Pietra, Daniela; Guglielmelli, Paola; Bordoni, Roberta; Casetti, Ilaria; Milanesi, Chiara; Sant’Antonio, Emanuela; Ferretti, Virginia; Pancrazzi, Alessandro; Rotunno, Giada; Severgnini, Marco; Pietrelli, Alessandro; Astori, Cesare; Fugazza, Elena; Pascutto, Cristiana; Boveri, Emanuela; Passamonti, Francesco; De Bellis, Gianluca; Vannucchi, Alessandro; Cazzola, Mario

2013-01-01

We studied mutations of MPL exon 10 in patients with essential thrombocythemia (ET) or primary myelofibrosis (PMF), first investigating a cohort of 892 consecutive patients. MPL mutation scanning was performed on granulocyte genomic DNA by using a high-resolution melt assay, and the mutant allele burden was evaluated by using deep sequencing. Somatic mutations of MPL, all but one involving codon W515, were detected in 26/661 (4%) patients with ET, 10/187 (5%) with PMF, and 7/44 (16%) patients with post-ET myelofibrosis. Comparison of JAK2 (V617F)–mutated and MPL-mutated patients showed only minor phenotypic differences. In an extended group of 62 MPL-mutated patients, the granulocyte mutant allele burden ranged from 1% to 95% and was significantly higher in patients with PMF or post-ET myelofibrosis compared with those with ET. Patients with higher mutation burdens had evidence of acquired copy-neutral loss of heterozygosity (CN-LOH) of chromosome 1p in granulocytes, consistent with a transition from heterozygosity to homozygosity for the MPL mutation in clonal cells. A significant association was found between MPL-mutant allele burden greater than 50% and marrow fibrosis. These observations suggest that acquired CN-LOH of chromosome 1p involving the MPL location may represent a molecular mechanism of fibrotic transformation in MPL-mutated myeloproliferative neoplasms. PMID:23575445

Age-dependent, negative heterozygosity-fitness correlations and local effects in an endangered Caribbean reptile, Iguana delicatissima.

PubMed

Judson, Jessica L Martin; Knapp, Charles R; Welch, Mark E

2018-02-01

Inbreeding depression can have alarming impacts on threatened species with small population sizes. Assessing inbreeding has therefore become an important focus of conservation research. In this study, heterozygosity-fitness correlations (HFCs) were measured by genotyping 7 loci in 83 adult and 184 hatchling Lesser Antillean Iguanas, Iguana delicatissima, at a communal nesting site in Dominica to assess the role of inbreeding depression on hatchling fitness and recruitment to the adult population in this endangered species. We found insignificant correlations between multilocus heterozygosity and multiple fitness proxies in hatchlings and adults. Further, multilocus heterozygosity did not differ significantly between hatchlings and adults, which suggests that the survivorship of homozygous hatchlings does not differ markedly from that of their heterozygous counterparts. However, genotypes at two individual loci were correlated with hatching date, a finding consistent with the linkage between specific marker loci and segregating deleterious recessive alleles. These results provide only modest evidence that inbreeding depression influences the population dynamics of I. delicatissima on Dominica.

False homozygous HLA genotyping results due to copy number neutral loss of heterozygosity in acquired aplastic anaemia.

PubMed

Heyrman, Bert; De Becker, Ann; Verheyden, Sonja; Demanet, Christian

2017-03-02

The aim of this case report is to draw attention on possible false human leucocyte antigen (HLA) genotyping in acquired aplastic anaemia prior to allogeneic haematopoietic stem cell transplantation. In acquired aplastic anaemia loss of heterozygosity (LOH) of chromosome 6p is known to occur in around 12%. We report false HLA genotyping results due to LOH and a coinciding steep rise in neutrophils following filgrastim stimulation in a patient with very severe aplastic anaemia. At diagnosis we obtained heterozygous results on peripheral blood. Failing to reach a partial response at 6 months with immune-suppressive therapy we repeated HLA genotyping, obtaining homozygous results. Repeated testing confirmed loss of HLA genotype heterozygosity. HLA genotyping on cells obtained by a buccal swab confirmed the previous HLA heterozygosity. A second course of filgrastim at the time of homozygous HLA genotyping resulted in a steep rise in neutrophils. Stopping filgrastim resulted in an equally steep drop. 2017 BMJ Publishing Group Ltd.

Interpreting aCGH-defined karyotypic changes in gliomas using copy number status, loss of heterozygosity and allelic ratios

PubMed Central

Cowell, John K; Lo, Ken C; Luce, Jesse; Hawthorn, Lesleyann

2009-01-01

We have used SNP mapping arrays to simultaneously record copy number changes, loss of heterozygosity and allele ratios (ploidy) in a series of 13 gliomas. This combined analysis has defined novel amplification events in this tumor type involving chr1:241544532-243005121 and chr18:54716681-54917277 which contain the AKT3 and ZNF532 genes respectively. The high resolution of this analysis has also identified homozygous deletions involving chr17:25600031-26490848 and Chr19:53883612-55061878. Throughout the karyotypes of these tumors, the combined analysis revealed counter intuitive relationships between copy number and LOH that requires reinterpretation of the significance of copy number gains and losses. It was not uncommon to observe copy number gains that were associated with loss of heterozygosity as well as copy number losses that were not. These events appeared to be related to ploidy status in the tumors as determined using allelic ratio calculations. Overall, this analysis of gliomas provides evidence for the need to perform more comprehensive interpretation of the CGH data beyond copy number analysis alone to evaluate the significance of individual events in the karyotypes. PMID:19818351

Effect of lead pollution on fitness and its dependence on heterozygosity in Drosophila subobscura.

PubMed

Tanaskovic, Marija; Novicic, Zorana Kurbalija; Kenig, Bojan; Stamenkovic-Radak, Marina; Andjelkovic, Marko

2015-12-01

Lead is one of the most present contaminants in the environment, and different species respond differently to this type of polution. If combined with genomic stress, lead may act synergistically, causing significant decrease of fitness components. We used two genetically diverse Drosophila subobscura populations (regarding both putatively adaptive inversion and microsatellite loci polymorphisms) originating from two ecologically distinct habitats. To establish different levels of genome heterozygosity, series of intraline, intrapopulation and interpopulation crosses were made. The progeny were reared on a standard medium and a medium with 200 μg/mL of lead acetate. Development time was significantly extended to all groups reared on lead. The progeny of intraline crosses showed significantly extended development time compared to all other groups. The obtained results suggest that genome heterozygosity reduces the effect of lead pollution.

Associations between heterozygosity and growth rate variables in three western forest trees

Treesearch

Jeffry B. Milton; Peggy Knowles; Kareen B. Sturgeon; Yan B. Linhart; Martha Davis

1981-01-01

For each of three species, quaking aspen, ponderosa pine, and lodgepole pine, we determined the relationships between a ranking of heterozygosity of individuals and measures of growth rate. Genetic variation was assayed by starch gel electrophoresis of enzymes. Growth rates were characterized by the mean, standard deviation, logarithm of the variance, and coefficient...

A Review of the Implications of Heterozygosity and Inbreeding on Germplasm Biodiversity and Its Conservation in the Silkworm, Bombyx mori

PubMed Central

Jingade, A.H.; Vijayan, K.; Somasundaram, P.; Srivasababu, G.K.; Kamble, C.K.

2011-01-01

Silkworm genebanks assume paramount importance as the reservoirs of biodiversity and source of alleles that can be easily retrieved for genetic enhancement of popular breeds. More than 4000 Bombyx mori L (Lepidoptera: Bombycidae) strains are currently available and these strains are maintained through continuous sibling mating. This repeated sibling mating makes the populations of each strain more homozygous, but leads to loss of unique and valuable genes through the process of inbreeding depression. Hence, it is essential to maintain a minimal degree of heterozygosity within the population of each silkworm strain, especially in the traditional geographic strains, to avoid such loss. As a result, accurate estimation of genetic diversity is becoming more important in silkworm genetic resources conservation. Application of molecular markers help estimate genetic diversity much more accurately than that of morphological traits. Since a minimal amount of heterozygosity in each silkworm strain is essential for better conservation by avoiding inbreeding depression, this article overviews both theoretical and practical importance of heterozygosity together with impacts of inbreeding depression and the merits and demerits of neutral molecular markers for measurements of both heterozygosity and inbreeding depression in the silkworm Bombyx mori. PMID:21521139

A review of the implications of heterozygosity and inbreeding on germplasm biodiversity and its conservation in the silkworm, Bombyx mori.

PubMed

Jingade, A H; Vijayan, K; Somasundaram, P; Srivasababu, G K; Kamble, C K

2011-01-01

Abstract Silkworm genebanks assume paramount importance as the reservoirs of biodiversity and source of alleles that can be easily retrieved for genetic enhancement of popular breeds. More than 4000 Bombyx mori L (Lepidoptera: Bombycidae) strains are currently available and these strains are maintained through continuous sibling mating. This repeated sibling mating makes the populations of each strain more homozygous, but leads to loss of unique and valuable genes through the process of inbreeding depression. Hence, it is essential to maintain a minimal degree of heterozygosity within the population of each silkworm strain, especially in the traditional geographic strains, to avoid such loss. As a result, accurate estimation of genetic diversity is becoming more important in silkworm genetic resources conservation. Application of molecular markers help estimate genetic diversity much more accurately than that of morphological traits. Since a minimal amount of heterozygosity in each silkworm strain is essential for better conservation by avoiding inbreeding depression, this article overviews both theoretical and practical importance of heterozygosity together with impacts of inbreeding depression and the merits and demerits of neutral molecular markers for measurements of both heterozygosity and inbreeding depression in the silkworm Bombyx mori.

Loss-of-heterozygosity facilitates passage through Haldane's sieve for Saccharomyces cerevisiae undergoing adaptation.

PubMed

Gerstein, A C; Kuzmin, A; Otto, S P

2014-05-07

Haldane's sieve posits that the majority of beneficial mutations that contribute to adaptation should be dominant, as these are the mutations most likely to establish and spread when rare. It has been argued, however, that if the dominance of mutations in their current and previous environments are correlated, Haldane's sieve could be eliminated. We constructed heterozygous lines of Saccharomyces cerevisiae containing single adaptive mutations obtained during exposure to the fungicide nystatin. Here we show that no clear dominance relationship exists across environments: mutations exhibited a range of dominance levels in a rich medium, yet were exclusively recessive under nystatin stress. Surprisingly, heterozygous replicates exhibited variable-onset rapid growth when exposed to nystatin. Targeted Sanger sequencing demonstrated that loss-of-heterozygosity (LOH) accounted for these growth patterns. Our experiments demonstrate that recessive beneficial mutations can avoid Haldane's sieve in clonal organisms through rapid LOH and thus contribute to rapid evolutionary adaptation.

Inferring relationships between pairs of individuals from locus heterozygosities

PubMed Central

Presciuttini, Silvano; Toni, Chiara; Tempestini, Elena; Verdiani, Simonetta; Casarino, Lucia; Spinetti, Isabella; Stefano, Francesco De; Domenici, Ranieri; Bailey-Wilson, Joan E

2002-01-01

Background The traditional exact method for inferring relationships between individuals from genetic data is not easily applicable in all situations that may be encountered in several fields of applied genetics. This study describes an approach that gives affordable results and is easily applicable; it is based on the probabilities that two individuals share 0, 1 or both alleles at a locus identical by state. Results We show that these probabilities (zi) depend on locus heterozygosity (H), and are scarcely affected by variation of the distribution of allele frequencies. This allows us to obtain empirical curves relating zi's to H for a series of common relationships, so that the likelihood ratio of a pair of relationships between any two individuals, given their genotypes at a locus, is a function of a single parameter, H. Application to large samples of mother-child and full-sib pairs shows that the statistical power of this method to infer the correct relationship is not much lower than the exact method. Analysis of a large database of STR data proves that locus heterozygosity does not vary significantly among Caucasian populations, apart from special cases, so that the likelihood ratio of the more common relationships between pairs of individuals may be obtained by looking at tabulated zi values. Conclusions A simple method is provided, which may be used by any scientist with the help of a calculator or a spreadsheet to compute the likelihood ratios of common alternative relationships between pairs of individuals. PMID:12441003

Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma

PubMed Central

Gatto, Francesco; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Several common oncogenic pathways have been implicated in the emergence of renowned metabolic features in cancer, which in turn are deemed essential for cancer proliferation and survival. However, the extent to which different cancers coordinate their metabolism to meet these requirements is largely unexplored. Here we show that even in the heterogeneity of metabolic regulation a distinct signature encompassed most cancers. On the other hand, clear cell renal cell carcinoma (ccRCC) strongly deviated in terms of metabolic gene expression changes, showing widespread down-regulation. We observed a metabolic shift that associates differential regulation of enzymes in one-carbon metabolism with high tumor stage and poor clinical outcome. A significant yet limited set of metabolic genes that explained the partial divergence of ccRCC metabolism correlated with loss of von Hippel-Lindau tumor suppressor (VHL) and a potential activation of signal transducer and activator of transcription 1. Further network-dependent analyses revealed unique defects in nucleotide, one-carbon, and glycerophospholipid metabolism at the transcript and protein level, which contrasts findings in other tumors. Notably, this behavior is recapitulated by recurrent loss of heterozygosity in multiple metabolic genes adjacent to VHL. This study therefore shows how loss of heterozygosity, hallmarked by VHL deletion in ccRCC, may uniquely shape tumor metabolism. PMID:24550497

Estimability and simple dynamical analyses of range (range-rate range-difference) observations to artificial satellites. [laser range observations to LAGEOS using non-Bayesian statistics

NASA Technical Reports Server (NTRS)

Vangelder, B. H. W.

1978-01-01

Non-Bayesian statistics were used in simulation studies centered around laser range observations to LAGEOS. The capabilities of satellite laser ranging especially in connection with relative station positioning are evaluated. The satellite measurement system under investigation may fall short in precise determinations of the earth's orientation (precession and nutation) and earth's rotation as opposed to systems as very long baseline interferometry (VLBI) and lunar laser ranging (LLR). Relative station positioning, determination of (differential) polar motion, positioning of stations with respect to the earth's center of mass and determination of the earth's gravity field should be easily realized by satellite laser ranging (SLR). The last two features should be considered as best (or solely) determinable by SLR in contrast to VLBI and LLR.

The Mars Observer differential one-way range demonstration

NASA Technical Reports Server (NTRS)

Kroger, P. M.; Border, J. S.; Nandi, S.

1994-01-01

Current methods of angular spacecraft positioning using station differenced range data require an additional observation of an extragalactic radio source (quasar) to estimate the timing offset between the reference clocks at the two Deep Space Stations. The quasar observation is also used to reduce the effects of instrumental and media delays on the radio metric observable by forming a difference with the spacecraft observation (delta differential one-way range, delta DOR). An experiment has been completed using data from the Global Positioning System satellites to estimate the station clock offset, eliminating the need for the quasar observation. The requirements for direct measurement of the instrumental delays that must be made in the absence of a quasar observation are assessed. Finally, the results of the 'quasar-free' differential one-way range, or DOR, measurements of the Mars Observer spacecraft are compared with those of simultaneous conventional delta DOR measurements.

An integer programming formulation of the parsimonious loss of heterozygosity problem.

PubMed

Catanzaro, Daniele; Labbé, Martine; Halldórsson, Bjarni V

2013-01-01

A loss of heterozygosity (LOH) event occurs when, by the laws of Mendelian inheritance, an individual should be heterozygote at a given site but, due to a deletion polymorphism, is not. Deletions play an important role in human disease and their detection could provide fundamental insights for the development of new diagnostics and treatments. In this paper, we investigate the parsimonious loss of heterozygosity problem (PLOHP), i.e., the problem of partitioning suspected polymorphisms from a set of individuals into a minimum number of deletion areas. Specifically, we generalize Halldórsson et al.'s work by providing a more general formulation of the PLOHP and by showing how one can incorporate different recombination rates and prior knowledge about the locations of deletions. Moreover, we show that the PLOHP can be formulated as a specific version of the clique partition problem in a particular class of graphs called undirected catch-point interval graphs and we prove its general $({\\cal NP})$-hardness. Finally, we provide a state-of-the-art integer programming (IP) formulation and strengthening valid inequalities to exactly solve real instances of the PLOHP containing up to 9,000 individuals and 3,000 SNPs. Our results give perspectives on the mathematics of the PLOHP and suggest new directions on the development of future efficient exact solution approaches.

Quantifying the increase in average human heterozygosity due to urbanisation.

PubMed

Rudan, Igor; Carothers, Andrew D; Polasek, Ozren; Hayward, Caroline; Vitart, Veronique; Biloglav, Zrinka; Kolcic, Ivana; Zgaga, Lina; Ivankovic, Davor; Vorko-Jovic, Ariana; Wilson, James F; Weber, James L; Hastie, Nick; Wright, Alan; Campbell, Harry

2008-09-01

The human population is undergoing a major transition from a historical metapopulation structure of relatively isolated small communities to an outbred structure. This process is predicted to increase average individual genome-wide heterozygosity (h) and could have effects on health. We attempted to quantify this increase in mean h. We initially sampled 1001 examinees from a metapopulation of nine isolated villages on five Dalmatian islands (Croatia). Village populations had high levels of genetic differentiation, endogamy and consanguinity. We then selected 166 individuals with highly specific personal genetic histories to form six subsamples, which could be ranked a priori by their predicted level of outbreeding. The measure h was then estimated in the 166 examinees by genotyping 1184 STR/indel markers and using two different computation methods. Compared to the value of mean h in the least outbred sample, values of h in the remaining samples increased successively with predicted outbreeding by 0.023, 0.038, 0.058, 0.067 and 0.079 (P<0.0001), where these values are measured on the same scale as the inbreeding coefficient (but opposite sign). We have shown that urbanisation was associated with an average increase in h of up to 0.08-0.10 in this Croatian metapopulation, regardless of the method used. Similar levels of differentiation have been described in many populations. Therefore, changes in the level of heterozygosity across the genome of this magnitude may be common during isolate break-up in humans and could have significant health effects through the established genetic mechanism of hybrid vigour/heterosis.

Phytophthora capsici - Loss of Heterozygosity (LOH): A Widespread Mechanism for Rapid Adaptation (7th Annual SFAF Meeting, 2012)

ScienceCinema

Mudge, Joanne

2018-01-15

Joanne Mudge on "Phytophthora capsici - Loss of Heterozygosity (LOH): A Widespread Mechanism for Rapid Mutation" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

Evidence of opposing fitness effects of parental heterozygosity and relatedness in a critically endangered marine turtle?

PubMed

Phillips, K P; Jorgensen, T H; Jolliffe, K G; Richardson, D S

2017-11-01

How individual genetic variability relates to fitness is important in understanding evolution and the processes affecting populations of conservation concern. Heterozygosity-fitness correlations (HFCs) have been widely used to study this link in wild populations, where key parameters that affect both variability and fitness, such as inbreeding, can be difficult to measure. We used estimates of parental heterozygosity and genetic similarity ('relatedness') derived from 32 microsatellite markers to explore the relationship between genetic variability and fitness in a population of the critically endangered hawksbill turtle, Eretmochelys imbricata. We found no effect of maternal MLH (multilocus heterozygosity) on clutch size or egg success rate, and no single-locus effects. However, we found effects of paternal MLH and parental relatedness on egg success rate that interacted in a way that may result in both positive and negative effects of genetic variability. Multicollinearity in these tests was within safe limits, and null simulations suggested that the effect was not an artefact of using paternal genotypes reconstructed from large samples of offspring. Our results could imply a tension between inbreeding and outbreeding depression in this system, which is biologically feasible in turtles: female-biased natal philopatry may elevate inbreeding risk and local adaptation, and both processes may be disrupted by male-biased dispersal. Although this conclusion should be treated with caution due to a lack of significant identity disequilibrium, our study shows the importance of considering both positive and negative effects when assessing how variation in genetic variability affects fitness in wild systems. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Dissecting Loss of Heterozygosity (LOH) in Neurofibromatosis Type 1-Associated Neurofibromas: Importance of Copy Neutral LOH

PubMed Central

Garcia-Linares, Carles; Fernández-Rodríguez, Juana; Terribas, Ernest; Mercadé, Jaume; Pros, Eva; Benito, Llúcia; Benavente, Yolanda; Capellà, Gabriel; Ravella, Anna; Blanco, Ignacio; Kehrer-Sawatzki, Hildegard; Lázaro, Conxi; Serra, Eduard

2011-01-01

Dermal neurofibromas (dNFs) are benign tumors of the peripheral nervous system typically associated with Neurofibromatosis type 1 (NF1) patients. Genes controlling the integrity of the DNA are likely to influence the number of neurofibromas developed because dNFs are caused by somatic mutational inactivation of the NF1 gene, frequently evidenced by loss of heterozygosity (LOH). We performed a comprehensive analysis of the prevalence and mechanisms of LOH in dNFs. Our study included 518 dNFs from 113 patients. LOH was detected in 25% of the dNFs (N = 129). The most frequent mechanism causing LOH was mitotic recombination, which was observed in 62% of LOH-tumors (N = 80), and which does not reduce the number of NF1 gene copies. All events were generated by a single crossover located between the centromere and the NF1 gene, resulting in isodisomy of 17q. LOH due to the loss of the NF1 gene accounted for a 38% of dNFs with LOH (N = 49), with deletions ranging in size from ∼80 kb to ∼8 Mb within 17q. In one tumor we identified the first example of a neurofibroma-associated second-hit type-2 NF1 deletion. Analysis of the prevalence of mechanisms causing LOH in dNFs in individual patients (possibly under genetic control) will elucidate whether there exist interindividual variation. Hum Mutat 32:78–90, 2011. © 2010 Wiley-Liss, Inc. PMID:21031597

HeFPipe: a complete analytical pipeline for heterozygosity-fitness correlation studies.

PubMed

Fisher, Mark A

2014-01-01

As the body of heterozygosity-fitness correlation (HFC) research grows, more and increasingly complicated tests have become an integral part of a typical HFC analysis (Chapman et al. 2009). Currently, no software is available to undertake conversion between the file formats required to conduct all of these tests and to conduct the main regression analyses at the core of all HFCs. Heterozygosity-Fitness Pipeline (HeFPipe) is a script written in Python that accomplishes both of these tasks for studies based on microsatellite data. HeFPipe is designed to be used from the command line terminal and will run on any Mac OSX computer. The script takes input in the form of allele reports from either the genotype-calling software, GeneMapper or GeneMarker, and reconfigures the data into GENEPOP (Raymond & Rousset 1995), Rhh (Alho et al. 2010), RMES (David et al. 2007) and GEPHAST (Amos & Acevedo-Whitehouse 2009) formats. The script is also equipped to reformat the output from GENEPOP on the Web (option 5) and Rhh into csv spreadsheets that can be incorporated into downstream analyses. HeFPipe accommodates user-provided lists of samples and markers to be included in or excluded from analyses. HeFPipe is equipped to create generalized linear models (GLMs) from both the main data set and subsets of the data. Finally, HeFPipe allows users to explore single-marker effects and conduct correlation analyses. The script, a comprehensive manual, a link to a series of video tutorials, and an example data set are available from GitHub (http://github.com/Atticus29/HeFPipe_rpos). © 2013 John Wiley & Sons Ltd.

Integument coloration signals reproductive success, heterozygosity, and antioxidant levels in chick-rearing black-legged kittiwakes

NASA Astrophysics Data System (ADS)

Leclaire, Sarah; White, Joël; Arnoux, Emilie; Faivre, Bruno; Vetter, Nathanaël; Hatch, Scott A.; Danchin, Étienne

2011-09-01

Carotenoid pigments are important for immunity and as antioxidants, and carotenoid-based colors are believed to provide honest signals of individual quality. Other colorless but more efficient antioxidants such as vitamins A and E may protect carotenoids from bleaching. Carotenoid-based colors have thus recently been suggested to reflect the concentration of such colorless antioxidants, but this has rarely been tested. Furthermore, although evidence is accruing for multiple genetic criteria for mate choice, carotenoid-based colors have rarely been shown to reflect both phenotypic and genetic quality. In this study, we investigated whether gape, tongue, eye-ring, and bill coloration of chick-rearing black-legged kittiwakes Rissa tridactyla reflected circulating levels of carotenoids and vitamins A and E. We further investigated whether integument coloration reflected phenotypic (body condition and fledging success) and genetic quality (heterozygosity). We found that the coloration of fleshy integuments was correlated with carotenoid and vitamin A levels and fledging success but only in males. Furthermore, the coloration of tongue and eye-ring was correlated with heterozygosity in both males and females. Integument colors might therefore be reliable signals of individual quality used by birds to adjust their parental care during the chick-rearing period.

Maternal heterozygosity and progeny fitness association in an inbred Scots pine population.

PubMed

Abrahamsson, S; Ahlinder, J; Waldmann, P; García-Gil, M R

2013-03-01

Associations between heterozygosity and fitness traits have typically been investigated in populations characterized by low levels of inbreeding. We investigated the associations between standardized multilocus heterozygosity (stMLH) in mother trees (obtained from12 nuclear microsatellite markers) and five fitness traits measured in progenies from an inbred Scots pine population. The traits studied were proportion of sound seed, mean seed weight, germination rate, mean family height of one-year old seedlings under greenhouse conditions (GH) and mean family height of three-year old seedlings under field conditions (FH). The relatively high average inbreeding coefficient (F) in the population under study corresponds to a mixture of trees with different levels of co-ancestry, potentially resulting from a recent bottleneck. We used both frequentist and Bayesian methods of polynomial regression to investigate the presence of linear and non-linear relations between stMLH and each of the fitness traits. No significant associations were found for any of the traits except for GH, which displayed negative linear effect with stMLH. Negative HFC for GH could potentially be explained by the effect of heterosis caused by mating of two inbred mother trees (Lippman and Zamir 2006), or outbreeding depression at the most heterozygote trees and its negative impact on the fitness of the progeny, while their simultaneous action is also possible (Lynch. 1991). However,since this effect wasn't detected for FH, we cannot either rule out that the greenhouse conditions introduce artificial effects that disappear under more realistic field conditions.

Social pairing of Seychelles warblers under reduced constraints: MHC, neutral heterozygosity, and age.

PubMed

Wright, David J; Brouwer, Lyanne; Mannarelli, Maria-Elena; Burke, Terry; Komdeur, Jan; Richardson, David S

2016-01-01

The prevalence and significance of precopulatory mate choice remains keenly debated. The major histocompatibility complex (MHC) plays a key role in vertebrate adaptive immunity, and variation at the MHC influences individual survival. Although MHC-dependent mate choice has been documented in certain species, many other studies find no such pattern. This may be, at least in part, because in natural systems constraints may reduce the choices available to individuals and prevent full expression of underlying preferences. We used translocations to previously unoccupied islands to experimentally reduce constraints on female social mate choice in the Seychelles warbler ( Acrocephalus sechellensis ), a species in which patterns of MHC-dependent extrapair paternity (EPP), but not social mate choice, have been observed. We find no evidence of MHC-dependent social mate choice in the new populations. Instead, we find that older males and males with more microsatellite heterozygosity are more likely to have successfully paired. Our data cannot resolve whether these patterns in pairing were due to male-male competition or female choice. However, our research does suggest that female Seychelles warblers do not choose social mates using MHC class I to increase fitness. It may also indicate that the MHC-dependent EPP observed in the source population is probably due to mechanisms other than female precopulatory mate choice based on MHC cues.

Social pairing of Seychelles warblers under reduced constraints: MHC, neutral heterozygosity, and age

PubMed Central

Wright, David J.; Brouwer, Lyanne; Mannarelli, Maria-Elena; Burke, Terry; Komdeur, Jan

2016-01-01

The prevalence and significance of precopulatory mate choice remains keenly debated. The major histocompatibility complex (MHC) plays a key role in vertebrate adaptive immunity, and variation at the MHC influences individual survival. Although MHC-dependent mate choice has been documented in certain species, many other studies find no such pattern. This may be, at least in part, because in natural systems constraints may reduce the choices available to individuals and prevent full expression of underlying preferences. We used translocations to previously unoccupied islands to experimentally reduce constraints on female social mate choice in the Seychelles warbler (Acrocephalus sechellensis), a species in which patterns of MHC-dependent extrapair paternity (EPP), but not social mate choice, have been observed. We find no evidence of MHC-dependent social mate choice in the new populations. Instead, we find that older males and males with more microsatellite heterozygosity are more likely to have successfully paired. Our data cannot resolve whether these patterns in pairing were due to male–male competition or female choice. However, our research does suggest that female Seychelles warblers do not choose social mates using MHC class I to increase fitness. It may also indicate that the MHC-dependent EPP observed in the source population is probably due to mechanisms other than female precopulatory mate choice based on MHC cues. PMID:26792973

BCR expression is decreased in meningiomas showing loss of heterozygosity of 22q within a new minimal deletion region.

PubMed

Wozniak, K; Piaskowski, S; Gresner, S M; Golanska, E; Bieniek, E; Bigoszewska, K; Sikorska, B; Szybka, M; Kulczycka-Wojdala, D; Zakrzewska, M; Zawlik, I; Papierz, W; Stawski, R; Jaskolski, D J; Och, W; Sieruta, M; Liberski, P P; Rieske, P

2008-05-01

Neurofibromin 2 (NF2), located on chromosome arm 22q, has been established as a tumor suppressor gene involved in meningioma pathogenesis. In our study, we investigated 149 meningiomas to determine whether there are additional tumor suppressor genes localized on chromosome 22q, apart from NF2, that might be involved in meningioma pathogenesis. The LOH analysis on chromosome 22q identified two regions of deletion: the first one, which is limited to the NF2 gene locus, and the second one, which is outside this location. The new minimal deletion region (MDR) included the following genes: BCR (breakpoint cluster region), RAB36 (a member of RAS oncogene family), GNAZ [guanine nucleotide binding protein (G protein), alpha-z polypeptide], and RTDR1 (rhabdoid tumor deletion region gene 1). The expression levels of all these genes, including NF2, were subsequently analyzed by quantitative real-time polymerase chain reaction. We observed a significantly lowered expression level of NF2 in meningiomas with 22q loss of heterozygosity (LOH) within NF2 region compared to the one in meningiomas with 22q retention of heterozygosity (ROH, P<0.05). Similarly, BCR showed a significantly lowered expression in meningiomas with 22q LOH within the new MDR compared to cases with 22q ROH (P<0.05). Our data, together with the already published information considering BCR function suggest that BCR can be considered as a candidate tumor suppressor gene localized on chromosome 22q which may be involved in meningioma pathogenesis.

Integument coloration signals reproductive success, heterozygosity, and antioxidant levels in chick-rearing black-legged kittiwakes

USGS Publications Warehouse

Leclaire, S.; White, J.; Arnoux, E.; Faivre, B.; Vetter, N.; Hatch, Shyla A.; Danchin, E.

2011-01-01

Carotenoid pigments are important for immunity and as antioxidants, and carotenoid-based colors are believed to provide honest signals of individual quality. Other colorless but more efficient antioxidants such as vitamins A and E may protect carotenoids from bleaching. Carotenoid-based colors have thus recently been suggested to reflect the concentration of such colorless antioxidants, but this has rarely been tested. Furthermore, although evidence is accruing for multiple genetic criteria for mate choice, carotenoid-based colors have rarely been shown to reflect both phenotypic and genetic quality. In this study, we investigated whether gape, tongue, eye-ring, and bill coloration of chick-rearing black-legged kittiwakes Rissa tridactyla reflected circulating levels of carotenoids and vitamins A and E. We further investigated whether integument coloration reflected phenotypic (body condition and fledging success) and genetic quality (heterozygosity). We found that the coloration of fleshy integuments was correlated with carotenoid and vitamin A levels and fledging success but only in males. Furthermore, the coloration of tongue and eye-ring was correlated with heterozygosity in both males and females. Integument colors might therefore be reliable signals of individual quality used by birds to adjust their parental care during the chick-rearing period. ?? Springer-Verlag 2011.

[A compound heterozygosity mutation in the interleukin-7 receptor-alpha gene resulted in severe combined immunodeficiency in a Chinese patient].

PubMed

Zhang, Zhi-yong; Zhao, Xiao-dong; Wang, Mo; Yu, Jie; An, Yun-fei; Yang, Xi-qiang

2009-09-01

Mutation in the interleukin-7 receptor-alpha (IL-7R alpha) chain causes a rare type of severe combined immunodeficiency (SCID) with presence of NK cells in the peripheral blood. Here we report the molecular and clinical characterization of a compound heterozygosity mutation in the interleukin-7 receptor-alpha gene that resulted in SCID in a patient firstly from China. A 5 month-old male patient and his parents were enrolled in this study. Since 15 days of age, the patient had had recurrent fever, persistent cough and diarrhea. He was in poor general condition with pyorrhea and ulceration of the BCG scar. His brother died of severe infection at 4 months of age. He was initially diagnosed as SCID according to clinical manifestation and immunological analysis. A panel of SCID candidate genes including IL-2RG, RAG1/RAG2 and IL-7R alpha of patient and his parents were amplified by polymerase chain reaction (PCR) from genomic DNA. Reverse transcription polymerase chain reaction (RT-PCR) was used to amplify the IL-7R alpha transcripts. Sequencing was performed directly on the PCR products forward and reversely. The serum immunoglobulin (Ig) profile was IgG 6867 mg/L (normal range, 3050 - 8870 mg/L); IgM 206 mg/L and IgA 249 mg/L, IgE 2.3 IU/ml (normal range < 150 IU/ml). The patient was treated with IVIG previously. There were no T-cells but increased percentage of B-cells (58%) and NK cells (42%) in the peripheral blood was found. Needle biopsies from enlarged axillary lymph node was identified positive for Mycobacterium bovis under microscope and by culture. The patient had a compound heterozygosity mutation in the IL-7R alpha gene:on one allele, there was a splice-junction mutation in intron 4 (intron 4(+1)G > A), for which his father was a carrier; whereas on the other allele, a nonsense mutation at position 638 in exon 5 with a premature stop codon (638 C > T, R206X) was identified, for which his mother was a carrier. The splice-junction mutation in intron 4 of IL-7R

CHEK2*1100delC Heterozygosity in Women With Breast Cancer Associated With Early Death, Breast Cancer–Specific Death, and Increased Risk of a Second Breast Cancer

PubMed Central

Weischer, Maren; Nordestgaard, Børge G.; Pharoah, Paul; Bolla, Manjeet K.; Nevanlinna, Heli; van't Veer, Laura J.; Garcia-Closas, Montserrat; Hopper, John L.; Hall, Per; Andrulis, Irene L.; Devilee, Peter; Fasching, Peter A.; Anton-Culver, Hoda; Lambrechts, Diether; Hooning, Maartje; Cox, Angela; Giles, Graham G.; Burwinkel, Barbara; Lindblom, Annika; Couch, Fergus J.; Mannermaa, Arto; Grenaker Alnæs, Grethe; John, Esther M.; Dörk, Thilo; Flyger, Henrik; Dunning, Alison M.; Wang, Qin; Muranen, Taru A.; van Hien, Richard; Figueroa, Jonine; Southey, Melissa C.; Czene, Kamila; Knight, Julia A.; Tollenaar, Rob A.E.M.; Beckmann, Matthias W.; Ziogas, Argyrios; Christiaens, Marie-Rose; Collée, Johanna Margriet; Reed, Malcolm W.R.; Severi, Gianluca; Marme, Frederik; Margolin, Sara; Olson, Janet E.; Kosma, Veli-Matti; Kristensen, Vessela N.; Miron, Alexander; Bogdanova, Natalia; Shah, Mitul; Blomqvist, Carl; Broeks, Annegien; Sherman, Mark; Phillips, Kelly-Anne; Li, Jingmei; Liu, Jianjun; Glendon, Gord; Seynaeve, Caroline; Ekici, Arif B.; Leunen, Karin; Kriege, Mieke; Cross, Simon S.; Baglietto, Laura; Sohn, Christof; Wang, Xianshu; Kataja, Vesa; Børresen-Dale, Anne-Lise; Meyer, Andreas; Easton, Douglas F.; Schmidt, Marjanka K.; Bojesen, Stig E.

2012-01-01

Purpose We tested the hypotheses that CHEK2*1100delC heterozygosity is associated with increased risk of early death, breast cancer–specific death, and risk of a second breast cancer in women with a first breast cancer. Patients and Methods From 22 studies participating in the Breast Cancer Association Consortium, 25,571 white women with invasive breast cancer were genotyped for CHEK2*1100delC and observed for up to 20 years (median, 6.6 years). We examined risk of early death and breast cancer–specific death by estrogen receptor status and risk of a second breast cancer after a first breast cancer in prospective studies. Results CHEK2*1100delC heterozygosity was found in 459 patients (1.8%). In women with estrogen receptor–positive breast cancer, multifactorially adjusted hazard ratios for heterozygotes versus noncarriers were 1.43 (95% CI, 1.12 to 1.82; log-rank P = .004) for early death and 1.63 (95% CI, 1.24 to 2.15; log-rank P < .001) for breast cancer–specific death. In all women, hazard ratio for a second breast cancer was 2.77 (95% CI, 2.00 to 3.83; log-rank P < .001) increasing to 3.52 (95% CI, 2.35 to 5.27; log-rank P < .001) in women with estrogen receptor–positive first breast cancer only. Conclusion Among women with estrogen receptor–positive breast cancer, CHEK2*1100delC heterozygosity was associated with a 1.4-fold risk of early death, a 1.6-fold risk of breast cancer–specific death, and a 3.5-fold risk of a second breast cancer. This is one of the few examples of a genetic factor that influences long-term prognosis being documented in an extensive series of women with breast cancer. PMID:23109706

CHEK2*1100delC heterozygosity in women with breast cancer associated with early death, breast cancer-specific death, and increased risk of a second breast cancer.

PubMed

Weischer, Maren; Nordestgaard, Børge G; Pharoah, Paul; Bolla, Manjeet K; Nevanlinna, Heli; Van't Veer, Laura J; Garcia-Closas, Montserrat; Hopper, John L; Hall, Per; Andrulis, Irene L; Devilee, Peter; Fasching, Peter A; Anton-Culver, Hoda; Lambrechts, Diether; Hooning, Maartje; Cox, Angela; Giles, Graham G; Burwinkel, Barbara; Lindblom, Annika; Couch, Fergus J; Mannermaa, Arto; Grenaker Alnæs, Grethe; John, Esther M; Dörk, Thilo; Flyger, Henrik; Dunning, Alison M; Wang, Qin; Muranen, Taru A; van Hien, Richard; Figueroa, Jonine; Southey, Melissa C; Czene, Kamila; Knight, Julia A; Tollenaar, Rob A E M; Beckmann, Matthias W; Ziogas, Argyrios; Christiaens, Marie-Rose; Collée, Johanna Margriet; Reed, Malcolm W R; Severi, Gianluca; Marme, Frederik; Margolin, Sara; Olson, Janet E; Kosma, Veli-Matti; Kristensen, Vessela N; Miron, Alexander; Bogdanova, Natalia; Shah, Mitul; Blomqvist, Carl; Broeks, Annegien; Sherman, Mark; Phillips, Kelly-Anne; Li, Jingmei; Liu, Jianjun; Glendon, Gord; Seynaeve, Caroline; Ekici, Arif B; Leunen, Karin; Kriege, Mieke; Cross, Simon S; Baglietto, Laura; Sohn, Christof; Wang, Xianshu; Kataja, Vesa; Børresen-Dale, Anne-Lise; Meyer, Andreas; Easton, Douglas F; Schmidt, Marjanka K; Bojesen, Stig E

2012-12-10

We tested the hypotheses that CHEK2*1100delC heterozygosity is associated with increased risk of early death, breast cancer-specific death, and risk of a second breast cancer in women with a first breast cancer. From 22 studies participating in the Breast Cancer Association Consortium, 25,571 white women with invasive breast cancer were genotyped for CHEK2*1100delC and observed for up to 20 years (median, 6.6 years). We examined risk of early death and breast cancer-specific death by estrogen receptor status and risk of a second breast cancer after a first breast cancer in prospective studies. CHEK2*1100delC heterozygosity was found in 459 patients (1.8%). In women with estrogen receptor-positive breast cancer, multifactorially adjusted hazard ratios for heterozygotes versus noncarriers were 1.43 (95% CI, 1.12 to 1.82; log-rank P = .004) for early death and 1.63 (95% CI, 1.24 to 2.15; log-rank P < .001) for breast cancer-specific death. In all women, hazard ratio for a second breast cancer was 2.77 (95% CI, 2.00 to 3.83; log-rank P < .001) increasing to 3.52 (95% CI, 2.35 to 5.27; log-rank P < .001) in women with estrogen receptor-positive first breast cancer only. Among women with estrogen receptor-positive breast cancer, CHEK2*1100delC heterozygosity was associated with a 1.4-fold risk of early death, a 1.6-fold risk of breast cancer-specific death, and a 3.5-fold risk of a second breast cancer. This is one of the few examples of a genetic factor that influences long-term prognosis being documented in an extensive series of women with breast cancer.

Loss of heterozygosity assay for molecular detection of cancer using energy-transfer primers and capillary array electrophoresis.

PubMed

Medintz, I L; Lee, C C; Wong, W W; Pirkola, K; Sidransky, D; Mathies, R A

2000-08-01

Microsatellite DNA loci are useful markers for the detection of loss of heterozygosity (LOH) and microsatellite instability (MI) associated with primary cancers. To carry out large-scale studies of LOH and MI in cancer progression, high-throughput instrumentation and assays with high accuracy and sensitivity need to be validated. DNA was extracted from 26 renal tumor and paired lymphocyte samples and amplified with two-color energy-transfer (ET) fluorescent primers specific for loci associated with cancer-induced chromosomal changes. PCR amplicons were separated on the MegaBACE-1000 96 capillary array electrophoresis (CAE) instrument and analyzed with MegaBACE Genetic Profiler v.1.0 software. Ninety-six separations were achieved in parallel in 75 minutes. Loss of heterozygosity was easily detected in tumor samples as was the gain/loss of microsatellite core repeats. Allelic ratios were determined with a precision of +/- 10% or better. Prior analysis of these samples with slab gel electrophoresis and radioisotope labeling had not detected these changes with as much sensitivity or precision. This study establishes the validity of this assay and the MegaBACE instrument for large-scale, high-throughput studies of the molecular genetic changes associated with cancer.

Contrasting effects of heterozygosity on survival and hookworm resistance in California sea lion pups.

PubMed

Acevedo-Whitehouse, Karina; Spraker, Terry R; Lyons, Eugene; Melin, Sharon R; Gulland, Frances; Delong, Robert L; Amos, William

2006-06-01

Low genetic heterozygosity is associated with loss of fitness in many natural populations. However, it remains unclear whether the mechanism is related to general (i.e. inbreeding) or local effects, in particular from a subset of loci lying close to genes under balancing selection. Here we analyse involving heterozygosity-fitness correlations on neonatal survival of California sea lions and on susceptibility to hookworm (Uncinaria spp.) infection, the single most important cause of pup mortality. We show that regardless of differences in hookworm burden, homozygosity is a key predictor of hookworm-related lesions, with no single locus contributing disproportionately. Conversely, the subsequent occurrence of anaemia due to blood loss in infected pups is overwhelmingly associated with homozygosity at one particular locus, all other loci showing no pattern. Our results suggest contrasting genetic mechanisms underlying two pathologies related to the same pathogen. First, relatively inbred pups are less able to expel hookworms and prevent their attachment to the intestinal mucosa, possibly due to a weakened immune response. In contrast, infected pups that are homozygous for a gene near to microsatellite Hg4.2 are strongly predisposed to anaemia. As yet, this gene is unknown, but could plausibly be involved in the blood-coagulation cascade. Taken together, these results suggest that pathogenic burden alone may not be the main factor regulating pathogen-related mortality in natural populations. Our study could have important implications for the conservation of small, isolated or threatened populations, particularly when they are at a risk of facing pathogenic challenges.

Inbreeding and disease resistance in a social insect: effects of heterozygosity on immunocompetence in the termite Zootermopsis angusticollis

PubMed Central

Calleri, Daniel V; McGrail Reid, Ellen; Rosengaus, Rebeca B; Vargo, Edward L; Traniello, James F.A

2006-01-01

Recent research has shown that low genetic variation in individuals can increase susceptibility to infection and group living may exacerbate pathogen transmission. In the eusocial diploid termites, cycles of outbreeding and inbreeding characterizing basal species can reduce genetic variation within nestmates during the life of a colony, but the relationship of genetic heterogeneity to disease resistance is poorly understood. Here we show that, one generation of inbreeding differentially affects the survivorship of isolated and grouped termites (Zootermopsis angusticollis) depending on the nature of immune challenge and treatment. Inbred and outbred isolated and grouped termites inoculated with a bacterial pathogen, exposed to a low dose of fungal pathogen or challenged with an implanted nylon monofilament had similar levels of immune defence. However, inbred grouped termites exposed to a relatively high concentration of fungal conidia had significantly greater mortality than outbred grouped termites. Inbred termites also had significantly higher cuticular microbial loads, presumably due to less effective grooming by nestmates. Genetic analyses showed that inbreeding significantly reduced heterozygosity and allelic diversity. Decreased heterozygosity thus appeared to increase disease susceptibility by affecting social behaviour or some other group-level process influencing infection control rather than affecting individual immune physiology. PMID:17002949

Relationships Between Long-Range Lightning Networks and TRMM/LIS Observations

NASA Technical Reports Server (NTRS)

Rudlosky, Scott D.; Holzworth, Robert H.; Carey, Lawrence D.; Schultz, Chris J.; Bateman, Monte; Cummins, Kenneth L.; Cummins, Kenneth L.; Blakeslee, Richard J.; Goodman, Steven J.

2012-01-01

Recent advances in long-range lightning detection technologies have improved our understanding of thunderstorm evolution in the data sparse oceanic regions. Although the expansion and improvement of long-range lightning datasets have increased their applicability, these applications (e.g., data assimilation, atmospheric chemistry, and aviation weather hazards) require knowledge of the network detection capabilities. The present study intercompares long-range lightning data with observations from the Lightning Imaging Sensor (LIS) aboard the Tropical Rainfall Measurement Mission (TRMM) satellite. The study examines network detection efficiency and location accuracy relative to LIS observations, describes spatial variability in these performance metrics, and documents the characteristics of LIS flashes that are detected by the long-range networks. Improved knowledge of relationships between these datasets will allow researchers, algorithm developers, and operational users to better prepare for the spatial and temporal coverage of the upcoming GOES-R Geostationary Lightning Mapper (GLM).

Inferring modes of colonization for pest species using heterozygosity comparisons and a shared-allele test.

PubMed

Sved, J A; Yu, H; Dominiak, B; Gilchrist, A S

2003-02-01

Long-range dispersal of a species may involve either a single long-distance movement from a core population or spreading via unobserved intermediate populations. Where the new populations originate as small propagules, genetic drift may be extreme and gene frequency or assignment methods may not prove useful in determining the relation between the core population and outbreak samples. We describe computationally simple resampling methods for use in this situation to distinguish between the different modes of dispersal. First, estimates of heterozygosity can be used to test for direct sampling from the core population and to estimate the effective size of intermediate populations. Second, a test of sharing of alleles, particularly rare alleles, can show whether outbreaks are related to each other rather than arriving as independent samples from the core population. The shared-allele statistic also serves as a genetic distance measure that is appropriate for small samples. These methods were applied to data on a fruit fly pest species, Bactrocera tryoni, which is quarantined from some horticultural areas in Australia. We concluded that the outbreaks in the quarantine zone came from a heterogeneous set of genetically differentiated populations, possibly ones that overwinter in the vicinity of the quarantine zone.

Inferring modes of colonization for pest species using heterozygosity comparisons and a shared-allele test.

PubMed Central

Sved, J A; Yu, H; Dominiak, B; Gilchrist, A S

2003-01-01

Long-range dispersal of a species may involve either a single long-distance movement from a core population or spreading via unobserved intermediate populations. Where the new populations originate as small propagules, genetic drift may be extreme and gene frequency or assignment methods may not prove useful in determining the relation between the core population and outbreak samples. We describe computationally simple resampling methods for use in this situation to distinguish between the different modes of dispersal. First, estimates of heterozygosity can be used to test for direct sampling from the core population and to estimate the effective size of intermediate populations. Second, a test of sharing of alleles, particularly rare alleles, can show whether outbreaks are related to each other rather than arriving as independent samples from the core population. The shared-allele statistic also serves as a genetic distance measure that is appropriate for small samples. These methods were applied to data on a fruit fly pest species, Bactrocera tryoni, which is quarantined from some horticultural areas in Australia. We concluded that the outbreaks in the quarantine zone came from a heterogeneous set of genetically differentiated populations, possibly ones that overwinter in the vicinity of the quarantine zone. PMID:12618417

Analysis of genetic composition and transmitted parental heterozygosity of natural 2n gametes in Populus tomentosa based on SSR markers.

PubMed

Han, Zhiqiang; Geng, Xining; Du, Kang; Xu, Congping; Yao, Pengqiang; Bai, Fengying; Kang, Xiangyang

2018-06-01

Natural 2n female gametes and transmission of parental heterozygosity by natural 2n gametes in Populus tomentosa are reported for the first time, which provides a new approach to polyploid breeding. Naturally occurring 2n pollen is widespread in Populus tomentosa and plays an important role in polyploid breeding. However, the competitiveness of 2n pollen is lower than that of haploid pollen during pollination and fertilization, so 2n pollen is less efficient at fertilizing haploid female gametes to produce polyploids. In theory, polyploids can also be obtained when 2n female gametes are fertilized by haploid pollen. Thus, the question becomes whether natural 2n female gametes exist in P. tomentosa, which can be answered by examining the genetic composition of natural 2n gametes. In this study, the origin of 87 triploids from the hybrid combination "X-2 × Z-5" was identified by SSR markers and 21% of natural 2n gametes were found to originate from female parents. Four SSR loci with low recombination rates were used to identify the genetic composition of natural 2n gametes. The results showed that the genetic composition of 2n female gametes was mainly characterized by SDR, while 2n male gametes were mainly produced by FDR. Moreover, the transmission of parental heterozygosity by natural 2n gametes, which is significantly different between female and male parents in FDR and SDR types, was analysed using 42 SSR primers. Here, we report naturally occurring 2n female gametes for the first time in P. tomentosa and reveal the genetic constitution and transmitted parental heterozygosity of these gametes. Our results provide a foundation for theoretical research into 2n gametes and their application in new polyploid breeding strategies.

Observing tectonic plate motions and deformations from satellite laser ranging

NASA Technical Reports Server (NTRS)

Christodoulidis, D. C.; Smith, D. E.; Kolenkiewicz, R.; Klosko, S. M.; Torrence, M. H.

1985-01-01

The scope of geodesy has been greatly affected by the advent of artificial near-earth satellites. The present paper provides a description of the results obtained from the reduction of data collected with the aid of satellite laser ranging. It is pointed out that dynamic reduction of satellite laser ranging (SLR) data provides very precise positions in three dimensions for the laser tracking network. The vertical components of the stations, through the tracking geometry provided by the global network and the accurate knowledge of orbital dynamics, are uniquely related to the center of mass of the earth. Attention is given to the observations, the methodologies for reducing satellite observations to estimate station positions, Lageos-observed tectonic plate motions, an improved temporal resolution of SLR plate motions, and the SLR vertical datum.

High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly Used Candida albicans Strains

PubMed Central

Abbey, Darren; Hickman, Meleah; Gresham, David; Berman, Judith

2011-01-01

Phenotypic diversity can arise rapidly through loss of heterozygosity (LOH) or by the acquisition of copy number variations (CNV) spanning whole chromosomes or shorter contiguous chromosome segments. In Candida albicans, a heterozygous diploid yeast pathogen with no known meiotic cycle, homozygosis and aneuploidy alter clinical characteristics, including drug resistance. Here, we developed a high-resolution microarray that simultaneously detects ∼39,000 single nucleotide polymorphism (SNP) alleles and ∼20,000 copy number variation loci across the C. albicans genome. An important feature of the array analysis is a computational pipeline that determines SNP allele ratios based upon chromosome copy number. Using the array and analysis tools, we constructed a haplotype map (hapmap) of strain SC5314 to assign SNP alleles to specific homologs, and we used it to follow the acquisition of loss of heterozygosity (LOH) and copy number changes in a series of derived laboratory strains. This high-resolution SNP/CGH microarray and the associated hapmap facilitated the phasing of alleles in lab strains and revealed detrimental genome changes that arose frequently during molecular manipulations of laboratory strains. Furthermore, it provided a useful tool for rapid, high-resolution, and cost-effective characterization of changes in allele diversity as well as changes in chromosome copy number in new C. albicans isolates. PMID:22384363

Studies on Training Ground Observers to Estimate Range to Aerial Targets.

ERIC Educational Resources Information Center

McCluskey, Michael R.; And Others

Six pilot studies were conducted to determine the effects of training on range estimation performance for aerial targets, and to identify some of the relevant variables. Observers were trained to estimate ranges of 350, 400, 800, 1,500, or 2,500 meters. Several variations of range estimation training methods were used, including immediate…

Laser-ranging scanning system to observe topographical deformations of volcanoes.

PubMed

Aoki, T; Takabe, M; Mizutani, K; Itabe, T

1997-02-20

We have developed a laser-ranging system to observe the topographical structure of volcanoes. This system can be used to measure the distance to a target by a laser and shows the three-dimensional topographical structure of a volcano with an accuracy of 30 cm. This accuracy is greater than that of a typical laser-ranging system that uses a corner-cube reflector as a target because the reflected light jitters as a result of inclination and unevenness of the target ground surface. However, this laser-ranging system is useful for detecting deformations of topographical features in which placement of a reflector is difficult, such as in volcanic regions.

Isolation and characterization of microsatellite loci from the Arctic cisco (Coregonus autumnalis)

USGS Publications Warehouse

Ramey, A.; Graziano, S.L.; Nielsen, J.L.

2008-01-01

Eight polymorphic microsatellite loci were isolated and characterized for the Arctic cisco, Coregonus autumnalis. Loci were evaluated in 21 samples from the Colville River subsistence fishery. The number of alleles per locus ranged from two to 18. Observed heterozygosity of loci varied from 0.10 to 1.00, and expected heterozygosity ranged from 0.09 to 0.92. All eight microsatellite markers were in Hardy-Weinberg equilibrium. The loci presented here will be useful in describing population structure and exploring populations of origin for Arctic cisco. ?? 2007 Blackwell Publishing Ltd.

Allele Imbalance or Loss of Heterozygosity, in Normal Appearing Breast Epithelium as a Novel Biomarker to Predict Future Breast Cancer

DTIC Science & Technology

2011-07-10

benign biopsy, had no atypia on the benign biopsy, and had no family history of breast cancer. For each breast cancer case, she selected one control...biopsies lacked atypia , and who had no fa mily history of breast cancer. 10-μ sections were cut from paraffin blocks and TDLUs were removed by laser...TITLE: Allele Imbalance or loss of heterozygosity, in normal- appearing breast epithelium as a novel biomarker to predict future breast cancer

An Observability Metric for Underwater Vehicle Localization Using Range Measurements

PubMed Central

Arrichiello, Filippo; Antonelli, Gianluca; Aguiar, Antonio Pedro; Pascoal, Antonio

2013-01-01

The paper addresses observability issues related to the general problem of single and multiple Autonomous Underwater Vehicle (AUV) localization using only range measurements. While an AUV is submerged, localization devices, such as Global Navigation Satellite Systems, are ineffective, due to the attenuation of electromagnetic waves. AUV localization based on dead reckoning techniques and the use of affordable motion sensor units is also not practical, due to divergence caused by sensor bias and drift. For these reasons, localization systems often build on trilateration algorithms that rely on the measurements of the ranges between an AUV and a set of fixed transponders using acoustic devices. Still, such solutions are often expensive, require cumbersome calibration procedures and only allow for AUV localization in an area that is defined by the geometrical arrangement of the transponders. A viable alternative for AUV localization that has recently come to the fore exploits the use of complementary information on the distance from the AUV to a single transponder, together with information provided by on-board resident motion sensors, such as, for example, depth, velocity and acceleration measurements. This concept can be extended to address the problem of relative localization between two AUVs equipped with acoustic sensors for inter-vehicle range measurements. Motivated by these developments, in this paper, we show that both the problems of absolute localization of a single vehicle and the relative localization of multiple vehicles can be treated using the same mathematical framework, and tailoring concepts of observability derived for nonlinear systems, we analyze how the performance in localization depends on the types of motion imparted to the AUVs. For this effect, we propose a well-defined observability metric and validate its usefulness, both in simulation and by carrying out experimental tests with a real marine vehicle during which the performance of an

PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite loci from the Arctic cisco (Coregonus autumnalis).

PubMed

Ramey, A; Graziano, S L; Nielsen, J L

2008-03-01

Eight polymorphic microsatellite loci were isolated and characterized for the Arctic cisco, Coregonus autumnalis. Loci were evaluated in 21 samples from the Colville River subsistence fishery. The number of alleles per locus ranged from two to 18. Observed heterozygosity of loci varied from 0.10 to 1.00, and expected heterozygosity ranged from 0.09 to 0.92. All eight microsatellite markers were in Hardy-Weinberg equilibrium. The loci presented here will be useful in describing population structure and exploring populations of origin for Arctic cisco. © 2007 Blackwell Publishing Ltd No claim to original US government works.

Heterozygosity-fitness correlations among wild populations of European tree frog (Hyla arborea) detect fixation load.

PubMed

Luquet, E; David, P; Lena, J-P; Joly, P; Konecny, L; Dufresnes, C; Perrin, N; Plenet, S

2011-05-01

Quantifying the impacts of inbreeding and genetic drift on fitness traits in fragmented populations is becoming a major goal in conservation biology. Such impacts occur at different levels and involve different sets of loci. Genetic drift randomly fixes slightly deleterious alleles leading to different fixation load among populations. By contrast, inbreeding depression arises from highly deleterious alleles in segregation within a population and creates variation among individuals. A popular approach is to measure correlations between molecular variation and phenotypic performances. This approach has been mainly used at the individual level to detect inbreeding depression within populations and sometimes at the population level but without consideration about the genetic processes measured. For the first time, we used in this study a molecular approach considering both the interpopulation and intrapopulation level to discriminate the relative importance of inbreeding depression vs. fixation load in isolated and non-fragmented populations of European tree frog (Hyla arborea), complemented with interpopulational crosses. We demonstrated that the positive correlations observed between genetic heterozygosity and larval performances on merged data were mainly caused by co-variations in genetic diversity and fixation load among populations rather than by inbreeding depression and segregating deleterious alleles within populations. Such a method is highly relevant in a conservation perspective because, depending on how populations lose fitness (inbreeding vs. fixation load), specific management actions may be designed to improve the persistence of populations. © 2011 Blackwell Publishing Ltd.

Loss of heterozygosity at 7p in Wilms' tumour development

PubMed Central

Powlesland, R M; Charles, A K; Malik, K T A; Reynolds, P A; Pires, S; Boavida, M; Brown, K W

2000-01-01

Chromosome 7p alterations have been implicated in the development of Wilms' tumour (WT) by previous studies of tumour cytogenetics, and by our analysis of a constitutional translocation (t(1;7)(q42;p15)) in a child with WT and radial aplasia. We therefore used polymorphic microsatellite markers on 7p for a loss of heterozygosity (LOH) study, and found LOH in seven out of 77 informative WTs (9%). The common region of LOH was 7p15–7p22, which contains the region disrupted by the t(1;7) breakpoint. Four WTs with 7p LOH had other genetic changes; a germline WT1 mutation with 11p LOH, LOH at 11p, LOH at 16q, and loss of imprinting of IGF2. Analysis of three tumour-associated lesions from 7p LOH cases revealed a cystic nephroma-like area also having 7p LOH. However, a nephrogenic rest and a contralateral WT from the two other cases showed no 7p LOH. No particular clinical phenotype was associated with the WTs which showed 7p LOH. The frequency and pattern of 7p LOH demonstrated in our studies indicate the presence of a tumour suppressor gene at 7p involved in the development of Wilms' tumour. © 2000 Cancer Research Campaign PMID:10646884

Loss of heterozygosity and microsatellite instability in chromosomal segments commonly deleted in squamous cell carcinoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Dyke, D.L.; Worsham, M.J.; Zarbo, R.J.

1994-09-01

To evaluate genetic loss in an unselected series of squamous cell carcinoma (SCC) of the head and neck region (SCCHN), including early stage tumors that do not proliferate aggressively in vitro, we have compared microsatellite repeat polymorphisms (MSRP) in normal blood DNA and tumor DNA from 44 patients with SCCHN, using nine MSRPs from 5q15-q21, proximal 8p, 9p21-p23, 18q21-qter, and 21q21. In previous cytogenetic studies, these chromosome segments were deleted in 40-60% of SCCHN and SCC of the female genital tract. Loss of heterozygosity (LOH) was observed from the ANK1 locus (8p21.1-p11.2) in 2/29 informative tumors. LOH was observed atmore » D5S98 (5q15-5q21) in 5/19, and at D21S11 (21q21) in 5/33 informative tumors. These LOH frequencies were lower than expected, which suggests that the critical region of deletion from these chromosome regions exludes the MSRPs studied here, especially for the 8p MSRP, which may reside in proximal 8p. Alternatively, the observed LOH rates may be appropriate for earlier pathologic stage tumors: total genetic loss increases with tumor stage, and the present study included more stage I and II tumors than did the cytogenetic studies. LOH was observed at D9S126, 1FN, and/or D9S199 (at 9p21, 9p22, & 9p23) in 16/38 informative tumors, and at D18S34 and/or MBP (at 18q21 & 18q22-qter) in 17/39 informative tumors. In addition, three tumors demonstrated microsatellite instability at the MBP locus, and one of these had an expansion at D9S199 as well. This tumor, HFH-SCC-20, also demonstrated microsatellite instability at many other MSRP loci. These results confirm that genetic loss from 9p and 18q is frequent in SCCHN, and demonstrate that microsatellite instability also occurs. Of 66 MSRP changes, 62 were LOH and 4 were microsatellite instabilities. These results also show the usefulness of analyses of MSRP LOH and microsatellite instability in squamous cell carcinoma.« less

Optimal Asteroid Mass Determination from Planetary Range Observations: A Study of a Simplified Test Model

NASA Technical Reports Server (NTRS)

Kuchynka, P.; Laskar, J.; Fienga, A.

2011-01-01

Mars ranging observations are available over the past 10 years with an accuracy of a few meters. Such precise measurements of the Earth-Mars distance provide valuable constraints on the masses of the asteroids perturbing both planets. Today more than 30 asteroid masses have thus been estimated from planetary ranging data (see [1] and [2]). Obtaining unbiased mass estimations is nevertheless difficult. Various systematic errors can be introduced by imperfect reduction of spacecraft tracking observations to planetary ranging data. The large number of asteroids and the limited a priori knowledge of their masses is also an obstacle for parameter selection. Fitting in a model a mass of a negligible perturber, or on the contrary omitting a significant perturber, will induce important bias in determined asteroid masses. In this communication, we investigate a simplified version of the mass determination problem. Instead of planetary ranging observations from spacecraft or radar data, we consider synthetic ranging observations generated with the INPOP [2] ephemeris for a test model containing 25000 asteroids. We then suggest a method for optimal parameter selection and estimation in this simplified framework.

Ranging algebraically with more observations than unknowns

NASA Astrophysics Data System (ADS)

Awange, J. L.; Fukuda, Y.; Takemoto, S.; Ateya, I. L.; Grafarend, E. W.

2003-07-01

In the recently developed Spatial Reference System that is designed to check and control the accuracy of the three-dimensional coordinate measuring machines and tooling equipment (Metronom US., Inc., Ann Arbor: http://www.metronomus.com), the coordinates of the edges of the instrument are computed from distances of the bars. The use of distances in industrial application is fast gaining momentum just as in Geodesy and in Geophysical applications and thus necessitating efficient algorithms to solve the nonlinear distance equations. Whereas the ranging problem with minimum known stations was considered in our previous contribution in the same Journal, the present contribution extends to the case where one is faced with many distance observations than unknowns (overdetermined case) as is usually the case in practise. Using the Gauss-Jacobi Combinatorial approach, we demonstrate how one can proceed to position without reverting to iterative and linearizing procedures such as Newton's or Least Squares approach.

New step toward geodetic range observations at the sea floor with the BBOBS system

NASA Astrophysics Data System (ADS)

Shiobara, H.; Shinohara, M.; Isse, T.

2011-12-01

Since 1999, we had developed the broadband ocean bottom seismometer (BBOBS) and its new generation model (BBOBS-NX), and performed several practical observations with them in these ten years to create a category of the ocean floor broadband seismology. Now, the BBOBS data is proved to be acceptable for broadband seismic analyses. In these studies, the period range of the data used is about 10 - 200 s, but in longer period range, i.e. geodetic range, is an unknown region in observations at the sea floor. The acoustic GPS link observation is one of successful methods to know horizontal movement of the sea floor, but it is difficult to obtain continuous data in time. The borehole tilt-meter system is ideal in observational conditions, but it is impossible to expand spatially dense observation network. On the other hand, high mobility of our BBOBS and BBOBS-NX can be a breakthrough for this kind of observation network. So that, based on our BBOBS technology, two kinds of attempts to expand observation range toward the geodetic one have been started since 2009. Our aim in these attempts is to extend observation periods more than one week long for detecting slow slip events, as a first step. Finally, we would like to build the observation network by using them. The first attempt is a precise pressure measurement to detect vertical displacement at the sea floor by attaching an absolute pressure gauge and a parasitic data logger to the original OBS data recorder. The stable frequency oscillator (MCXO) in the data recorder is useful for precise pressure measurement of the gauge with frequency outputs. Although the final resolution of the pressure becomes smaller than 1 Pa, we still have problems due to the drift of the gauge and some scale of sea level change in practical observations. The total precision of the pressure value is also affected by the shift and drift of the frequency standard to measure frequency output signals of the gauge. In our measurements, this effect

Evaluation of Long-Range Lightning Detection Networks Using TRMM/LIS Observations

NASA Technical Reports Server (NTRS)

Rudlosky, Scott D.; Holzworth, Robert H.; Carey, Lawrence D.; Schultz, Chris J.; Bateman, Monte; Cecil, Daniel J.; Cummins, Kenneth L.; Petersen, Walter A.; Blakeslee, Richard J.; Goodman, Steven J.

2011-01-01

Recent advances in long-range lightning detection technologies have improved our understanding of thunderstorm evolution in the data sparse oceanic regions. Although the expansion and improvement of long-range lightning datasets have increased their applicability, these applications (e.g., data assimilation, atmospheric chemistry, and aviation weather hazards) require knowledge of the network detection capabilities. Toward this end, the present study evaluates data from the World Wide Lightning Location Network (WWLLN) using observations from the Lightning Imaging Sensor (LIS) aboard the Tropical Rainfall Measurement Mission (TRMM) satellite. The study documents the WWLLN detection efficiency and location accuracy relative to LIS observations, describes the spatial variability in these performance metrics, and documents the characteristics of LIS flashes that are detected by WWLLN. Improved knowledge of the WWLLN detection capabilities will allow researchers, algorithm developers, and operational users to better prepare for the spatial and temporal coverage of the upcoming GOES-R Geostationary Lightning Mapper (GLM).

Identification of a region of frequent loss of heterozygosity at 11q24 in colorectal cancer.

PubMed

Connolly, K C; Gabra, H; Millwater, C J; Taylor, K J; Rabiasz, G J; Watson, J E; Smyth, J F; Wyllie, A H; Jodrell, D I

1999-06-15

Loss of heterozygosity (LOH) at 11q23-qter occurs frequently in ovarian and other cancers, but for colorectal cancer, the evidence is conflicting. Seven polymorphic loci were analyzed between D11S897 and D11S969 in 50 colorectal tumors. Two distinct LOH regions were detected, suggesting possible sites for tumor-suppressor genes involved in colorectal neoplasia: a large centromeric region between D11S897 and D11S925, and a telomeric 4.9-Mb region between D11S912 and D11S969. There was no correlation with clinicopathological features. This analysis describes a region of LOH in the region 11q23.3-24.3 for the first time in colorectal cancer and provides complementary evidence for the ongoing effort to identify the gene(s) involved.

Mild Microcytic Anemia in an Infant with a Compound Heterozygosity for Hb C (HBB: c.19G > A) and Hb Osu Christiansborg (HBB: c.157G > A).

PubMed

Boucher, Maria O; Chui, David H K; Woda, Bruce A; Newburger, Peter E

2016-06-01

We report an infant with a compound heterozygosity for Hb C (HBB: c.19G > A) and Hb Osu Christiansborg (HBB: c.157G > A) and a phenotype of mild microcytic anemia with target cell morphology but without overt hemolysis.

Copy neutral loss of heterozygosity: a novel chromosomal lesion in myeloid malignancies

PubMed Central

O'Keefe, Christine; McDevitt, Michael A.

2010-01-01

Single nucleotide polymorphism arrays (SNP-A) have recently been widely applied as a powerful karyotyping tool in numerous translational cancer studies. SNP-A complements traditional metaphase cytogenetics with the unique ability to delineate a previously hidden chromosomal defect, copy neutral loss of heterozygosity (CN-LOH). Emerging data demonstrate that selected hematologic malignancies exhibit abundant CN-LOH, often in the setting of a normal metaphase karyotype and no previously identified clonal marker. In this review, we explore emerging biologic and clinical features of CN-LOH relevant to hematologic malignancies. In myeloid malignancies, CN-LOH has been associated with the duplication of oncogenic mutations with concomitant loss of the normal allele. Examples include JAK2, MPL, c-KIT, and FLT3. More recent investigations have focused on evaluation of candidate genes contained in common CN-LOH and deletion regions and have led to the discovery of tumor suppressor genes, including c-CBL and family members, as well as TET2. Investigations into the underlying mechanisms generating CN-LOH have great promise for elucidating general cancer mechanisms. We anticipate that further detailed characterization of CN-LOH lesions will probably facilitate our discovery of a more complete set of pathogenic molecular lesions, disease and prognosis markers, and better understanding of the initiation and progression of hematologic malignancies. PMID:20107230

Four new cases of double heterozygosity for BRCA1 and BRCA2 gene mutations: clinical, pathological, and family characteristics.

PubMed

Zuradelli, Monica; Peissel, Bernard; Manoukian, Siranoush; Zaffaroni, Daniela; Barile, Monica; Pensotti, Valeria; Cavallari, Ugo; Masci, Giovanna; Mariette, Frederique; Benski, Anne Caroline; Santoro, Armando; Radice, Paolo

2010-11-01

Double heterozygosity (DH) for BRCA1 and BRCA2 mutations is a very rare finding, particularly in non-Ashkenazi individuals, and only a few cases have been reported to date. In addition, little is known on the pathological features of the tumors that occur in DH cases and on their family history of cancer. Four carriers of pathogenic mutations in both BRCA1 and BRCA2 were identified among women who underwent genetic counseling for hereditary susceptibility to breast and ovarian carcinoma at three different Italian institutions. Clinical, pathological, and family history data were collected from medical records and during genetic counseling sessions. All identified DH cases developed breast carcinoma and three of them were also diagnosed with ovarian carcinoma. Mean ages of breast and ovarian cancer diagnosis were 42.7 and 48.6 years, respectively. The majority of breast cancers showed a BRCA1-related phenotype, being negative for hormone receptors and HER2. Two cases reported different gastrointestinal tumors among relatives. Although the individuals described in this study show more severe clinical features in comparison to previously reported BRCA1 and BRCA2 DH cases, our observations support the hypothesis of a non specific phenotype of DH cases in terms of age of disease onset. In addition, our observations indicate that in DH patients breast carcinogenesis appears to be driven mainly by the mutations in BRCA1. The possible association of DH for BRCA gene mutations with gastrointestinal tumors is in keeping with previous reports, but needs to be confirmed by further analyses.

Loss of heterozygosity at D8S262: an early genetic event of hepatocarcinogenesis.

PubMed

Zhu, Qiao; Gong, Li; Liu, Xiaoyan; Wang, Jun; Ren, Pin; Zhang, Wendong; Yao, Li; Han, Xiujuan; Zhu, Shaojun; Lan, Miao; Li, Yanhong; Zhang, Wei

2015-06-16

Hepatocellular carcinoma (HCC) is a multi-factor, multi-step, multi-gene and complicated process resulting from the accumulation of sequential genetic and epigenetic alterations. An important change among them is from precancerous lesions to HCC. However, only few studies have been reported about the sequential genetic changes during hepatocarcinogenesis. We observed firstly molecular karyotypes of 10 matched HCC using Affymetrix single-nucleotide polymorphism (SNP) 6.0 arrays, and found chromosomal fragments with high incidence (more than 70%) of loss of heterozygosity (LOH). Then, we selected 28 microsatellite markers at some gene spanning these chromosomal fragments, and examined the frequency of LOH of 128 matched HCC and 43 matched precancerous lesions-dysplastic nodules (DN) by a PCR-based analysis. Finally, we investigated the expression of proteins encoded by these genes in HCC, DN and the surrounding hepatic tissues. The result of Affymetrix SNP6.0 arrays demonstrated that more than 70% (7/10) cases had chromosomal fragment deletion on 4q13.3-35.1, 8p23.2-21.2, 16q11.2-24.3, and 17p13.3-12. Among 28 microsatellite markers selected, LOH frequencies at D8S262 for DN and HCC were found to be the highest, 51.2% and 72.7%, respectively. Immunohistochemically, the positive rate of its adjacent gene CSMD1 in HCC, DN, and the surrounding hepatic tissues were 27.3% (35/128), 75% (33/44), and 82% (105/128), respectively. LOH at D8S262 may be associated with an early genetic event of hepatocarcinogenesis, and a predictor for the monitor and prevention of HCC. The virtual slides for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1557074981159099 .

Developmental Stability Covaries with Genome-Wide and Single-Locus Heterozygosity in House Sparrows

PubMed Central

Vangestel, Carl; Mergeay, Joachim; Dawson, Deborah A.; Vandomme, Viki; Lens, Luc

2011-01-01

Fluctuating asymmetry (FA), a measure of developmental instability, has been hypothesized to increase with genetic stress. Despite numerous studies providing empirical evidence for associations between FA and genome-wide properties such as multi-locus heterozygosity, support for single-locus effects remains scant. Here we test if, and to what extent, FA co-varies with single- and multilocus markers of genetic diversity in house sparrow (Passer domesticus) populations along an urban gradient. In line with theoretical expectations, FA was inversely correlated with genetic diversity estimated at genome level. However, this relationship was largely driven by variation at a single key locus. Contrary to our expectations, relationships between FA and genetic diversity were not stronger in individuals from urban populations that experience higher nutritional stress. We conclude that loss of genetic diversity adversely affects developmental stability in P. domesticus, and more generally, that the molecular basis of developmental stability may involve complex interactions between local and genome-wide effects. Further study on the relative effects of single-locus and genome-wide effects on the developmental stability of populations with different genetic properties is therefore needed. PMID:21747940

HuH-7 reference genome profile: complex karyotype composed of massive loss of heterozygosity.

PubMed

Kasai, Fumio; Hirayama, Noriko; Ozawa, Midori; Satoh, Motonobu; Kohara, Arihiro

2018-05-17

Human cell lines represent a valuable resource as in vitro experimental models. A hepatoma cell line, HuH-7 (JCRB0403), has been used extensively in various research fields and a number of studies using this line have been published continuously since it was established in 1982. However, an accurate genome profile, which can be served as a reliable reference, has not been available. In this study, we performed M-FISH, SNP microarray and amplicon sequencing to characterize the cell line. Single cell analysis of metaphases revealed a high level of heterogeneity with a mode of 60 chromosomes. Cytogenetic results demonstrated chromosome abnormalities involving every chromosome in addition to a massive loss of heterozygosity, which accounts for 55.3% of the genome, consistent with the homozygous variants seen in the sequence analysis. We provide empirical data that the HuH-7 cell line is composed of highly heterogeneous cell populations, suggesting that besides cell line authentication, the quality of cell lines needs to be taken into consideration in the future use of tumor cell lines.

Determination of genetic polymorphism in Guney Karaman local Turkish sheep breed by using STR markers

NASA Astrophysics Data System (ADS)

Karslı, Taki; Balcıoǧlu, Murat Soner

2017-04-01

The objective of this study was to assess genetic diversity of Güney Karaman Turkish local sheep breed. A total of 29 samples were genotyped by using 14 STR markers. All markers were polymorphic. The number of alleles in Güney Karaman sheep breed ranged from 3 to 11 per locus, with a mean of 7.42. The average observed and expected heterozygosity was 0.659 and 0.794, respectively. Mean inbreeding coefficient (Fis) value was found 0.175. The PIC values ranged from 0.569 to 0.860 with a mean of 0.743. The findings of this research demonstrate at moderate level gene diversity and heterozygosity with lower inbreeding in Güney Karaman sheep breed.

Development of microsatellite markers from loquat, Eriobotrya japonica (Thunb.) Lindl.

PubMed

Gisbert, A D; Lopez-Capuz, I; Soriano, J M; Llacer, G; Romero, C; Badenes, M L

2009-05-01

Loquat (Eriobotrya japonica) is a minor fruit which has become an interesting alternative into the European fruit industry. This interest resulted in a loquat germplasm collection established at the Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain. Currently, it is the main reservoir of this species outside Asia. We developed and characterized the first 21 polymorphic microsatellite loci from a CT/AG-enriched loquat genomic library. The observed heterozygosity ranged between 0.20 and 1.00, expected heterozygosity ranged between 0.17 and 0.81, three markers were multilocus and eight loci departed significantly from Hardy-Weinberg equilibrium. These markers will facilitate diversity and genetic studies into the species. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Isolation and characterization of polymorphic microsatellite loci from Zelkova schneideriana Hand.-Mazz.

PubMed

Liu, H L; Zhang, R Q; Geng, M L; Zhu, J Y; Ma, J L

2014-12-03

Zelkova schneideriana is a highly valued hardwood species. An improved technique for isolating codominant compound microsatellite markers was used to develop simple sequence repeat markers for Z. schneideriana. A total of 12 microsatellite loci were identified. Overall, the number of alleles per locus ranged from 8-19, with an average of 11.75. Observed heterozygosity and expected heterozygosity values ranged from 0.109-0.709 and 0.832-0.929, respectively. Polymorphic information content is from 0.803-0.915, with an average of 0.854. These markers will be very important for future research related to the genetic diversity, population structure, patterns of gene flow, and mating system of this species.

Characterization of 12 microsatellite loci for the Pacific lamprey, Entosphenus tridentatus (Petromyzontidae), and cross-amplification in five other lamprey species.

PubMed

Spice, E K; Whitesel, T A; McFarlane, C T; Docker, M F

2011-12-22

The Pacific lamprey (Entosphenus tridentatus) is an anadromous fish that is of conservation concern in North America and Asia. Data on Pacific lamprey population structure are scarce and conflicting, impeding conservation efforts. We optimized 12 polymorphic microsatellite loci for the Pacific lamprey. Three to 13 alleles per locus were observed in a sample of 51 fish collected from the West Fork Illinois River, Oregon. Observed heterozygosity ranged from 0.235 to 0.902 and expected heterozygosity ranged from 0.214 to 0.750. Cross-species amplification produced 8 to 12 polymorphic loci in four other Entosphenus species and in the western brook lamprey (Lampetra richardsoni). Two loci appear to be diagnostic for distinguishing Entosphenus from Lampetra. These markers will be valuable for evaluating population structure and making conservation decisions for E. tridentatus and other lamprey species.

Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka).

PubMed

McClelland, Erin K; Ming, Tobi J; Tabata, Amy; Kaukinen, Karia H; Beacham, Terry D; Withler, Ruth E; Miller, Kristina M

2013-09-01

The major histocompatibility complex (MHC), an important component of the vertebrate immune system, provides an important suite of genes to examine the role of genetic diversity at non-neutral loci for population persistence. We contrasted patterns of diversity at the two classical MHC loci in sockeye salmon (Oncorhynchus nerka), MHC class I (UBA) and MHC class II (DAB), and neutral microsatellite loci across 70 populations spanning the species range from Washington State to Japan. There was no correlation in allelic richness or heterozygosity between MHC loci or between MHC loci and microsatellites. The two unlinked MHC loci may be responding to different selective pressures; the distribution of FST values for the two loci was uncorrelated, and evidence for both balancing and directional selection on alleles and lineages of DAB and UBA was observed in populations throughout the species range but rarely on both loci within a population. These results suggest that fluctuating selection has resulted in the divergence of MHC loci in contemporary populations. © 2013 John Wiley & Sons Ltd.

The effect of multiple simple Robertsonian heterozygosity on chromosome pairing and fertility of wild-stock house mice (Mus musculus domesticus).

PubMed

Wallace, B M N; Searle, J B; Everett, C A

2002-01-01

The influence of Robertsonian (Rb) heterozygosity on fertility has been the subject of much study in the house mouse. However, these studies have been largely directed at single simple heterozygotes (heterozygous for a single Rb metacentric) or complex heterozygotes (heterozygous for several to many metacentrics which share common chromosome arms). In this paper we describe studies on male multiple simple heterozygotes, specifically the F(1) products of crosses between wild-stock mice homozygous for four or seven metacentrics and wild-stock mice with a standard all-acrocentric karyotype; these F(1) products were characterized by four and seven trivalents at meiosis I, respectively. Mice with the same karyotype, but two different genetic backgrounds were examined. Although a range of meiotic and fertility studies were conducted, particular emphasis was paid to analysis of chromosome pairing, previously not well-described in multiple simple heterozygous mice. The progression of spermatocytes through prophase I was followed by electron microscopy of surface spread material. As previously shown for single simple Rb heterozygotes, the trivalents that characterize multiple simple heterozygotes initially showed delayed pairing of the centromeric region and later showed side arm formation, resulting from non-homologous pairing by the centromeric ends of the acrocentric chromosomes. In the four trivalent groups of mice, 15 and 32% of trivalents showed unpairing in the centromeric region at mid pachytene; equivalent values were 29 and 39% for the seven trivalent groups. Pairing abnormalities (largely attachments and interlocks between trivalents and between a trivalent and the XY configuration) were observed in 18 and 23% of mid pachytene cells in the four trivalent groups and 36 and 49% of cells in the seven trivalent groups. The greater level of pachytene irregularity (unpairing and pairing abnormalities) in seven versus four trivalent heterozygotes was mirrored in terms

Shifting species ranges and changing phenology: A new approach to mining social media for ecosystems observations

NASA Astrophysics Data System (ADS)

Fuka, M. Z.; Osborne-Gowey, J. D.; Fuka, D. R.

2013-12-01

Geoscientists & ecologists are increasingly using social media to solicit 'citizen scientists' to participate in the data collection process. However, social media users are also a largely untapped resource of spontaneous, unsolicited observations of the natural world. Of particular interest are observations of species phenology & range to better develop a predictive understanding of how ecosystems are affected by a changing climate and human-mediated influences. Social media users' observations include information on phenological & biological phenomena such as flowers blooming, native & invasive species sightings, unusual behaviors, animal tracks, droppings, damage, feeding, nesting, etc. Our AGU2011 pilot study on the North American armadillo suggests that useful observational data can be extracted from Twitter to map current species ranges to compare with past ranges. We have expanded that work by mining Twitter for a number of North American species and ecosystem observations to determine usefulness for environmental applications such as: 1) supplementing existing databases, 2) identifying outlier phenomena, 3) guiding additional crowd-sourced studies and data collection efforts, 4) recruiting citizen scientists, 5) gauging sentiment about the observations and 6) informing ecosystems policy-making and education. We present the results for our evaluation of a representative sample from a list of 200+ species for which we've collected data since August 2011. Our results include frequency of reports and sightings by day, week and month, where the number of observations range from a few per month to ten or more per day. We discuss challenges, best practices and tools for distilling information from crowd-sourced observations gathered via Twitter in the form of 140-character 'tweets'. For example, geolocation is a critical issue. Despite the prevalence of smart phones, specific latitudinal and longitudinal coordinates are included in fewer than 10% of the

Individual Ranging Behaviour Patterns in Commercial Free-Range Layers as Observed through RFID Tracking

PubMed Central

Larsen, Hannah; Cronin, Greg M.; Gebhardt-Henrich, Sabine G.; Smith, Carolynn L.; Hemsworth, Paul H.; Rault, Jean-Loup

2017-01-01

Simple Summary Understanding of how free-range laying hens on commercial farms utilize the outdoor space provided is limited. In order to optimise use of the range, it is important to understand whether hens vary in their ranging behaviour, both between and within individual hens. In our study, we used individual tracking technology to assess how hens in two commercial free-range flocks used the range and whether they varied in their use of the range. We assessed use of three areas at increasing distance from the shed; the veranda [0–2.4 m], close range [2.4–11.4 m], and far range [>11.4 m]. Most hens accessed the range every day (68.6% in Flock A, and 82.2% in Flock B), and most hens that ranged accessed all three areas (73.7% in Flock A, and 84.5% in Flock B). Hens spent half of their time outside in the veranda adjacent to the shed. We found that some hens within the flocks would range consistently (similar duration and frequency) daily, whereas others would range inconsistently. Hens that were more consistent in their ranging behaviour spent more time on the range overall than those that were inconsistent. These different patterns of range use should be taken into account to assess the implications of ranging for laying hens. Abstract In this exploratory study, we tracked free-range laying hens on two commercial flocks with Radio Frequency Identification (RFID) technology with the aim to examine individual hen variation in range use. Three distinct outdoor zones were identified at increasing distances from the shed; the veranda [0–2.4 m], close range [2.4–11.4 m], and far range [>11.4 m]. Hens’ movements between these areas were tracked using radio frequency identification technology. Most of the hens in both flocks (68.6% in Flock A, and 82.2% in Flock B) accessed the range every day during the study. Of the hens that accessed the range, most hens accessed all three zones (73.7% in Flock A, and 84.5% in Flock B). Hens spent half of their time

Stress-induced loss of heterozygosity in Candida: a possible missing link in the ability to evolve.

PubMed

Rosenberg, Susan M

2011-01-01

Diploid organisms are buffered against the effects of mutations by carrying two sets of each gene, which allows compensation if one is mutated. But recombination between "mom" and "dad" chromosomes causes loss of heterozygosity (LOH), stretches of "mom-only" or "dad-only" DNA sequence, suddenly revealing effects of mutations accumulated in entire chromosome arms. LOH creates new phenotypes from old mutations, drives cancer development and evolution, and, in a new study by Forche et al., is shown to be induced by stress in Candida albicans [Forche A, et al, mBio 2(4):e00129-11, 2011]. Stress-induced LOH could speed evolution of Candida specifically when it is poorly adapted to its environment. Moreover, the findings may provide a missing link between recombination-dependent mutagenesis in bacteria and yeast, suggesting that both might be stress induced, both maximizing genetic variation when populations could benefit most from diversity.

Applications of laser ranging and VLBI observations for selenodetic control

NASA Technical Reports Server (NTRS)

Fajemirokun, F. A.

1971-01-01

The observation equations necessary to utilize lunar laser ranging and very long baseline interferometry measurements were developed for the establishment of a primary control network on the moon. The network consists of coordinates of moon points in the selenodetic Cartesian coordinate system, which is fixed to the lunar body, oriented along the three principal axes of inertia of the moon, and centered at the lunar center of mass. The observation equations derived are based on a general model in which the unknown parameters included: the selenodetic Cartesian coordinates, the geocentric coordinates of earth stations, parameters of the orientation of the selenodetic coordinate system with respect to a fixed celestial system, the parameters of the orientation of the average terrestrial coordinate system with respect to a fixed celestial coordinate system, and the geocentric coordinates of the center of mass of the moon, given by a lunar ephemeris.

Genetic differentiation of the pine wilt disease vector Monochamus alternatus (Coleoptera: Cerambycidae) over a mountain range - revealed from microsatellite DNA markers.

PubMed

Shoda-Kagaya, E

2007-04-01

To study the dispersal process of the pine sawyer Monochamus alternatus (Hope) in frontier populations, a microsatellite marker-based genetic analysis was performed on expanding populations at the northern limit of its range in Japan. In Asian countries, M. alternatus is the main vector of pine wilt disease, the most serious forest disease in Japan. Sawyers were collected from nine sites near the frontier of the pine wilt disease damage area. A mountain range divides the population into western and eastern sides. Five microsatellite loci were examined and a total of 188 individuals was genotyped from each locus with the number of alleles ranged from two to nine. The mean observed heterozygosity for all loci varied from 0.282 to 0.480 in the nine sites, with an overall mean of 0.364. None of the populations have experienced a significant bottleneck. Significant differentiation was found across the mountain range, but the genetic composition was similar amongst populations of each side. It is believed that the mountain range acts as a geographical barrier to dispersal and that gene flow without a geographical barrier is high. On the west side of the mountain range, a pattern of isolation by distance was detected. This was likely to be caused by secondary contact of different colonizing routes on a small spatial scale. Based on these data, a process linking genetic structure at local (kilometres) and regional spatial scales (hundreds of kilometres) was proposed.

Development and characterization of 16 microsatellite markers for the Louisiana pine snake, Pituophis ruthveni, and two congeners of conservation concern

Treesearch

Matthew A. Kwiatkowski; Christopher M. Somers; Ray G. Poulin; D. Craig Rudolph; Jessica Martino; Tracey D. Tuberville; Cris Hagen; Stacey L. Lance

2010-01-01

We isolated and characterized 16 microsatellite loci from the Louisiana pine snake, Pituophis ruthveni. Loci were screened in 24 individuals from locations throughout its distribution in Louisiana and Texas. The number of alleles per locus ranged from 4 to 12, observed heterozygosity ranged from 0.200 to 0.875, and the probability of identity ranged from 0.043 to 0.298...

Individual Ranging Behaviour Patterns in Commercial Free-Range Layers as Observed through RFID Tracking.

PubMed

Larsen, Hannah; Cronin, Greg M; Gebhardt-Henrich, Sabine G; Smith, Carolynn L; Hemsworth, Paul H; Rault, Jean-Loup

2017-03-09

In this exploratory study, we tracked free-range laying hens on two commercial flocks with Radio Frequency Identification (RFID) technology with the aim to examine individual hen variation in range use. Three distinct outdoor zones were identified at increasing distances from the shed; the veranda [0-2.4 m], close range [2.4-11.4 m], and far range [>11.4 m]. Hens' movements between these areas were tracked using radio frequency identification technology. Most of the hens in both flocks (68.6% in Flock A, and 82.2% in Flock B) accessed the range every day during the study. Of the hens that accessed the range, most hens accessed all three zones (73.7% in Flock A, and 84.5% in Flock B). Hens spent half of their time outdoors in the veranda area. Within-individual consistency of range use (daily duration and frequency) varied considerably, and hens which were more consistent in their daily range use spent more time on the range overall ( p < 0.001). Understanding variation within and between individuals in ranging behaviour may help elucidate the implications of ranging for laying hens.

Identification and characterization of microsatellite loci in two socially complex old world tropical babblers (Family Timaliidae).

PubMed

Kaiser, Sara A; Danner, J E; Bergner, Laura; Fleischer, Robert C

2015-11-24

Although the highest diversity of birds occurs in tropical regions, little is known about the genetic mating systems of most tropical species. We describe microsatellite markers isolated in the chestnut-crested yuhina (Staphida everetti), endemic to the island of Borneo, and the grey-throated babbler (Stachyris nigriceps), widely distributed across Southeast Asia. Both species belong to the avian family Timaliidae and are highly social, putatively cooperatively breeding birds in which helpers attend the nests of members of their social group. We obtained DNA from individuals in social groups breeding in Kinabalu Park, Malaysian Borneo. We used a shotgun sequencing approach and 454-technology to identify 36 microsatellite loci in the yuhina and 40 in the babbler. We tested 13 primer pairs in yuhinas and 20 in babblers and characterized eight polymorphic loci in 20 unrelated female yuhinas and 21 unrelated female babblers. Polymorphism at the yuhina loci ranged from 3 to 9 alleles, observed heterozygosities from 0.58 to 1.00, and expected heterozygosities from 0.64 to 0.81. Polymorphism at the babbler loci ranged from 3 to 12 alleles, observed heterozygosities from 0.14 to 0.90 and expected heterozygosities from 0.14 to 0.87. One locus in the yuhina deviated significantly from Hardy-Weinberg equilibrium. We detected nonrandom allele associations between two pairs of microsatellite loci in each species. Microsatellite markers will be used to describe the genetic mating system of these socially complex species and to measure genetic parentage and relatedness within social groups.

Compound heterozygosity of SHOX-encompassing and downstream PAR1 deletions results in Langer mesomelic dysplasia (LMD).

PubMed

Campos-Barros, Angel; Benito-Sanz, Sara; Ross, Judith L; Zinn, Andrew R; Heath, Karen E

2007-05-01

We present the clinical and molecular characteristics of a multi-generation family in which the proband presented with clinical features of Langer mesomelic dysplasia (LMD) whilst different family members had a diagnosis of Léri-Weill dyschondrosteosis (LWD) and/or pseudoachondroplasia (PSACH). In the LMD proband two different deletions were identified in the pseudoautosomal 1 region (PAR1) of the X and Y chromosomes: a SHOX-encompassing deletion inherited from his father and a downstream PAR1 deletion, which did not include SHOX, inherited from his mother. The individuals with PSACH features presented the previously described G719D mutation in the C-terminal globular domain of the cartilage oligomeric matrix protein gene (COMP). The LMD proband described here represents the first LMD case due to compound heterozygosity for deletions of the two different PAR1 regions, SHOX-encompassing and downstream from SHOX, that have been shown to be implicated in the pathogenesis of LWD and LMD.

Microsatellites for Carpotroche brasiliensis (Flacourtiaceae), a useful species for agroforestry and ecosystem conservation.

PubMed

Bittencourt, Flora; Alves, Jackeline S; Gaiotto, Fernanda A

2015-12-01

We developed microsatellite markers for Carpotroche brasiliensis (Flacourtiaceae), a dioecious tree that is used as a food resource by midsize animals of the Brazilian fauna. We designed 30 primer pairs using next-generation sequencing and classified 25 pairs as polymorphic. Observed heterozygosity ranged from 0.5 to 1.0, and expected heterozygosity ranged from 0.418 to 0.907. The combined probability of exclusion was greater than 0.999 and the combined probability of identity was less than 0.001, indicating that these microsatellites are appropriate for investigations of genetic structure, individual identification, and paternity testing. The developed molecular tools may contribute to future studies of population genetics, answering ecological and evolutionary questions regarding efficient conservation strategies for C. brasiliensis.

Mesoscale influence on long-range transport — evidence from ETEX modelling and observations

NASA Astrophysics Data System (ADS)

Sørensen, Jens Havskov; Rasmussen, Alix; Ellermann, Thomas; Lyck, Erik

During the first European Tracer Experiment (ETEX) tracer gas was released from a site in Brittany, France, and subsequently observed over a range of 2000 km. Hourly measurements were taken at the National Environmental Research Institute (NERI) located at Risø, Denmark, using two measurement techniques. At this location, the observed concentration time series shows a double-peak structure occurring between two and three days after the release. By using the Danish Emergency Response Model of the Atmosphere (DERMA), which is developed at the Danish Meteorological Institute (DMI), simulations of the dispersion of the tracer gas have been performed. Using numerical weather-prediction data from the European Centre for Medium-Range Weather Forecast (ECMWF) by DERMA, the arrival time of the tracer is quite well predicted, so also is the duration of the passage of the plume, but the double-peak structure is not reproduced. However, using higher-resolution data from the DMI version of the HIgh Resolution Limited Area Model (DMI-HIRLAM), DERMA reproduces the observed structure very well. The double-peak structure is caused by the influence of a mesoscale anti-cyclonic eddy on the tracer gas plume about one day earlier.

New Horizons: Long-Range Kuiper Belt Targets Observed by the Hubble Space Telescope

NASA Technical Reports Server (NTRS)

Benecchi, S. D.; Noll, K. S.; Weaver, H. A.; Spencer, J. R.; Stern, S. A.; Buie, M. W.; Parker, A. H.

2014-01-01

We report on Hubble Space Telescope (HST) observations of three Kuiper Belt Objects (KBOs), discovered in our dedicated ground-based search campaign, that are candidates for long-range observations from the New Horizons spacecraft: 2011 epochY31, 2011 HZ102, and 2013 LU35. Astrometry with HST enables both current and future critical accuracy improvements for orbit precision, required for possible New Horizons observations, beyond what can be obtained from the ground. Photometric colors of all three objects are red, typical of the Cold Classical dynamical population within which they reside; they are also the faintest KBOs to have had their colors measured. None are observed to be binary with HST above separations of approx. 0.02 arcsec (approx. 700 km at 44 AU) and delta m less than or equal to 0.5.

Loss of heterozygosity on chromosome 11q13 in two families with acromegaly/gigantism is independent of mutations of the multiple endocrine neoplasia type I gene.

PubMed

Gadelha, M R; Prezant, T R; Une, K N; Glick, R P; Moskal, S F; Vaisman, M; Melmed, S; Kineman, R D; Frohman, L A

1999-01-01

Familial acromegaly/gigantism occurring in the absence of multiple endocrine neoplasia type I (MEN-1) or the Carney complex has been reported in 18 families since the biochemical diagnosis of GH excess became available, and the genetic defect is unknown. In the present study we examined 2 unrelated families with isolated acromegaly/gigantism. In family A, 3 of 4 siblings were affected, with ages at diagnosis of 19, 21, and 23 yr. In family B, 5 of 13 siblings exhibited the phenotype and were diagnosed at 13, 15, 17, 17, and 24 yr of age. All 8 affected patients had elevated basal GH levels associated with high insulin-like growth factor I levels and/or nonsuppressible serum GH levels during an oral glucose tolerance test. GHRH levels were normal in affected members of family A. An invasive macroadenoma was found in 6 subjects, and a microadenoma was found in 1 subject from family B. The sequence of the GHRH receptor complementary DNA in 1 tumor from family A was normal. There was no history of consanguinity in either family, and the past medical history and laboratory results excluded MEN-1 and the Carney complex in all affected and unaffected screened subjects. Five of 8 subjects have undergone pituitary surgery to date, and paraffin-embedded pituitary blocks were available for analysis. Loss of heterozygosity on chromosome 11q13 was studied by comparing microsatellite polymorphisms of leukocyte and tumor DNA using PYGM (centromeric) and D11S527 (telomeric), markers closely linked to the MEN-1 tumor suppressor gene. All tumors exhibited a loss of heterozygosity at both markers. Sequencing of the MEN-1 gene revealed no germline mutations in either family, nor was a somatic mutation found in tumor DNA from one subject in family A. The integrity of the MEN-1 gene in this subject was further supported by demonstration of the presence of MEN-1 messenger ribonucleic acid, as assessed by RT-PCR. These data indicate that loss of heterozygosity in these affected family

Identification of flexible structures by frequency-domain observability range context

NASA Astrophysics Data System (ADS)

Hopkins, M. A.

2013-04-01

The well known frequency-domain observability range space extraction (FORSE) algorithm provides a powerful multivariable system-identification tool with inherent flexibility, to create state-space models from frequency-response data (FRD). This paper presents a method of using FORSE to create "context models" of a lightly damped system, from which models of individual resonant modes can be extracted. Further, it shows how to combine the extracted models of many individual modes into one large state-space model. Using this method, the author has created very high-order state-space models that accurately match measured FRD over very broad bandwidths, i.e., resonant peaks spread across five orders-of-magnitude of frequency bandwidth.

Airborne lidar observations of long-range transport in the free troposphere

NASA Technical Reports Server (NTRS)

Shipley, S. T.; Browell, E. V.; Mcdougal, D. S.; Orndorff, B. L.; Haagenson, P.

1984-01-01

Airborne lidar measurements of ozone and aerosols in the lower troposphere show the presence of pollutant layers above the mixed layer. Two case studies are analyzed to identify probable source regions and mechanisms for material injection into the free troposphere above local mixed layers. An elevated haze/oxidant layer observed over South Carolina on Aug. 2, 1980, was found to originate in cumulus convection over Georgia on Aug. 1, 1980. An extensive haze/oxidant layer observed over southeastern Virginia on July 31, 1981, is shown to have been in contact with the New England mixed layer on July 30, 1981. This transported air mass is estimated to contribute approximately 30 percent of the ozone maximum measured at the surface in the Norfolk, VA, area on July 31, 1981. Such elevated 'reservoir' layers are transported over long ranges and are not detected by sensors which are confined to the surface.

OSSE observations of NGC 1275 in the 0.05-10.0 MeV range

NASA Astrophysics Data System (ADS)

Osako, C. Y.; Ulmer, M. P.; Grabelsky, D. A.; Purcell, W. R.; Strickman, M. S.; Johnson, W. N.; Kinzer, R. L.; Kurfess, J. D.; Jung, G. V.

1994-11-01

We made observations of NGC 1275 with the Compton Gamma-Ray Observatory's Oriented Scintillation Spectrometer Experiment (OSSE) between 1991 November 28 and December 12. We did not detect the source during this viewing period. Our 3 sigma upper limit to a detection in the approximately 50-90 keV range is 6 x 10-6 photons/sq cm/s/keV. This flux is more than 10 times lower than the 3 sigma detection in the same energy range reported by Rothschild et al. for their OSO 7 observations. Our results are discussed in comparison with radio observations and models for the X-ray emission, and we show that it is likely that most of the approx. greater than 10 keV photons come from the nuclear region of NGC 1275. We find no significant correlation between the variable radio intensity and the hard X-ray flux of the entire NGC 1275 source. Simultaneous Very Large Baseline Array and gamma-ray observations are needed to test the self-Compton synchrotron models for gamma-ray emission from the core of NGC 1275. Our results also provide a lower limit to the magnetic field of approximately 2 x 10-7 gauss for the approximately 5 min radio source centered on NGC 1275.

Half of 23 Belgian dog breeds has a compromised genetic diversity, as revealed by genealogical and molecular data analysis.

PubMed

Wijnrocx, K; François, L; Stinckens, A; Janssens, S; Buys, N

2016-10-01

The genetic diversity in 23 dog breeds raised in Belgium was investigated using both genealogical analysis and microsatellite markers. Some of these breeds are native breeds, with only small populations maintained. Pedigree and molecular data, obtained from the Belgian kennel club, were used to calculate the inbreeding coefficients, realised effective population size as well as probabilities of gene origin and average observed heterozygosity. Inbreeding coefficients ranged from 0.8 to 44.7% and realised effective population size varied between 3.2 and 829.1, according to the used method and breed. Mean observed heterozygosity ranged from 0.47 to 0.73. Both pedigree and molecular methods reveal low genetic diversity and presence of bottlenecks, especially in native Belgian breeds with small population sizes. Furthermore, principal component analysis on the set of investigated diversity parameters revealed no groups of breeds that could be identified in which similar breeding strategies could be applied to maintain genetic diversity. © 2016 Blackwell Verlag GmbH.

Quantum gases. Observation of many-body dynamics in long-range tunneling after a quantum quench.

PubMed

Meinert, Florian; Mark, Manfred J; Kirilov, Emil; Lauber, Katharina; Weinmann, Philipp; Gröbner, Michael; Daley, Andrew J; Nägerl, Hanns-Christoph

2014-06-13

Quantum tunneling is at the heart of many low-temperature phenomena. In strongly correlated lattice systems, tunneling is responsible for inducing effective interactions, and long-range tunneling substantially alters many-body properties in and out of equilibrium. We observe resonantly enhanced long-range quantum tunneling in one-dimensional Mott-insulating Hubbard chains that are suddenly quenched into a tilted configuration. Higher-order tunneling processes over up to five lattice sites are observed as resonances in the number of doubly occupied sites when the tilt per site is tuned to integer fractions of the Mott gap. This forms a basis for a controlled study of many-body dynamics driven by higher-order tunneling and demonstrates that when some degrees of freedom are frozen out, phenomena that are driven by small-amplitude tunneling terms can still be observed. Copyright © 2014, American Association for the Advancement of Science.

Soil moisture sensing with aircraft observations of the diurnal range of surface temperature

NASA Technical Reports Server (NTRS)

Schmugge, T. J.; Blanchard, B.; Anderson, A.; Wang, V.

1977-01-01

Aircraft observations of the surface temperature were made by measurements of the thermal emission in the 8-14 micrometers band over agricultural fields around Phoenix, Arizona. The diurnal range of these surface temperature measurements were well correlated with the ground measurement of soil moisture in the 0-2 cm layer. The surface temperature observations for vegetated fields were found to be within 1 or 2 C of the ambient air temperature indicating no moisture stress. These results indicate that for clear atmospheric conditions remotely sensed surface temperatures are a reliable indicator of soil moisture conditions and crop status.

Tonopah Test Range Air Monitoring: CY2016 Meteorological, Radiological, and Wind Transported Particulate Observations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chapman, Jenny; Nikolich, George; Shadel, Craig

In 1963, the U.S. Department of Energy (DOE) (formerly the Atomic Energy Commission [AEC]), implemented Operation Roller Coaster on the Tonopah Test Range (TTR) and an adjacent area of the Nevada Test and Training Range (NTTR) (formerly the Nellis Air Force Range). This operation resulted in radionuclide-contaminated soils at the Clean Slate I, II, and III sites. This report documents observations made during ongoing monitoring of radiological, meteorological, and dust conditions at stations installed adjacent to Clean Slate I and Clean Slate III, and at the TTR Sandia National Laboratories (SNL) Range Operations Control (ROC) center. The primary objective ofmore » the monitoring effort is to determine if wind blowing across the Clean Slate sites is transporting particles of radionuclide-contaminated soil beyond the physical and administrative boundaries of the sites.« less

Range of earth structure nonuniqueness implied by body wave observations.

NASA Technical Reports Server (NTRS)

Wiggins, R. A.; Mcmechan, G. A.; Toksoz, M. N.

1973-01-01

The Herglotz-Wiechert integral for the direct inversion of ray parameter versus distance curves can be manipulated to find the envelope of all possible models consistent with geometrical body wave observations (travel time and ray parameter versus distance). Such an extremal inversion approach has been used to find the uncertainty bounds for the velocity structure in the mantle and core. It is found, for example, that there is an uncertainty of plus or minus 40 km in the radius of the inner core boundary, plus or minus 18 km at the core-mantle boundary, and plus or minus 35 km at the 435-km transition zone. The velocity uncertainty is about plus or minus 0.08 km/sec for P and S waves in the lower mantle and about plus or minus 0.20 km/sec in the core. Experiments with various combinations of ray types in the core indicate that rather crude observations of SKKS-SKS travel times confine the range of possible models far more dramatically than do the most precise estimates of PmKP travel times. Comparisons of results from extremal inversion and linearized perturbation inversions indicate that body wave behavior is too strongly nonlinear for linearized schemes to be effective for predicting uncertainty.

Α₁-antitrypsin PiMZ heterozygosity has an independent aggravating effect on liver fibrosis in alcoholic liver disease.

PubMed

Goltz, Diane; Hittetiya, Kanishka; Vössing, Lena Marie; Kirfel, Jutta; Spengler, Ulrich; Fischer, Hans-Peter

2014-11-01

Heterozygous α1-antitrypsin deficiency type PiZ (PiMZ) results in chronic liver injury and predisposes to hepatocellular carcinoma. Gene frequency of the PiZ allele ranges from 0.005 to 0.027 in Western and Central Europe; therefore, there is a substantial risk of coincidence with chronic alcohol abuse. This retrospective case-control study evaluates the impact of PiMZ genotype on the development of chronic liver disease in alcohol consuming patients. Six thousand eight hundred eighty-six consecutive liver specimens were immunohistochemically tested for PiZ-deposits. From 254 PiZ-positive patients, the liver biopsies of 30 PiMZ adults without concomitant liver disease other than alcoholic liver disease (ALD) were selected and matched to PiMM (wild type) patients with respect to age, gender and lifetime daily alcohol ingestion (LDAI). Histomorphological changes were assessed using the SAF score and by digital image analysis. Liver cirrhosis was significantly more frequent in PIMZ patients than in matched PiMM patients (PiMM 9/30 vs. PiMZ 14/30, p = 0.04). Comparison of the extent of fibrosis in PiMZ and PiMM livers by two-way ANOVA indicated that the amount of LDAI has a major effect in PiMZ and PiMM patients (30.04 % of total variation, p < 0.0001), whereas PIMZ genotype has a minor but independent effect on liver fibrosis as assessed by digital planimetric evaluation (9.27 % of total variation, p = 0.005). Semiquantitative assessment was in agreement with this finding. Histomorphological findings support that PiMZ heterozygosity has an independent aggravating effect on liver fibrosis, even though the pathogenic effect of alcohol consumption is much stronger.

Isolation and characterization of 21 polymorphic microsatellite loci in the Japanese dace (Tribolodon hakonensis)

USGS Publications Warehouse

Koizumi, Noriyuki; Quinn, Thomas W.; Park, Myeongsoo; Fike, Jennifer A.; Nishida, Kazuya; Takemura, Takeshi; Watabe, Keiji; Mori, Atsushi

2011-01-01

Twenty one polymorphic microsatellite loci for the Japanese dace (Tribolodon hakonensis) were isolated and characterized. The number of observed alleles per locus in 32 individuals ranged from 3 to 30. The observed and expected heterozygosities ranged from 0.125 to 0.969 and from 0.175 to 0.973, respectively. All loci conformed to Hardy–Weinberg equilibrium, no linkage disequilibrium was observed between pairs of loci and no loci showed evidence of null alleles. These microsatellite loci will be useful for investigating the intraspecific genetic variation and population structure of this species.

Performance of PHOTONIS' low light level CMOS imaging sensor for long range observation

NASA Astrophysics Data System (ADS)

Bourree, Loig E.

2014-05-01

Identification of potential threats in low-light conditions through imaging is commonly achieved through closed-circuit television (CCTV) and surveillance cameras by combining the extended near infrared (NIR) response (800-10000nm wavelengths) of the imaging sensor with NIR LED or laser illuminators. Consequently, camera systems typically used for purposes of long-range observation often require high-power lasers in order to generate sufficient photons on targets to acquire detailed images at night. While these systems may adequately identify targets at long-range, the NIR illumination needed to achieve such functionality can easily be detected and therefore may not be suitable for covert applications. In order to reduce dependency on supplemental illumination in low-light conditions, the frame rate of the imaging sensors may be reduced to increase the photon integration time and thus improve the signal to noise ratio of the image. However, this may hinder the camera's ability to image moving objects with high fidelity. In order to address these particular drawbacks, PHOTONIS has developed a CMOS imaging sensor (CIS) with a pixel architecture and geometry designed specifically to overcome these issues in low-light level imaging. By combining this CIS with field programmable gate array (FPGA)-based image processing electronics, PHOTONIS has achieved low-read noise imaging with enhanced signal-to-noise ratio at quarter moon illumination, all at standard video frame rates. The performance of this CIS is discussed herein and compared to other commercially available CMOS and CCD for long-range observation applications.

Signatures of the Martian rotation parameters in the Doppler and range observables

NASA Astrophysics Data System (ADS)

Yseboodt, Marie; Dehant, Véronique; Péters, Marie-Julie

2017-09-01

The position of a Martian lander is affected by different aspects of Mars' rotational motions: the nutations, the precession, the length-of-day variations and the polar motion. These various motions have a different signature in a Doppler observable between the Earth and a lander on Mars' surface. Knowing the correlations between these signatures and the moments when these signatures are not null during one day or on a longer timescale is important to identify strategies that maximize the geophysical return of observations with a geodesy experiment, in particular for the ones on-board the future NASA InSight or ESA-Roscosmos ExoMars2020 missions. We provide first-order formulations of the signature of the rotation parameters in the Doppler and range observables. These expressions are functions of the diurnal rotation of Mars, the lander position, the planet radius and the rotation parameter. Additionally, the nutation signature in the Doppler observable is proportional to the Earth declination with respect to Mars. For a lander on Mars close to the equator, the motions with the largest signature in the Doppler observable are due to the length-of-day variations, the precession rate and the rigid nutations. The polar motion and the liquid core signatures have a much smaller amplitude. For a lander closer to the pole, the polar motion signature is enhanced while the other signatures decrease. We also numerically evaluate the amplitudes of the rotation parameters signature in the Doppler observable for landers on other planets or moons.

Loss of heterozygosity at 7q22 and mutation analysis of the CDP gene in human epithelial ovarian tumors.

PubMed

Neville, P J; Thomas, N; Campbell, I G

2001-02-01

Many tumor types including that of the ovary show loss of heterozygosity (LOH) on chromosome arm 7q, which suggests the existence of at least one tumor suppressor gene (TSG) on this chromosome arm. We have studied the region surrounding the putative tumor suppressor gene CUTL1 at 7q22 in 127 epithelial ovarian tumors. LOH was found across 7q22 in 31% of malignant and 14% of benign ovarian tumors. In 16% of the tumors the LOH appeared to be centered on the CUTL1 gene. This gene has been implicated previously as a TSG in both uterine leiomyomas and breast carcinoma. However, mutation analysis of the CUTL1 gene in 47 tumors with 7q22 LOH failed to identify any somatic alterations in the coding regions. This finding suggests that CUTL1 may not be the target of the 7q22 LOH in ovarian cancers.

High Frequency of Copy-Neutral Loss of Heterozygosity in Patients with Myelofibrosis.

PubMed

Rego de Paula Junior, Milton; Nonino, Alexandre; Minuncio Nascimento, Juliana; Bonadio, Raphael S; Pic-Taylor, Aline; de Oliveira, Silviene F; Wellerson Pereira, Rinaldo; do Couto Mascarenhas, Cintia; Forte Mazzeu, Juliana

2018-01-01

Myelofibrosis is the rarest and most severe type of Philadelphia-negative classical myeloproliferative neoplasms. Although mutually exclusive driver mutations in JAK2, MPL, or CALR that activate JAK-STAT pathway have been related to the pathogenesis of the disease, chromosome abnormalities have also been associated with the phenotype and prognosis of the disease. Here, we report the use of a chromosomal microarray platform consisting of both oligo and SNP probes to improve the detection of chromosome abnormalities in patients with myelofibrosis. Sixteen patients with myelofibrosis were tested, and the results were compared to karyotype analysis. Driver mutations in JAK2, MPL, or CALR were investigated by PCR and MLPA. Conventional cytogenetics revealed chromosome abnormalities in 3 out of 16 cases (18.7%), while chromosomal microarray analysis detected copy-number variations (CNV) or copy-neutral loss of heterozygosity (CN-LOH) alterations in 11 out of 16 (68.7%) patients. These included 43 CN-LOH, 14 deletions, 1 trisomy, and 1 duplication. Ten patients showed multiple chromosomal abnormalities, varying from 2 to 13 CNVs or CN-LOHs. Mutational status for JAK2, CALR, and MPL by MLPA revealed a total of 3/16 (18.7%) patients positive for the JAK2 V617F mutation, 9 with CALR deletion or insertion and 1 positive for MPL mutation. Considering that most of the CNVs identified were smaller than the karyotype resolution and the high frequency of CN-LOHs in our study, we propose that chromosomal microarray platforms that combine oligos and SNP should be used as a first-tier genetic test in patients with myelofibrosis. © 2018 S. Karger AG, Basel.

Microsatellite primers for two threatened orchids in Florida: Encyclia tampensis and Cyrtopodium punctatum (Orchidaceae)1

PubMed Central

Weremijewicz, Joanna; Almonte, Jasmin I.; Hilaire, Vanessa S.; Lopez, Frank D.; Lu, Stephen H.; Marrero, Sarah M.; Martinez, Catherine M.; Zarate, Edson A.; Lam, Ana K.; Ferguson, Samantha A. N.; Petrakis, Nicolas Z.; Peeples, Kelsey A.; Taylor, Ebony D.; Leon, Natalie M.; Valdes, Carolina; Hass, Michael; Reeve, Andrew B.; Palow, Danielle T.; Downing, Jason L.

2016-01-01

Premise of the study: The Million Orchid Project at Fairchild Tropical Botanic Garden is an initiative to propagate native orchids for reintroduction into Miami’s urban landscapes. The aim of this study was to develop microsatellites for Encyclia tampensis and Cyrtopodium punctatum (Orchidaceae). Methods and Results: Ten microsatellites were developed for each species. For E. tampensis sampled from the natural population, allele numbers ranged from one to four, with an average observed heterozygosity (Ho) of 0.314 and average expected heterozygosity (He) of 0.281. For the individuals from cultivation, allele numbers ranged from one to six, with an average Ho of 0.35 and an average He of 0.224. For C. punctatum, allele numbers ranged from one to three, with an average Ho of 0.257 and an average He of 0.272. Conclusions: These microsatellites will be used to assess the genetic diversity of natural and cultivated populations with the intention of guiding genetic breeding under the Million Orchid Project. PMID:27144103

Microsatellite primers for two threatened orchids in Florida: Encyclia tampensis and Cyrtopodium punctatum (Orchidaceae).

PubMed

Weremijewicz, Joanna; Almonte, Jasmin I; Hilaire, Vanessa S; Lopez, Frank D; Lu, Stephen H; Marrero, Sarah M; Martinez, Catherine M; Zarate, Edson A; Lam, Ana K; Ferguson, Samantha A N; Petrakis, Nicolas Z; Peeples, Kelsey A; Taylor, Ebony D; Leon, Natalie M; Valdes, Carolina; Hass, Michael; Reeve, Andrew B; Palow, Danielle T; Downing, Jason L

2016-04-01

The Million Orchid Project at Fairchild Tropical Botanic Garden is an initiative to propagate native orchids for reintroduction into Miami's urban landscapes. The aim of this study was to develop microsatellites for Encyclia tampensis and Cyrtopodium punctatum (Orchidaceae). Ten microsatellites were developed for each species. For E. tampensis sampled from the natural population, allele numbers ranged from one to four, with an average observed heterozygosity (H o) of 0.314 and average expected heterozygosity (H e) of 0.281. For the individuals from cultivation, allele numbers ranged from one to six, with an average H o of 0.35 and an average H e of 0.224. For C. punctatum, allele numbers ranged from one to three, with an average H o of 0.257 and an average H e of 0.272. These microsatellites will be used to assess the genetic diversity of natural and cultivated populations with the intention of guiding genetic breeding under the Million Orchid Project.

Enhanced SO2 Concentrations Observed over Northern India: Role of Long-range Transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mallik, C.; Lal, S.; Naja, M.

2013-01-17

Volcanic emissions and coal burning are among the major sources of SO2 over the continental environment. In this study, we show episodes of long-range transport of volcanic SO2 from Africa to Northern India using satellite observations. Monthly averaged SO2 from OMI were of the order of 0.6-0.9 DU during November, 2008 over the Indo-Gangetic Plain (IGP), which far exceeded background values (<0.3 DU) retrieved from observations across different locations over North India during 2005-2010. The columnar SO2 loadings were much higher on November 6 over most of the IGP and even exceeded 6 DU, a factor of 10 higher thanmore » background levels at some places. These enhanced SO2 levels were, however, not reciprocated in satellite derived NO2 or CO columns, indicating transport from a non-anthropogenic source of SO2. Backward trajectory analysis revealed strong winds in the free troposphere, which originated from the Dalaffilla volcanic eruption over the Afar region of Ethiopia during November 4-6, 2008. Wind streams and stable atmospheric conditions were conducive to the long-range transport of volcanic plume into the IGP. As most of the local aerosols over IGP region are below 3 km, a well separated layer at 4-5 km is observed from CALIPSO, most likely as a result of this transport. Apart from known anthropogenic sources, the additional transport of volcanic SO2 over the IGP region would have implications to air quality and radiation balance over this region.« less

Seismic structures in the inner and outer core constrained by the PKP observations near the caustic distance range

NASA Astrophysics Data System (ADS)

Yu, W.; Wen, L.; Niu, F.

2002-05-01

We have extensively collected PKP waveforms around the PKP caustic distance range (141o - 147o) recorded in several dense regional arrays and the Global Seismic Network covering from 1990 to 2000. PKP observations at this distance range (141o - 147o) are usually purposely avoided in travel time analyses, because of the interference of various PKP branches. The observations there, however, will be extremely useful for constraining the seismic structures at both the top of the inner core and the bottom of the outer core. Moreover, because PKIKP phases sample a depth range of 100 km - 170 km below the inner-core boundary at this distant range, their observations fill the sampling depth gap between the PKiKP-PKIKP observations at the smaller distances and the PKPbc-PKIKP phases at the larger distances. Before the PKP caustics (141o - 145o), the diffracted PKP phases near the B caustics (PKPBdiff) and PKiKP phases are discernible in the long-period seismograms, and their differential travel times and waveforms could be used to constrain seismic structures at the bottom of the outer core and/or at the base of the mantle. The observed long-period PKiKP-PKPBdiff waveforms exhibit a hemispheric difference between those sampling the "eastern" and "western" hemispheres, with those sampling the "western" hemisphere showing larger time separations between the two phases. These observations can be explained by models with P velocity gradients of 0.0806 (km/s)/ 200 km for the "western" hemisphere and 0.114 (km/s)/200 km for the "eastern" hemisphere at the bottom of the outer core. Alternatively, these observations can also be explained by models with different velocity structures at the bottom 200 km of the mantle with P velocity variations in an order of 3 percent with respect to PREM. Broadband PKP observations after the PKP caustics (145o - 147o), on the other hand, provide high-quality constraints on the seismic structures at both the top of the inner core and the bottom of

Lowered Diversity and Increased Inbreeding Depression within Peripheral Populations of Wild Rice Oryza rufipogon.

PubMed

Gao, Li-Zhi; Gao, Cheng-Wen

2016-01-01

The distribution of genetic variability from the interior towards the periphery of a species' range is of great interest to evolutionary biologists. Although it has been long presumed that population genetic variation should decrease as a species' range is approached, results of empirical investigations still remain ambiguous. Knowledge regarding patterns of genetic variability as well as affected factors is particularly not conclusive in plants. To determine genetic divergence in peripheral populations of the wild rice Oryza rufipogon Griff. from China, genetic diversity and population structure were studied in five northern & northeastern peripheral and 16 central populations using six microsatellite loci. We found that populations resided at peripheries of the species possessed markedly decreased microsatellite diversity than those located in its center. Population size was observed to be positively correlated with microsatellite diversity. Moreover, there are significantly positive correlations between levels of microsatellite diversity and distances from the northern and northeastern periphery of this species. To investigate genetic structure and heterozygosity variation between generations of O. rufipogon, a total of 2382 progeny seeds from 186 maternal families were further assayed from three peripheral and central populations, respectively. Peripheral populations exhibited significantly lower levels of heterozygosities than central populations for both seed and maternal generations. In comparisons with maternal samples, significantly low observed heterozygosity (HO) and high heterozygote deficit within populations (FIS) values were detected in seed samples from both peripheral and central populations. Significantly lower observed heterozygosity (HO) and higher FIS values were further observed in peripheral populations than those in central populations for seed samples. The results indicate an excess of homozygotes and thus high inbreeding depression in

Tonopah Test Range Air Monitoring: CY2015 Meteorological, Radiological, and Airborne Particulate Observations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nikolich, George; Shadel, Craig; Chapman, Jenny

2016-09-01

In 1963, the U.S. Department of Energy (DOE) (formerly the Atomic Energy Commission [AEC]), implemented Operation Roller Coaster on the Tonopah Test Range (TTR) and an adjacent area of the Nevada Test and Training Range (NTTR) (formerly the Nellis Air Force Range). The operation resulted in radionuclide-contaminated soils at the Clean Slate I, II, and III sites. This report documents observations made during ongoing monitoring of radiological, meteorological, and dust conditions at stations installed adjacent to Clean Slate I and Clean Slate III, and at the TTR Sandia National Laboratories (SNL) Range Operations Control (ROC) center. The primary objective ofmore » the monitoring effort is to determine if winds blowing across the Clean Slate sites are transporting particles of radionuclide-contaminated soil beyond the physical and administrative boundaries of the sites. Radionuclide assessment of airborne particulates in 2015 found the gross alpha and gross beta values of dust collected from the filters at the monitoring stations are consistent with background conditions. The meteorological and particle monitoring indicate that conditions for wind-borne contaminant movement exist at the Clean Slate sites and that, although the transport of radionuclide-contaminated soil by suspension has not been detected, movement by saltation is occurring.« less

Social perceptions versus meteorological observations of snow and winter along the Front Range

NASA Astrophysics Data System (ADS)

Milligan, William James, IV

This research aims to increase understanding of Front Range residents' perceptions of snow, winter and hydrologic events. This study also investigates how an individual's characteristics may shape perceptions of winter weather and climate. A survey was administered to determine if perceptions of previous winters align with observed meteorological data. The survey also investigated how individual characteristics influence perceptions of snow and winter weather. The survey was conducted primarily along the Front Range area of the state of Colorado in the United States of America. This is a highly populated semi-arid region that acts as an interface between the agricultural plains to the east that extend to the Mississippi River and the Rocky Mountains to the west. The climate is continental, and while many people recreate in the snowy areas of the mountains, most live where annual snowfall amounts are low. Precipitation, temperature, and wind speed datasets from selected weather stations were analyzed to determine correct survey responses. Survey analysis revealed that perceptions of previous winters do not necessarily align with observed meteorological data. The mean percentage of correct responses to all survey questions was 36.8%. Further analysis revealed that some individual characteristics (e.g. winter recreation, source of winter weather information) did influence correct responses to survey questions.

Life stage, not climate change, explains observed tree range shifts.

PubMed

Máliš, František; Kopecký, Martin; Petřík, Petr; Vladovič, Jozef; Merganič, Ján; Vida, Tomáš

2016-05-01

Ongoing climate change is expected to shift tree species distribution and therefore affect forest biodiversity and ecosystem services. To assess and project tree distributional shifts, researchers may compare the distribution of juvenile and adult trees under the assumption that differences between tree life stages reflect distributional shifts triggered by climate change. However, the distribution of tree life stages could differ within the lifespan of trees, therefore, we hypothesize that currently observed distributional differences could represent shifts over ontogeny as opposed to climatically driven changes. Here, we test this hypothesis with data from 1435 plots resurveyed after more than three decades across the Western Carpathians. We compared seedling, sapling and adult distribution of 12 tree species along elevation, temperature and precipitation gradients. We analyzed (i) temporal shifts between the surveys and (ii) distributional differences between tree life stages within both surveys. Despite climate warming, tree species distribution of any life stage did not shift directionally upward along elevation between the surveys. Temporal elevational shifts were species specific and an order of magnitude lower than differences among tree life stages within the surveys. Our results show that the observed range shifts among tree life stages are more consistent with ontogenetic differences in the species' environmental requirements than with responses to recent climate change. The distribution of seedlings substantially differed from saplings and adults, while the distribution of saplings did not differ from adults, indicating a critical transition between seedling and sapling tree life stages. Future research has to take ontogenetic differences among life stages into account as we found that distributional differences recently observed worldwide may not reflect climate change but rather the different environmental requirements of tree life stages. © 2016

Life-stage, not climate change, explains observed tree range shifts

PubMed Central

Máliš, František; Kopecký, Martin; Petřík, Petr; Vladovič, Jozef; Merganič, Ján; Vida, Tomáš

2017-01-01

Ongoing climate change is expected to shift tree species distribution and therefore affect forest biodiversity and ecosystem services. To assess and project tree distributional shifts, researchers may compare the distribution of juvenile and adult trees under the assumption that differences between tree life-stages reflect distributional shifts triggered by climate change. However, the distribution of tree life-stages could differ within the lifespan of trees, therefore we hypothesize that currently observed distributional differences could represent shifts over ontogeny as opposed to climatically driven changes. Here we test this hypothesis with data from 1435 plots resurveyed after more than three decades across the Western Carpathians. We compared seedling, sapling and adult distribution of 12 tree species along elevation, temperature and precipitation gradients. We analyzed i) temporal shifts between the surveys and ii) distributional differences between tree life-stages within both surveys. Despite climate warming, tree species distribution of any life-stage did not shift directionally upward along elevation between the surveys. Temporal elevational shifts were species-specific and an order of magnitude lower than differences among tree life-stages within the surveys. Our results show that the observed range shifts among tree life-stages are more consistent with ontogenetic differences in the species’ environmental requirements than with responses to recent climate change. The distribution of seedlings substantially differed from saplings and adults, while the distribution of saplings did not differ from adults, indicating a critical transition between seedling and sapling tree life-stages. Future research has to take ontogenetic differences among life-stages into account as we found that distributional differences recently observed worldwide may not reflect climate change but rather the different environmental requirements of tree life-stages. PMID:26725258

STS-56 Earth observation of Karakorum Range of north India

NASA Image and Video Library

1993-04-17

STS-56 Earth observation shows of some of the highest mountain peaks in the world taken from Discovery, Orbiter Vehicle (OV) 103, as it passed over India and China. The top of the view shows one of the snow and ice-covered massifs in the great Karakorum Range of north India. A star-shaped peak at top left reaches 23,850 feet. Glaciers can be seen in valleys at these high elevations. The international border between India to the south (top) and China (bottom) snakes left to right along a river near the top of the scene, then veers into the muntains at top left. Larger valleys, despite their elevation (all in excess of 14,000 feet), are occupied by transport routes joining points in India, China and the southern republics of the CIS. The ancient Silk Route between China and the Middle East lies not far to the north (outside the bottom of the frame).

Different mechanisms of radiation-induced loss of heterozygosity in two human lymphoid cell lines from a single donor

NASA Technical Reports Server (NTRS)

Wiese, C.; Gauny, S. S.; Liu, W. C.; Cherbonnel-Lasserre, C. L.; Kronenberg, A.

2001-01-01

Allelic loss is an important mutational mechanism in human carcinogenesis. Loss of heterozygosity (LOH) at an autosomal locus is one outcome of the repair of DNA double-strand breaks (DSBs) and can occur by deletion or by mitotic recombination. We report that mitotic recombination between homologous chromosomes occurred in human lymphoid cells exposed to densely ionizing radiation. We used cells derived from the same donor that express either normal TP53 (TK6 cells) or homozygous mutant TP53 (WTK1 cells) to assess the influence of TP53 on radiation-induced mutagenesis. Expression of mutant TP53 (Met 237 Ile) was associated with a small increase in mutation frequencies at the hemizygous HPRT (hypoxanthine phosphoribosyl transferase) locus, but the mutation spectra were unaffected at this locus. In contrast, WTK1 cells (mutant TP53) were 30-fold more susceptible than TK6 cells (wild-type TP53) to radiation-induced mutagenesis at the TK1 (thymidine kinase) locus. Gene dosage analysis combined with microsatellite marker analysis showed that the increase in TK1 mutagenesis in WTK1 cells could be attributed, in part, to mitotic recombination. The microsatellite marker analysis over a 64-cM region on chromosome 17q indicated that the recombinational events could initiate at different positions between the TK1 locus and the centromere. Virtually all of the recombinational LOH events extended beyond the TK1 locus to the most telomeric marker. In general, longer LOH tracts were observed in mutants from WTK1 cells than in mutants from TK6 cells. Taken together, the results demonstrate that the incidence of radi-ation-induced mutations is dependent on the genetic background of the cell at risk, on the locus examined, and on the mechanisms for mutation available at the locus of interest.

Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

PubMed Central

Garzón-Martínez, Gina A.; Osorio-Guarín, Jaime A.; Delgadillo-Durán, Paola; Mayorga, Franklin; Enciso-Rodríguez, Felix E.; Landsman, David

2015-01-01

The genus Physalis is common in the Americas and includes several economically important species, among them Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNPs) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation FST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies. PMID:26550601

Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers.

PubMed

Garzón-Martínez, Gina A; Osorio-Guarín, Jaime A; Delgadillo-Durán, Paola; Mayorga, Franklin; Enciso-Rodríguez, Felix E; Landsman, David; Mariño-Ramírez, Leonardo; Barrero, Luz Stella

2015-12-01

The genus Physalis is common in the Americas and includes several economically important species, among them Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNPs) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation F ST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies.

Conspecific Crop-Weed Introgression Influences Evolution of Weedy Rice (Oryza sativa f. spontanea) across a Geographical Range

PubMed Central

Xia, Han-Bing; Wang, Wei; Xia, Hui; Zhao, Wei; Lu, Bao-Rong

2011-01-01

Background Introgression plays an important role in evolution of plant species via its influences on genetic diversity and differentiation. Outcrossing determines the level of introgression but little is known about the relationships of outcrossing rates, genetic diversity, and differentiation particularly in a weedy taxon that coexists with its conspecific crop. Methodology/Principal Findings Eleven weedy rice (Oryza sativa f. spontanea) populations from China were analyzed using microsatellite (SSR) fingerprints to study outcrossing rate and its relationship with genetic variability and differentiation. To estimate outcrossing, six highly polymorphic SSR loci were used to analyze >5500 progeny from 216 weedy rice families, applying a mixed mating model; to estimate genetic diversity and differentiation, 22 SSR loci were analyzed based on 301 weedy individuals. Additionally, four weed-crop shared SSR loci were used to estimate the influence of introgression from rice cultivars on weedy rice differentiation. Outcrossing rates varied significantly (0.4∼11.7%) among weedy rice populations showing relatively high overall Nei's genetic diversity (0.635). The observed heterozygosity was significantly correlated with outcrossing rates among populations (r2 = 0.783; P<0.001) although no obvious correlation between outcrossing rates and genetic diversity parameters was observed. Allelic introgression from rice cultivars to their coexisting weedy rice was detected. Weedy rice populations demonstrated considerable genetic differentiation that was correlated with their spatial distribution (r2 = 0.734; P<0.001), and possibly also influenced by the introgression from rice cultivars. Conclusions/Significance Outcrossing rates can significantly affect heterozygosity of populations, which may shape the evolutionary potential of weedy rice. Introgression from the conspecific crop rice can influence the genetic differentiation and possibly evolution of its coexisting

Ataxia-telangiectasia gene (ATM) mutation heterozygosity in breast cancer: a narrative review.

PubMed

Jerzak, K J; Mancuso, T; Eisen, A

2018-04-01

Despite the fact that heterozygosity for a pathogenic ATM variant is present in 1%-2% of the adult population, clinical guidelines to inform physicians and genetic counsellors about optimal management in that population are lacking. In this narrative review, we describe the challenges and controversies in the management of women who are heterozygous for a pathogenic ATM variant with respect to screening for breast and other malignancies, to choices for systemic therapy, and to decisions about radiation therapy. Given that the lifetime risk for breast cancer in women who are heterozygous for a pathogenic ATM variant is likely greater than 25%, those women should undergo annual mammographic screening starting at least by 40 years of age. For women in this group who have a strong family history of breast cancer, earlier screening with both magnetic resonance imaging and mammography should be considered. High-quality data to inform the management of established breast cancer in carriers of pathogenic ATM variants are lacking. Although deficiency in the ATM gene product might confer sensitivity to dna-damaging pharmaceuticals such as inhibitors of poly (adp-ribose) polymerase or platinum agents, prospective clinical trials have not been conducted in the relevant patient population. Furthermore, the evidence with respect to radiation therapy is mixed; some data suggest increased toxicity, and other data suggest improved clinical benefit from radiation in women who are carriers of a pathogenic ATM variant. As in the 2017 U.S. National Comprehensive Cancer Network guidelines, we recommend high-risk imaging for women in Ontario who are heterozygous for a pathogenic ATM variant. Currently, ATM carrier status should not influence decisions about systemic or radiation therapy in the setting of an established breast cancer diagnosis.

Partial rescue of defects in Cited2-deficient embryos by HIF-1alpha heterozygosity.

PubMed

Xu, Bing; Doughman, Yongqiu; Turakhia, Mona; Jiang, Weihong; Landsettle, Chad E; Agani, Faton H; Semenza, Gregg L; Watanabe, Michiko; Yang, Yu-Chung

2007-01-01

Hypoxia inducible factor-1 (HIF-1) initiates key cellular and tissue responses to physiological and pathological hypoxia. Evidence from in vitro and structural analyses supports a critical role for Cited2 in down-regulating HIF-1-mediated transcription by competing for binding with oxygen-sensitive HIF-1alpha to transcriptional co-activators CBP/p300. We previously detected elevated expression of HIF-1 target genes in Cited2(-/-) embryonic hearts, indicating that Cited2 inhibits HIF-1 transactivation in vivo. In this study, we show for the first time that highly hypoxic cardiac regions in mouse embryos corresponded to the sites of defects in Cited2(-/-) embryos and that defects of the outflow tract, interventricular septum, cardiac vasculature, and hyposplenia were largely rescued by HIF-1alpha haploinsufficiency. The hypoxia of the outflow tract and interventricular septum peaked at E13.5 and dissipated by E15.5 in wild-type hearts, but persisted in E15.5 Cited2(-/-) hearts. The persistent hypoxia and abnormal vasculature in the myocardium of interventricular septum in E15.5 Cited2(-/-) hearts were rescued with decreased HIF-1alpha gene dosage. Accordingly, mRNA levels of HIF-1-responsive genes were reduced in Cited2(-/-) embryonic hearts by HIF-1alpha heterozygosity. These findings suggest that a precise level of HIF-1 transcriptional activity critical for normal development is triggered by differential hypoxia and regulated through feedback inhibition by Cited2.

Isolation and characterization of 16 microsatellite loci in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae: Scolytinae)

Treesearch

C. S. Davis; K. E. Mock; B. J. Bentz; S. M. Bromilow; N. V. Bartell; B. W. Murray; A. D. Roe; J. E. K. Cooke

2009-01-01

We isolated 16 polymorphic microsatellite loci in the mountain pine beetle (Dendroctonus ponderosae Hopkins) and developed conditions for amplifying these markers in four multiplex reactions. Three to 14 alleles were detected per locus across two sampled populations. Observed and expected heterozygosities ranged from 0.000 to 0.902 and from 0.100 to 0.830, respectively...

Compound heterozygosity for Hb S [beta6(A3)GluVal, GAG-->GTG] and a new thalassemic mutation [beta132(H10)Lys-->term, AAA-->TAA] detected in a family from West Africa.

PubMed

Frischknecht, Hannes; Troxler, Heinz; Greiner, Jeanette; Hengartner, Heinz; Dutly, Fabrizio

2008-01-01

We describe a Hb S/beta-thalassemia (beta-thal) mutation involving an AT transition at codon 132 of the beta-globin gene. The mutation, in the heterozygous state, unlike several other mutations in exon 3, shows no signs of dominant thalassemia but those of a typical beta(0) carrier. Compound heterozygosity with Hb S [beta6(A3)GluVal, GAGGTG] showed a severe clinical picture.

Loss of heterozygosity in yeast can occur by ultraviolet irradiation during the S phase of the cell cycle.

PubMed

Daigaku, Yasukazu; Mashiko, Satsuki; Mishiba, Keiichiro; Yamamura, Saburo; Ui, Ayako; Enomoto, Takemi; Yamamoto, Kazuo

2006-08-30

A CAN1/can1Delta heterozygous allele that determines loss of heterozygosity (LOH) was used to study recombination in Saccharomyces cerevisiae cells exposed to ultraviolet (UV) light at different points in the cell cycle. With this allele, recombination events can be detected as canavanine-resistant mutations after exposure of cells to UV radiation, since a significant fraction of LOH events appear to arise from recombination between homologous chromosomes. The radiation caused a higher level of LOH in cells that were in the S phase of the cell cycle relative to either cells at other points in the cell cycle or unsynchronized cells. In contrast, the inactivation of nucleotide excision repair abolished the cell cycle-specific induction by UV of LOH. We hypothesize that DNA lesions, if not repaired, were converted into double-strand breaks during stalled replication and these breaks could be repaired through recombination using a non-sister chromatid and probably also the sister chromatid. We argue that LOH may be an outcome used by yeast cells to recover from stalled replication at a lesion.

Loss of heterozygosity 4q24 and TET2 mutations associated with myelodysplastic/myeloproliferative neoplasms

PubMed Central

Jankowska, Anna M.; Szpurka, Hadrian; Tiu, Ramon V.; Makishima, Hideki; Afable, Manuel; Huh, Jungwon; O'Keefe, Christine L.; Ganetzky, Rebecca; McDevitt, Michael A.

2009-01-01

Chromosomal abnormalities are frequent in myeloid malignancies, but in most cases of myelodysplasia (MDS) and myeloproliferative neoplasms (MPN), underlying pathogenic molecular lesions are unknown. We identified recurrent areas of somatic copy number–neutral loss of heterozygosity (LOH) and deletions of chromosome 4q24 in a large cohort of patients with myeloid malignancies including MDS and related mixed MDS/MPN syndromes using single nucleotide polymorphism arrays. We then investigated genes in the commonly affected area for mutations. When we sequenced TET2, we found homozygous and hemizygous mutations. Heterozygous and compound heterozygous mutations were found in patients with similar clinical phenotypes without LOH4q24. Clinical analysis showed most TET2 mutations were present in patients with MDS/MPN (58%), including CMML (6/17) or sAML (32%) evolved from MDS/MPN and typical MDS (10%), suggesting they may play a ubiquitous role in malignant evolution. TET2 mutations affected conserved domains and the N terminus. TET2 is widely expressed in hematopoietic cells but its function is unknown, and it lacks homology to other known genes. The frequency of mutations in this candidate myeloid regulatory gene suggests an important role in the pathogenesis of poor prognosis MDS/MPN and sAML and may act as a disease gene marker for these often cytogenetically normal disorders. PMID:19372255

Wide-Range Multiwavelength Observations of Northern TeV Blazars With MAGIC / HESS, Suzaku And KVA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayashida, M.; /Munich, Max Planck Inst.; Rugamer, S.

2007-11-14

We have conducted multiwavelength observations of several northern TeV blazars employing the ground-based {gamma}-ray observatories MAGIC and HESS, the optical KVA telescope, and the Suzaku X-ray satellite. The data taken in 2006 establish measurements of the contemporaneous spectral energy distributions of the rapidly variable blazar emission over a wide range of frequencies. Results allow us to test leptonic and hadronic emission and particle acceleration models which predict different correlations between the optical, X-ray, and very high energy {gamma}-ray emissions. In this presentation, we report on the highlights of the results of these observations.

Body odour preferences in men and women: do they aim for specific MHC combinations or simply heterozygosity?

PubMed Central

Wedekind, C; Füri, S

1997-01-01

The major histocompatibility complex (MHC) is an immunologically important group of genes that appears to be under natural as well as sexual selection. Several hypotheses suggest that certain MHC-allele combinations (usually heterozygous ones) are superior under selective pressure by pathogens. This could influence mate choice in a way that preferences function to create MHC-heterozygous offspring, or that they function to create specific allele combinations that are beneficial under the current environmental conditions through their complementary or epistatic effects. To test these hypotheses, we asked 121 men and women to score the odours of six T-shirts, worn by two women and four men. Their scorings of pleasantness correlated negatively with the degree of MHC similarity between smeller and T-shirt-wearer in men and women who were not using the contraceptive pill (but not in Pill-users). Depending on the T-shirt-wearer, the amount of variance in the scorings of odour pleasantness that was explained by the degree of MHC similarity (r2) varied between nearly 0 and 23%. There was no apparent effect of gender in this correlation: the highest r2 was actually reached with one of the male odours sniffed by male smellers. Men and women who were reminded of their own mate/ex-mate when sniffing a T-shirt had significantly fewer MHC-alleles in common with this T-shirt-wearer than expected by chance. This suggests that the MHC or linked genes influence human mate choice. We found no significant effect when we tested for an influence of the MHC on odour preferences after the degree of similarity between T-shirt-wearer and smeller was statistically controlled for. This suggests that in our study populations the MHC influences body odour preferences mainly, if not exclusively, by the degree of similarity or dissimilarity. The observed preferences would increase heterozygosity in the progeny. They do not seem to aim for more specific MHC combinations. PMID:9364787

A far-ultraviolet atlas of symbiotic stars observed with IUE. 1. The SWP range

NASA Technical Reports Server (NTRS)

Meier, S. R.; Kafatos, M.; Fahey, R. P.; Michalitsianos, A. G.

1994-01-01

This atlas contains sample spectra from the far-ultraviolet observations of 32 symbiotic stars obtained with the International Ultraviolet Explorer (IUE) satellite. In all, 394 low-resolution spectra from the short-wavelength primary (SWP) camera covering the range 1200-2000 A have been extracted from the IUE archive, calibrated, and measured. Absolute line fluxes and wavelengths for the prominent emission lines have been tabulated. Tables of both the general properties of these symbiotics and of features specific to the spectrum of each are included. The spectra shown are representative of the different classes of symbiotic stars that are currently in the IUE archive. These include known eclipsing systems and those that have been observed in outburst (as well as quiescence).

Autosomal InDel polymorphisms for population genetic structure and differentiation analysis of Chinese Kazak ethnic group

PubMed Central

Kong, Tingting; Chen, Yahao; Guo, Yuxin; Wei, Yuanyuan; Jin, Xiaoye; Xie, Tong; Mu, Yuling; Dong, Qian; Wen, Shaoqing; Zhou, Boyan; Zhang, Li; Shen, Chunmei; Zhu, Bofeng

2017-01-01

In the present study, we assessed the genetic diversities of the Chinese Kazak ethnic group on the basis of 30 well-chosen autosomal insertion and deletion loci and explored the genetic relationships between Kazak and 23 reference groups. We detected the level of the expected heterozygosity ranging from 0.3605 at HLD39 locus to 0.5000 at HLD136 locus and the observed heterozygosity ranging from 0.3548 at HLD39 locus to 0.5283 at HLD136 locus. The combined power of discrimination and the combined power of exclusion for all 30 loci in the studied Kazak group were 0.999999999999128 and 0.9945, respectively. The dataset generated in this study indicated the panel of 30 InDels was highly efficient in forensic individual identifcation but may not have enough power in paternity cases. The results of the interpopulation differentiations, PCA plots, phylogenetic trees and STRUCTURE analyses showed a close genetic affiliation between the Kazak and Uigur group. PMID:28915619

How Continuous Observations of Shortwave Reflectance Spectra Can Narrow the Range of Shortwave Climate Feedbacks

NASA Astrophysics Data System (ADS)

Feldman, D.; Collins, W. D.; Wielicki, B. A.; Shea, Y.; Mlynczak, M. G.; Kuo, C.; Nguyen, N.

2017-12-01

Shortwave feedbacks are a persistent source of uncertainty for climate models and a large contributor to the diagnosed range of equilibrium climate sensitivity (ECS) for the international multi-model ensemble. The processes that contribute to these feedbacks affect top-of-atmosphere energetics and produce spectral signatures that may be time-evolving. We explore the value of such spectral signatures for providing an observational constraint on model ECS by simulating top-of-atmosphere shortwave reflectance spectra across much of the energetically-relevant shortwave bandpass (300 to 2500 nm). We present centennial-length shortwave hyperspectral simulations from low, medium and high ECS models that reported to the CMIP5 archive as part of an Observing System Simulation Experiment (OSSE) in support of the CLimate Absolute Radiance and Refractivity Observatory (CLARREO). Our framework interfaces with CMIP5 archive results and is agnostic to the choice of model. We simulated spectra from the INM-CM4 model (ECS of 2.08 °K/2xCO2), the MIROC5 model (ECS of 2.70 °K/2xCO2), and the CSIRO Mk3-6-0 (ECS of 4.08 °K/2xCO2) based on those models' integrations of the RCP8.5 scenario for the 21st Century. This approach allows us to explore how perfect data records can exclude models of lower or higher climate sensitivity. We find that spectral channels covering visible and near-infrared water-vapor overtone bands can potentially exclude a low or high sensitivity model with under 15 years' of absolutely-calibrated data. These different spectral channels are sensitive to model cloud radiative effect and cloud height changes, respectively. These unprecedented calculations lay the groundwork for spectral simulations of perturbed-physics ensembles in order to identify those shortwave observations that can help narrow the range in shortwave model feedbacks and ultimately help reduce the stubbornly-large range in model ECS.

Genetic divergence between Melipona quadrifasciata Lepeletier (Hymenoptera, Apidae) populations.

PubMed

Tavares, Mara Garcia; Pietrani, Nathalia Teixeira; de Castro Durvale, Maxwell; Resende, Helder Canto; de Oliveira Campos, Lucio Antonio

2013-03-01

Melipona quadrifasciata is a stingless bee widely found throughout the Brazilian territory, with two recognized subspecies, M. quadrifasciata anthidioides, that exhibits interrupted metasomal stripes, and M. quadrifasciata quadrifasciata, with continuous metasomal stripes. This study aimed to estimate the genetic variability of these subspecies. For this purpose, 127 colonies from 15 Brazilian localities were analyzed, using nine species-specific microsatellite primers. At these loci, the number of alleles ranged from three to 15 (mean: 7.2), and the observed heterozygosity (Ho) ranged from 0.03-0.21, while the expected heterozygosity (He) ranged from 0.23-0.47. The genetic distances among populations ranged from 0.03-0.45. The FST multilocus value (0.23) indicated that the populations sampled were structured, and the clustering analysis showed the formation of two subgroups and two more distant populations. The first group contained the subspecies M. quadrifasciata quadrifasciata, and the other, the subspecies M. quadrifasciata anthidioides and the two M. quadrifasciata populations with continuous metasomal stripes from northern Minas Gerais. These results confirmed that the yellow metasomal stripes alone are not a good means for correctly identifying the different subspecies of M. quadrifasciata.

Genetic divergence between Melipona quadrifasciata Lepeletier (Hymenoptera, Apidae) populations

PubMed Central

Tavares, Mara Garcia; Pietrani, Nathalia Teixeira; de Castro Durvale, Maxwell; Resende, Helder Canto; de Oliveira Campos, Lucio Antonio

2013-01-01

Melipona quadrifasciata is a stingless bee widely found throughout the Brazilian territory, with two recognized subspecies, M. quadrifasciata anthidioides, that exhibits interrupted metasomal stripes, and M. quadrifasciata quadrifasciata, with continuous metasomal stripes. This study aimed to estimate the genetic variability of these subspecies. For this purpose, 127 colonies from 15 Brazilian localities were analyzed, using nine species-specific microsatellite primers. At these loci, the number of alleles ranged from three to 15 (mean: 7.2), and the observed heterozygosity (Ho) ranged from 0.03–0.21, while the expected heterozygosity (He) ranged from 0.23–0.47. The genetic distances among populations ranged from 0.03–0.45. The FST multilocus value (0.23) indicated that the populations sampled were structured, and the clustering analysis showed the formation of two subgroups and two more distant populations. The first group contained the subspecies M. quadrifasciata quadrifasciata, and the other, the subspecies M. quadrifasciata anthidioides and the two M. quadrifasciata populations with continuous metasomal stripes from northern Minas Gerais. These results confirmed that the yellow metasomal stripes alone are not a good means for correctly identifying the different subspecies of M. quadrifasciata. PMID:23569416

Further localization of the gene for nevoid basal cell carcinoma syndrome (NBCCS) in 15 Australasian families: Linkage and loss of heterozygosity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chenevix-Trench, G.; Wicking, C.; Berkman, J.

Nevoid basal cell carcinoma syndrome (NBCCS; basal cell nevus syndrome or Gorlin syndrome) is a cancer-predisposition syndrome characterized by multiple basal cell carcinomas (BCCs) and diverse developmental defects. The gene for NBCCS has been mapped to 9q23.1-q31 in North Americal and European families. In addition, loss of heterozygosity (LOH) for genetic markers in this region has been detected in sporadic BCCs, indicating that the NBCCs gene is probably a tumor-suppressor gene. In this study the authors have determined that the NBCCS gene is also linked to this region in Australasian pedigrees and that there is no significant evidence of heterogeneity.more » They have defined the localization of the gene by multipoint and haplotype analysis of 15 families, using four microsatellite markers. LOH at these loci was detected in 50% of sporadic BCCs, a rate that is significantly higher than that in other skin lesions used as controls. 21 refs., 3 figs., 2 tabs.« less

Microsatellite markers for the native Texas perennial grass, Panicum hallii (Poaceae).

PubMed

Lowry, David B; Purmal, Colin T; Meyer, Eli; Juenger, Thomas E

2012-03-01

We developed microsatellites for Panicum hallii for studies of gene flow, population structure, breeding experiments, and genetic mapping. Next-generation (454) genomic sequence data were used to design markers. Eighteen robust markers were discovered, 15 of which were polymorphic across six accessions of P. hallii var. hallii. Fourteen of the markers cross-amplified in a P. capillare accession. For the 15 polymorphic markers, the total number of alleles per locus ranged from two to 26 (mean: 11.0) across six populations (11-19 individuals per population). Observed heterozygosity (mean: 0.031) was 13.7 times lower than the expected heterozygosity (mean: 0.426). The deficit of heterozygous individuals is consistent with P. hallii having a high rate of self-fertilization. These markers will be useful for studies in P. hallii and related species.

Observation of Prethermalization in Long-Range Interacting Spin Chains (Open Access, Author’s Manuscript)

DTIC Science & Technology

2016-08-03

instance, quantum systems that are near-integrable usually fail to thermalize in an experimentally realistic time scale and, instead, relax to quasi ...However, it is possible to observe quasi -stationary states, often called prethermal, that emerge within an experimentally accessible time scale. Previous...generalized Gibbs ensemble (GGE) [10–13]. Here we experimentally study the relaxation dynamics of a chain of up to 22 spins evolving under a long-range

Rare copy number alterations and copy-neutral loss of heterozygosity revealed in ameloblastomas by high-density whole-genome microarray analysis.

PubMed

Diniz, Marina Gonçalves; Duarte, Alessandra Pires; Villacis, Rolando A; Guimarães, Bruna V A; Duarte, Luiz Cláudio Pires; Rogatto, Sílvia R; Gomez, Ricardo Santiago; Gomes, Carolina Cavaliéri

2017-05-01

Ameloblastoma (unicystic, UA, or multicystic, MA) is a rare tumor associated with bone destruction and facial deformity. Its malignant counterpart is the ameloblastic carcinoma (AC). The BRAFV600E mutation is highly prevalent in all these tumors subtypes and cannot account for their different clinical behaviors. We assessed copy number alterations (CNAs) and copy-neutral loss of heterozygosity (cnLOH) in UA (n = 2), MA (n = 3), and AC (n = 1) using the CytoScan HD Array (Affymetrix) and the BRAFV600E status. RT-qPCR was applied in four selected genes (B4GALT1, BAG1, PKD1L2, and PPP2R5A) covered by rare alterations, also including three MA and four normal oral tissues. Fifty-seven CNAs and cnLOH were observed in the ameloblastomas and six CNAs in the AC. Seven of the CNAs were rare (six in UA and one in MA), four of them encompassing genes (gains of 7q11.21, 1q32.3, and 9p21.1 and loss of 16q23.2). We found positive correlation between rare CNA gene dosage and the expression of B4GALT1, BAG1, PKD1L2, and PPP2R5A. The AC and 1 UA were BRAF wild-type; however, this UA showed rare genomic alterations encompassing genes associated with RAF/MAPK activation. Ameloblastomas show rare CNAs and cnLOH, presenting a specific genomic profile with no overlapping of the rare alterations among UA, MA, and AC. These genomic changes might play a role in tumor evolution and in BRAFV600E-negative tumors. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lamour, Kurt H.; Mudge, Joann; Gobena, Daniel

2012-02-07

The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diversemore » isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30percent of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.« less

Preliminary Observations of Population Genetics and Relatedness of the Broadnose Sevengill Shark, Notorynchus cepedianus, in Two Northeast Pacific Estuaries

PubMed Central

Larson, Shawn; Farrer, Debbie; Lowry, Dayv; Ebert, David A.

2015-01-01

The broadnose sevengill shark, Notorynchus cepedianus, a common coastal species in the eastern North Pacific, was sampled during routine capture and tagging operations conducted from 2005–2012. One hundred and thirty three biopsy samples were taken during these research operations in Willapa Bay, Washington and in San Francisco Bay, California. Genotypic data from seven polymorphic microsatellites (derived from the related sixgill shark, Hexanchus griseus) were used to describe N. cepedianus genetic diversity, population structure and relatedness. Diversity within N. cepedianus was found to be low to moderate with an average observed heterozygosity of 0.41, expected heterozygosity of 0.53, and an average of 5.1 alleles per microsatellite locus. There was no evidence of a recent population bottleneck based on genetic data. Analyses of genetic differences between the two sampled estuaries suggest two distinct populations with some genetic mixing of sharks sampled during 2005–2006. Relatedness within sampled populations was high, with percent relatedness among sharks caught in the same area indicating 42.30% first-order relative relationships (full or half siblings). Estuary-specific familial relationships suggest that management of N. cepedianus on the U.S. West Coast should incorporate stock-specific management goals to conserve this ecologically important predator. PMID:26052706

Photonic orbital angular momentum in starlight. Further analysis of the 2011 Starfire Optical Range Observations

NASA Astrophysics Data System (ADS)

Oesch, Denis W.; Sanchez, Darryl J.

2014-07-01

Context. Each attempt by the Atmospheric Simulation and Adaptive-optics Laboratory Testbed (ASALT) research group to detect turbulence-induced photonic orbital angular momentum (POAM) has been successful, spanning laboratory, simulation and field experiments, with the possible exception of the 2011 Starfire Optical Range (SOR) astronomical observations, a search for POAM induced by astronomical sources. Aims: The purposes of this work are to discuss how POAM from astronomical turbulent assemblages of molecules or atoms (TAMA) would appear in observations and then to reanalyze the data from the 2011 SOR observations using a more refined technique as a demonstration of POAM in starlight. Methods: This work uses the method of projections used previously in analysis of terrestrial data. Results: Using the method of projections, the noise floor of the system was reevaluated and is found to be no greater than 1%. Reevaluation of the 2011 SOR observations reveals that a POAM signal is evident in all of the data. Conclusions: POAM signals have been found in every instance of extended propagation through turbulence conducted by the ASALT research group, including the 2011 SOR observations. POAM is an inevitable result of the propagation of optical waves through turbulence. We express our gratitude to the Air Force Office of Scientific Research for their support of this research.

Comparative Serum Fatty Acid Profiles of Captive and Free-Ranging Cheetahs (Acinonyx jubatus) in Namibia.

PubMed

Tordiffe, Adrian S W; Wachter, Bettina; Heinrich, Sonja K; Reyers, Fred; Mienie, Lodewyk J

2016-01-01

Cheetahs (Acinonyx jubatus) are highly specialised large felids, currently listed as vulnerable on the IUCN red data list. In captivity, they are known to suffer from a range of chronic non-infectious diseases. Although low heterozygosity and the stress of captivity have been suggested as possible causal factors, recent studies have started to focus on the contribution of potential dietary factors in the pathogenesis of these diseases. Fatty acids are an important component of the diet, not only providing a source of metabolisable energy, but serving other important functions in hormone production, cellular signalling as well as providing structural components in biological membranes. To develop a better understanding of lipid metabolism in cheetahs, we compared the total serum fatty acid profiles of 35 captive cheetahs to those of 43 free-ranging individuals in Namibia using gas chromatography-mass spectrometry. The unsaturated fatty acid concentrations differed most remarkably between the groups, with all of the polyunsaturated and monounsaturated fatty acids, except arachidonic acid and hypogeic acid, detected at significantly lower concentrations in the serum of the free-ranging animals. The influence of age and sex on the individual fatty acid concentrations was less notable. This study represents the first evaluation of the serum fatty acids of free-ranging cheetahs, providing critical information on the normal fatty acid profiles of free-living, healthy individuals of this species. The results raise several important questions about the potential impact of dietary fatty acid composition on the health of cheetahs in captivity.

Constaints on Lorentz symmetry violations using lunar laser ranging observations

NASA Astrophysics Data System (ADS)

Bourgoin, Adrien

2016-12-01

General Relativity (GR) and the standard model of particle physics provide a comprehensive description of the four interactions of nature. A quantum gravity theory is expected to merge these two pillars of modern physics. From unification theories, such a combination would lead to a breaking of fundamental symmetry appearing in both GR and the standard model of particle physics as the Lorentz symmetry. Lorentz symmetry violations in all fields of physics can be parametrized by an effective field theory framework called the standard-model extension (SME). Local Lorentz Invariance violations in the gravitational sector should impact the orbital motion of bodies inside the solar system, such as the Moon. Thus, the accurate lunar laser ranging (LLR) data can be analyzed in order to study precisely the lunar motion to look for irregularities. For this purpose, ELPN (Ephéméride Lunaire Parisienne Numérique), a new lunar ephemeris has been integrated in the SME framework. This new numerical solution of the lunar motion provides time series dated in temps dynamique barycentrique (TDB). Among that series, we mention the barycentric position and velocity of the Earth-Moon vector, the lunar libration angles, the time scale difference between the terrestrial time and TDB and partial derivatives integrated from variational equations. ELPN predictions have been used to analyzed LLR observations. In the GR framework, the residuals standard deviations has turned out to be the same order of magnitude compare to those of INPOP13b and DE430 ephemerides. In the framework of the minimal SME, LLR data analysis provided constraints on local Lorentz invariance violations. Spetial attention was paid to analyze uncertainties to provide the most realistic constraints. Therefore, in a first place, linear combinations of SME coefficients have been derived and fitted to LLR observations. In a second time, realistic uncertainties have been determined with a resampling method. LLR data

Systematic observations of long-range transport events and climatological backscatter profiles with the DWD ceilometer network

NASA Astrophysics Data System (ADS)

Mattis, Ina; Müller, Gerhard; Wagner, Frank; Hervo, Maxime

2015-04-01

The German Meteorological Service (DWD) operates a network of about 60 CHM15K-Nimbus ceilometers for cloud base height observations. Those very powerful ceilometers allow for the detection and characterization of aerosol layers. Raw data of all network ceilometers are transferred online to DWD's data analysis center at the Hohenpeißenberg Meteorological Observatory. There, the occurrence of aerosol layers from long-range transport events in the free troposphere is systematically monitored on daily basis for each single station. If possible, the origin of the aerosol layers is determined manually from the analysis of the meteorological situation and model output. We use backward trajectories as well as the output of the MACC and DREAM models for the decision, whether the observed layer originated in the Sahara region, from forest fires in North America or from another, unknown source. Further, the magnitude of the observed layers is qualitatively estimated taking into account the geometrical layer depth, signal intensity, model output and nearby sun photometer or lidar observations (where available). All observed layers are attributed to one of the categories 'faint', 'weak', 'medium', 'strong', or 'extreme'. We started this kind of analysis in August 2013 and plan to continue this systematic documentation of long-range transport events of aerosol layers to Germany on long-term base in the framework of our GAW activities. Most of the observed aerosol layers have been advected from the Sahara region to Germany. In the 15 months between August 2013 and November 2014 we observed on average 46 days with Sahara dust layers per station, but only 16 days with aerosol layers from forest fires. The occurrence of Sahara dust layers vary with latitude. We observed only 28 dusty days in the north, close to the coasts of North Sea and Baltic Sea. In contrast, in southern Germany, in Bavarian Pre-Alps and in the Black Forest mountains, we observed up to 59 days with dust. At

HLA-B27 homozygosity has no influence on radiographic damage in ankylosing spondylitis: Observation Study of Korean spondyloArthropathy Registry (OSKAR) data.

PubMed

Kim, Tae-Jong; Sung, Il-Hoon; Lee, Seunghun; Joo, Kyung Bin; Choi, Jung Hyun; Park, Dong-Jin; Park, Yong-Wook; Lee, Shin-Seok; Kim, Tae-Hwan

2013-10-01

To evaluate the influence of homozygosity for HLA-B27 on the radiographic damage in ankylosing spondylitis (AS). A total of 368 AS patients with positive HLA-B27 status from the Observation Study of Korean spondyloArthropathy Registry (OSKAR) cohort were recruited for this study. HLA-B27 positive patients out of all AS patients were assessed for whether they had homozygosity or heterozygosity for HLA-B27. First, all data were stratified in relation to the carrier state of positive HLA-B27 for cross-sectional survey. Then we compared the radiographic damage score between groups. Second, we evaluated collected clinical and radiographic parameters at two different time points. Then we compared radiographic progression between groups. To use the mSASSS, cervical and lumbar spinal radiographs were examined by two experienced bone and joint radiologists (S. Lee, K.B. Joo). The agreement between the two readers regarding mSASSS was very good: ICC coefficient 0.70 (95% CI 0.60-0.81). The mean age (SD) of the AS patients was 37.0 (9.2) years, and the mean disease duration (SD) was 15.6 (9.1) years. Of these patients, 34.5% (127 patients) had HLA-B27 homozygosity. The mean mSASSS unit (SEM) was not significantly different between groups (homozygosity 28.57±4.12 vs heterozygosity 23.34±3.44, P=0.344) on cross-sectional survey. When it comes to radiographic progression between groups over 5 years, there was no significant difference in spite of adjusting for confounding variable (homozygosity 4.98±0.98 vs heterozygosity 4.21±0.82, P=0.562). The carrier state of positive HLA-B27 plays no role in determining the radiographic progression in AS. Copyright © 2013 Société française de rhumatologie. Published by Elsevier SAS. All rights reserved.

Observation of prethermalization in long-range interacting spin chains

PubMed Central

Neyenhuis, Brian; Zhang, Jiehang; Hess, Paul W.; Smith, Jacob; Lee, Aaron C.; Richerme, Phil; Gong, Zhe-Xuan; Gorshkov, Alexey V.; Monroe, Christopher

2017-01-01

Although statistical mechanics describes thermal equilibrium states, these states may or may not emerge dynamically for a subsystem of an isolated quantum many-body system. For instance, quantum systems that are near-integrable usually fail to thermalize in an experimentally realistic time scale, and instead relax to quasi-stationary prethermal states that can be described by statistical mechanics, when approximately conserved quantities are included in a generalized Gibbs ensemble (GGE). We experimentally study the relaxation dynamics of a chain of up to 22 spins evolving under a long-range transverse-field Ising Hamiltonian following a sudden quench. For sufficiently long-range interactions, the system relaxes to a new type of prethermal state that retains a strong memory of the initial conditions. However, the prethermal state in this case cannot be described by a standard GGE; it rather arises from an emergent double-well potential felt by the spin excitations. This result shows that prethermalization occurs in a broader context than previously thought, and reveals new challenges for a generic understanding of the thermalization of quantum systems, particularly in the presence of long-range interactions. PMID:28875166

Pancreatic Agenesis due to Compound Heterozygosity for a Novel Enhancer and Truncating Mutation in the PTF1A Gene.

PubMed

Gabbay, Monica; Ellard, Sian; De Franco, Elisa; Moisés, Regina S

2017-09-01

Neonatal diabetes, defined as the onset of diabetes within the first six months of life, is very rarely caused by pancreatic agenesis. Homozygous truncating mutations in the PTF1A gene, which encodes a transcriptional factor, have been reported in patients with pancreatic and cerebellar agenesis, whilst mutations located in a distal pancreatic-specific enhancer cause isolated pancreatic agenesis. We report an infant, born to healthy non-consanguineous parents, with neonatal diabetes due to pancreatic agenesis. Initial genetic investigation included sequencing of KCNJ11, ABCC8 and INS genes, but no mutations were found. Following this, 22 neonatal diabetes associated genes were analyzed by a next generation sequencing assay. We found compound heterozygous mutations in the PTF1A gene: A frameshift mutation in exon 1 (c.437_462 del, p.Ala146Glyfs*116) and a mutation affecting a highly conserved nucleotide within the distal pancreatic enhancer (g.23508442A>G). Both mutations were confirmed by Sanger sequencing. Isolated pancreatic agenesis resulting from compound heterozygosity for truncating and enhancer mutations in the PTF1A gene has not been previously reported. This report broadens the spectrum of mutations causing pancreatic agenesis.

Pancreatic Agenesis due to Compound Heterozygosity for a Novel Enhancer and Truncating Mutation in the PTF1A Gene

PubMed Central

Gabbay, Monica; Ellard, Sian; De Franco, Elisa; Moisés, Regina S.

2017-01-01

Neonatal diabetes, defined as the onset of diabetes within the first six months of life, is very rarely caused by pancreatic agenesis. Homozygous truncating mutations in the PTF1A gene, which encodes a transcriptional factor, have been reported in patients with pancreatic and cerebellar agenesis, whilst mutations located in a distal pancreatic-specific enhancer cause isolated pancreatic agenesis. We report an infant, born to healthy non-consanguineous parents, with neonatal diabetes due to pancreatic agenesis. Initial genetic investigation included sequencing of KCNJ11, ABCC8 and INS genes, but no mutations were found. Following this, 22 neonatal diabetes associated genes were analyzed by a next generation sequencing assay. We found compound heterozygous mutations in the PTF1A gene: A frameshift mutation in exon 1 (c.437_462 del, p.Ala146Glyfs*116) and a mutation affecting a highly conserved nucleotide within the distal pancreatic enhancer (g.23508442A>G). Both mutations were confirmed by Sanger sequencing. Isolated pancreatic agenesis resulting from compound heterozygosity for truncating and enhancer mutations in the PTF1A gene has not been previously reported. This report broadens the spectrum of mutations causing pancreatic agenesis. PMID:28663161

Boundaries on Range-Range Constrained Admissible Regions for Optical Space Surveillance

NASA Astrophysics Data System (ADS)

Gaebler, J. A.; Axelrad, P.; Schumacher, P. W., Jr.

We propose a new type of admissible-region analysis for track initiation in multi-satellite problems when apparent angles measured at known stations are the only observable. The goal is to create an efficient and parallelizable algorithm for computing initial candidate orbits for a large number of new targets. It takes at least three angles-only observations to establish an orbit by traditional means. Thus one is faced with a problem that requires N-choose-3 sets of calculations to test every possible combination of the N observations. An alternative approach is to reduce the number of combinations by making hypotheses of the range to a target along the observed line-of-sight. If realistic bounds on the range are imposed, consistent with a given partition of the space of orbital elements, a pair of range possibilities can be evaluated via Lambert’s method to find candidate orbits for that that partition, which then requires Nchoose- 2 times M-choose-2 combinations, where M is the average number of range hypotheses per observation. The contribution of this work is a set of constraints that establish bounds on the range-range hypothesis region for a given element-space partition, thereby minimizing M. Two effective constraints were identified, which together, constrain the hypothesis region in range-range space to nearly that of the true admissible region based on an orbital partition. The first constraint is based on the geometry of the vacant orbital focus. The second constraint is based on time-of-flight and Lagrange’s form of Kepler’s equation. A complete and efficient parallelization of the problem is possible on this approach because the element partitions can be arbitrary and can be handled independently of each other.

Observations of Inland Snowpack-driven Bromine Chemistry near the Brooks Range, Alaska

NASA Astrophysics Data System (ADS)

Peterson, P.; Pöhler, D.; Sihler, H.; Zielcke, J.; S., General; Friess, U.; Platt, U.; Simpson, W. R.; Nghiem, S. V.; Shepson, P. B.; Stirm, B. H.; Pratt, K.

2017-12-01

The snowpack produces high amounts of reactive bromine in the polar regions during spring. The resulting atmospheric bromine chemistry depletes boundary layer ozone to near-zero levels and alters oxidation of atmospheric pollutants, particularly elemental mercury. To improve our understanding of the spatial extent of this bromine chemistry in Arctic coastal regions, the Purdue Airborne Laboratory for Atmospheric Research (ALAR), equipped with the Heidelberg Imaging differential optical absorption spectroscopy (DOAS) instrument, measured the spatial distribution of BrO, an indicator of active bromine chemistry, over northern Alaska during the March 2012 BRomine Ozone Mercury Experiment (BROMEX). Here we show that this bromine chemistry, commonly associated with snow-covered sea ice regions in the Arctic Ocean, is active 200 km inland in the foothills of the Brooks Range. Profiles retrieved from limb-viewing measurements show this event was located near the snowpack surface, with measured BrO mole ratios of 20 pmol mol-1 in a 500 m thick layer. This observed bromine chemistry is likely enabled by deposition of transported sea salt aerosol or gas phase bromine species from prior activation events to the snowpack. These observations of halogen activation hundreds of km from the coast suggest the impacts of this springtime bromine chemistry are not restricted to sea ice regions and directly adjacent coastal regions.

Rates of loss of heterozygosity and mitotic recombination in NF2 schwannomas, sporadic vestibular schwannomas and schwannomatosis schwannomas.

PubMed

Hadfield, K D; Smith, M J; Urquhart, J E; Wallace, A J; Bowers, N L; King, A T; Rutherford, S A; Trump, D; Newman, W G; Evans, D G

2010-11-25

Biallelic inactivation of the NF2 gene occurs in the majority of schwannomas. This usually involves a combination of a point mutation or multiexon deletion, in conjunction with either a second point mutation or loss of heterozygosity (LOH). We have performed DNA sequence and dosage analysis of the NF2 gene in a panel of 239 schwannoma tumours: 97 neurofibromatosis type 2 (NF2)-related schwannomas, 104 sporadic vestibular schwannomas (VS) and 38 schwannomatosis-related schwannomas. In total, we identified germline NF2 mutations in 86 out of 97 (89%) NF2 patients and a second mutational event in 77 out of 97 (79%). LOH was by far the most common form of second hit. A combination of microsatellite analysis with either conventional comparative genomic hybridization (CGH) or multiplex ligation-dependent probe amplification (MLPA) identified mitotic recombination (MR) as the cause of LOH in 14 out of 72 (19%) total evaluable tumours. Among sporadic VS, at least one NF2 mutation was identified by sequence analysis or MLPA in 65 out of 98 (66%) tumours. LOH occurred in 54 out of 96 (56%) evaluable tumours, but MR only accounted for 5 out of 77 (6%) tested. LOH was present in 28 out of 34 (82%) schwannomatosis-related schwannomas. In all eight patients who had previously tested positive for a germline SMARCB1 mutation, this involved loss of the whole, or part of the long arm, of chromosome 22. In contrast, 5 out of 22 (23%) tumours from patients with no germline SMARCB1 mutation exhibited MR. High-resolution Affymetrix SNP6 genotyping and copy number (CN) analysis (Affymetrix, Santa Clara, CA, USA) were used to determine the chromosomal breakpoint locations in tumours with MR. A range of unique recombination sites, spanning approximately 11.4 Mb, were identified. This study shows that MR is a mechanism of LOH in NF2 and SMARCB1-negative schwannomatosis-related schwannomas, occurring less frequently in sporadic VS. We found no evidence of MR in SMARCB1-positive

Compound Heterozygosity for Null Mutations and a Common Hypomorphic Risk Haplotype in TBX6 Causes Congenital Scoliosis.

PubMed

Takeda, Kazuki; Kou, Ikuyo; Kawakami, Noriaki; Iida, Aritoshi; Nakajima, Masahiro; Ogura, Yoji; Imagawa, Eri; Miyake, Noriko; Matsumoto, Naomichi; Yasuhiko, Yukuto; Sudo, Hideki; Kotani, Toshiaki; Nakamura, Masaya; Matsumoto, Morio; Watanabe, Kota; Ikegawa, Shiro

2017-03-01

Congenital scoliosis (CS) occurs as a result of vertebral malformations and has an incidence of 0.5-1/1,000 births. Recently, TBX6 on chromosome 16p11.2 was reported as a disease gene for CS; about 10% of Chinese CS patients were compound heterozygotes for rare null mutations and a common haplotype defined by three SNPs in TBX6. All patients had hemivertebrae. We recruited 94 Japanese CS patients, investigated the TBX6 locus for both mutations and the risk haplotype, examined transcriptional activities of mutant TBX6 in vitro, and evaluated clinical and radiographic features. We identified TBX6 null mutations in nine patients, including a missense mutation that had a loss of function in vitro. All had the risk haplotype in the opposite allele. One of the mutations showed dominant negative effect. Although all Chinese patients had one or more hemivertebrae, two Japanese patients did not have hemivertebra. The compound heterozygosity of null mutations and the common risk haplotype in TBX6 also causes CS in Japanese patients with similar incidence. Hemivertebra was not a specific type of spinal malformation in TBX6-associated CS (TACS). A heterozygous TBX6 loss-of-function mutation has been reported in a family with autosomal-dominant spondylocostal dysostosis, but it may represent a spectrum of the same disease with TACS. © 2017 WILEY PERIODICALS, INC.

Constraints on the Mass and Location of Planet 9 set by Range and VLBI Observations of Cassini

NASA Astrophysics Data System (ADS)

Jacobson, Robert Arthur; Folkner, William; Park, Ryan; Williams, James

2018-04-01

Batygin and Brown, 2016 AJ, found that Kuiper belt objects (KBOs) with well determined orbits having periods greater than 4000 years are apsidally aligned. They attribute this orbital clustering to the existence of a distant planet, Planet 9, well beyond Neptune, with a mass roughly ten times that of Earth. If such a planet exists, it would affect the motion of the known solar system planets, in particular Saturn, which is well observed with radiometric ranging from the Cassini spacecraft and VLBI observations of Cassini. The current planetary ephemerides do not account for the postulated Planet 9, yet their fit to the observational data shows no obvious effect that could be attributed to neglecting that planet. However, it is possible that the effect could be absorbed by the estimated parameters used to determine the ephemerides. Those parameters include the planetary orbital elements, mass of the Sun, and the masses of the asteroids that perturb the Martian orbit. We recently updated the Cassini data set and extended it through the end of the mssion in 2017 September. We analyze the sensitivity of these data to the tidal perturbations caused by the postulated Planet 9 for a range of positions on the sky and tidal parameters (the ratio of the mass of Planet 9 to the cube of its distance from Saturn). We determine an upper bound on the tidal parameter and the most probable directions consistent with the observational data.

Isolation and characterization of 50 nuclear microsatellite markers for Cathaya argyrophylla, a Chinese endemic conifer.

PubMed

Wang, Zhao-Shan; Sun, Hai-Qin; Wang, Hong-Wei; Ge, Song

2010-11-01

Microsatellite primers were developed for the endangered Cathaya argyrophylla (Pinaceae) to investigate its genetic diversity and population genetic structure, as well as its evolutionary history. • Fifty dinucleotide microsatellite loci were identified in two populations. The number of alleles per locus ranged from 1 to 6, with a mean of 2.84. The observed and expected heterozygosities ranged from 0 to 0.889 and from 0 to 0.779, respectively. • These markers will facilitate further studies on the population genetics and evolutionary history of Cathaya argyrophylla.

Development and characterization of polymorphic microsatellitemarkers for the crested caracara, Caracara cheriway

USGS Publications Warehouse

Vaughn, Erin E.; Dwyer, James F.; Morrison, Joan L.; Culver, Melanie

2015-01-01

We isolated novel microsatellites from the crested caracara (Caracara cheriway) with a shotgun pyrosequencing approach. We tested 80 loci for polymorphism among 20 individuals from the threatened Florida population. Fourteen loci were polymorphic. The mean number of alleles was 2.21 (range 2–3) and the mean observed heterozygosity was 0.41 (range 0.15–0.65). None of the 14 polymorphic loci exhibited significant linkage disequilibrium nor did they deviate significantly from Hardy–Weinberg expectations. We also report 16 monomorphic loci.

Development and characterization of 12 microsatellite markers for the Island Night Lizard (Xantusia riversiana), a threatened species endemic to the Channel Islands, California, USA

USGS Publications Warehouse

O'Donnell, Ryan P.; Drost, Charles A.; Mock, Karen E.

2014-01-01

The Island Night Lizard is a federally threatened species endemic to the Channel Islands of California. Twelve microsatellite loci were developed for use in this species and screened in 197 individuals from across San Nicolas Island, California. The number of alleles per locus ranged from 6 to 21. Observed heterozygosities ranged from 0.520 to 0.843. These microsatellite loci will be used to investigate population structure, effective population size, and gene flow across the island, to inform protection and management of this species.

Characterization of microsatellite loci from two-spotted octopus Octopus bimaculatus Verrill 1883 from pyrosequencing reads

USGS Publications Warehouse

Domínguez-Contreras, J. F.; Munguía-Vega, A.; Ceballos-Vázquez, B. P.; Arellano-Martínez, M.; Culver, Melanie

2014-01-01

We characterized 22 novel microsatellite loci in the two-spotted octopus Octopus bimaculatus using 454 pyrosequencing reads. All loci were polymorphic and will be used in studies of marine connectivity aimed at increasing sustainability of the resource. The mean number alleles per locus was 13.09 (range 7–19) and observed heterozygosities ranged from 0.50 to 1.00. Four loci pairs were linked and three deviated from Hardy–Weinberg equilibrium. Eighteen and 12 loci were polymorphic in Octopus bimaculoides and Octopus hubbsorum, respectively.

Genetic Variation of Beet Armyworm (Lepidoptera: Noctuidae) Populations Detected Using Microsatellite Markers in Iran.

PubMed

Golikhajeh, Neshat; Naseri, Bahram; Razmjou, Jabraeil; Hosseini, Reza; Aghbolaghi, Marzieh Asadi

2018-05-28

In order to understand the population genetic diversity and structure of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), a serious pest of sugar beet in Iran and the world, we genotyped 133 individuals from seven regions in Iran using four microsatellite loci. Significant difference was seen between the observed and expected heterozygosity in all loci. A lower observed heterozygosity than expected heterozygosity indicated a low heterozygosity in these populations. The value of F showed a high genetic differentiation, so that the mean of Fst was 0.21. Molecular analysis variance showed significant differences within and among populations with group variance accounted for 71 and 21%, respectively. No correlation was found between pair-wise Fst and geographic distance by Mantel test. Bayesian clustering analysis grouped all regions to two clusters. These data suggested that a combination of different factors, such as geographic distance, environmental condition, and physiological behavior in addition to genetic factors, could play an important role in forming variation within and between S. exigua populations.

Tumour TIF1 mutations and loss of heterozygosity related to cancer-associated myositis.

PubMed

Pinal-Fernandez, Iago; Ferrer-Fabregas, Berta; Trallero-Araguas, Ernesto; Balada, Eva; Martínez, Maria Angeles; Milisenda, Jose César; Aparicio-Español, Gloria; Labrador-Horrillo, Moises; Garcia-Patos, Vicente; Grau-Junyent, Josep M; Selva-O'Callaghan, Albert

2018-02-01

To analyse the influence of genetic alterations and differential expression of transcription intermediary factor 1 (TIF1) genes in the pathophysiology of cancer-associated myositis (CAM). Paired blood and tumour DNA samples from patients with anti-TIF1γ-positive CAM and from controls were analysed by whole-exome sequencing for the presence of somatic mutations and loss of heterozygosity (LOH) in their TIF1 genes. The genesis and maintenance of the autoimmune process were investigated immunohistochemically by studying TIF1γ expression in the different tissues involved in CAM (skin, muscle and tumour) based on the immunohistochemical H-score. From seven patients with anti-TIF1γ-positive CAM, we detected one somatic mutation and five cases of LOH in one or more of the four TIF1 genes compared with just one case of LOH in tumours from TIF1γ-negative myositis patients (86% vs 17%; P = 0.03). Compared with type-matched control tumours from non-myositis patients, TIF1γ staining was more intense in tumours from anti-TIF1γ-positive patients (H-score 255 vs 196; P = 0.01). Also, TIF1γ staining in muscle was slightly more intense in anti-TIF1γ-positive than in anti-TIF1γ-negative myositis (H-score 22 vs 5; P = 0.03). In contrast, intense TIF1γ staining was detected in the skin of both myositis and control patients. Tumours from paraneoplastic anti-TIF1γ-positive patients showed an increased number of genetic alterations, such as mutations and LOH, in TIF1 genes. These genetic alterations, in the context of a high expression of TIF1γ in the tumour, muscle and skin of these patients may be key to understanding the genesis of paraneoplastic myositis. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Loss of heterozygosity on chromosome 11p15.5 and relapse in hepatoblastomas.

PubMed

Chitragar, S; Iyer, V K; Agarwala, S; Gupta, S D; Sharma, A; Wari, M N

2011-01-01

IGF2 is a tumor suppressor gene at locus 11p15. Many hepatoblastomas have loss of heterozygosity (LOH) at this locus. Earlier studies have not demonstrated any association between LOH and prognosis. Aim of the study was to evaluate the prognostic significance of LOH at 11p15.5 in hepatoblastomas. DNA was isolated from normal liver and tumor tissue in 20 patients with hepatoblastoma. PCR was performed and cases were classified as LOH present, absent or non-informative. Patients' follow-up data was analyzed using Fischer's exact test and Kaplan-Meier survival analysis for relapse-free survival (RFS) in relation to LOH. Ethical clearance was obtained from the institutional ethics board. All cases were informative for at least one microsatellite marker used. 4 of the 20 cases (20%) had LOH at 11p15.5. One patient died in the immediate postoperative period. 5 of 19 patients relapsed (26%). Of 4 patients who had LOH, 3 (75%) relapsed, the time to relapse being 7, 7 and 9 months, respectively. Of the 15 cases without LOH, 2 (13.3%) relapsed. 4 patients had mixed epithelial and mesenchymal histology; 3 of them had LOH. The 2 groups with and without LOH were well matched. The RFS for patients with LOH (n=4) was 13% (mean survival time [MST]: 8.7 months; 95CI 6.7-10.7), while the RFS for cases without LOH (n=15) was 75% (MST: 100.7 months; 95CI 74.5-126.8). Mixed epithelial and mesenchymal histology is more frequently associated with LOH on chromosome 11p15.5 than pure epithelial histology. LOH on chromosome 11p15.5 is associated with a significantly increased incidence of relapse and a significantly shorter relapse-free survival in patients with hepatoblastoma. The risk of relapse is higher and the RFS lower both in standard-risk and high-risk patients with hepatoblastoma if they demonstrate the presence of LOH at 11p15.5. © Georg Thieme Verlag KG Stuttgart · New York.

Novel microsatellite development and characterization for Phacelia formosula (Hydrophyllaceae).

PubMed

Riser, James P; Schwabe, Anna L; Neale, Jennifer Ramp

2017-07-01

Microsatellite primers were developed to characterize genetic diversity and structuring in the genus Phacelia (Hydrophyllaceae) and to further conservation efforts for P. formosula . Fifteen novel microsatellite primers were developed for P. formosula . These were characterized for genetic variation in three separate P. formosula populations. Two to nine alleles were found per locus. Overall observed heterozygosity and expected heterozygosity ranged from 0.000 to 0.800 and 0.000 to 0.840, respectively. Additionally, these loci were successfully amplified and showed polymorphism in P. gina-glenneae and a potential new Phacelia species. These microsatellite markers will be useful in assessing genetic diversity, structuring, and gene flow within and among populations of the rare P. formosula , in addition to related Phacelia species. These markers will provide important genetic data needed for appropriate conservation and management of these rare plants.

Genetic diversity of Brazilian natural populations of Anthonomus grandis Boheman (Coleoptera: Curculionidae), the major cotton pest in the New World.

PubMed

Martins, W F S; Ayres, C F J; Lucena, W A

2007-01-27

Twenty-five RAPD loci and 6 isozyme loci were studied to characterize the genetic variability of natural populations of Anthonomus grandis from two agroecosystems of Brazil. The random-amplified polymorphic DNA data disclosed a polymorphism that varied from 52 to 84% and a heterozygosity of 0.189 to 0.347. The index of genetic differentiation (GST) among the six populations was 0.258. The analysis of isozymes showed a polymorphism and a heterozygosity ranging from 25 to 100% and 0.174 to 0.277, respectively. The genetic differentiation (FST) among the populations obtained by isozyme data was 0.544. It was possible to observe rare alleles in the populations from the Northeast region. The markers examined allowed us to distinguish populations from large-scale, intensive farming region (cotton belts) versus populations from areas of small-scale farming

Development and characterization of EST-SSR markers for Artocarpus hypargyreus (Moraceae).

PubMed

Liu, Haijun; Tan, Weizheng; Sun, Hongbin; Liu, Yu; Meng, Kaikai; Liao, Wenbo

2016-12-01

Polymorphic microsatellite markers were developed for Artocarpus hypargyreus (Moraceae), a threatened species endemic to China, to investigate the genetic diversity and structure of the species. Based on the transcriptome data of A. hypargyreus , 63 primer pairs were preliminarily designed and tested, of which 34 were successfully amplified and 10 displayed clear polymorphisms across the 67 individuals from four populations of A. hypargyreus . The results showed the number of alleles per locus ranged from three to 10, and the observed heterozygosity and expected heterozygosity per locus varied from 0.000 to 0.706 and from 0.328 to 0.807, respectively. These microsatellite markers will be useful in exploring genetic diversity and structure of A. hypargyreus . Furthermore, most loci were successfully cross-amplified in A. nitidus and A. heterophyllus , indicating that they will be of great value for genetic study across this genus.

Assessment of the accuracy of global geodetic satellite laser ranging observations and estimated impact on ITRF scale: estimation of systematic errors in LAGEOS observations 1993-2014

NASA Astrophysics Data System (ADS)

Appleby, Graham; Rodríguez, José; Altamimi, Zuheir

2016-12-01

Satellite laser ranging (SLR) to the geodetic satellites LAGEOS and LAGEOS-2 uniquely determines the origin of the terrestrial reference frame and, jointly with very long baseline interferometry, its scale. Given such a fundamental role in satellite geodesy, it is crucial that any systematic errors in either technique are at an absolute minimum as efforts continue to realise the reference frame at millimetre levels of accuracy to meet the present and future science requirements. Here, we examine the intrinsic accuracy of SLR measurements made by tracking stations of the International Laser Ranging Service using normal point observations of the two LAGEOS satellites in the period 1993 to 2014. The approach we investigate in this paper is to compute weekly reference frame solutions solving for satellite initial state vectors, station coordinates and daily Earth orientation parameters, estimating along with these weekly average range errors for each and every one of the observing stations. Potential issues in any of the large number of SLR stations assumed to have been free of error in previous realisations of the ITRF may have been absorbed in the reference frame, primarily in station height. Likewise, systematic range errors estimated against a fixed frame that may itself suffer from accuracy issues will absorb network-wide problems into station-specific results. Our results suggest that in the past two decades, the scale of the ITRF derived from the SLR technique has been close to 0.7 ppb too small, due to systematic errors either or both in the range measurements and their treatment. We discuss these results in the context of preparations for ITRF2014 and additionally consider the impact of this work on the currently adopted value of the geocentric gravitational constant, GM.

Northwest Basin and Range tectonic deformation observed with the Global Positioning System, 1999-2003

USGS Publications Warehouse

Hammond, W.C.; Thatcher, W.

2005-01-01

We use geodetic velocities obtained with the Global Positioning System (GPS) to quantify tectonic deformation of the northwest Basin and Range province of the western United States. The results are based on GPS data collected in 1999 and 2003 across five new quasi-linear networks in northern Nevada, northeast California, and southeast Oregon. The velocities show ???3 mm/yr westward movement of northern Nevada with respect to stable North America. West of longitude 119??W the velocities increase and turn northwest, parallel to Sierra Nevada/Great Valley microplate motion, and similar to velocities previously obtained to the south. The observations are explained by a kinematic model with three domains that rotate around Euler poles in eastern Oregon and western Idaho. Northeast California experiences internal dextral shear deformation (11.2 ?? 3.6 nstrain/yr) subparallel to Pacific/North America motion. Relative motions of the domains imply 2-5 mm/yr approximately east-west extension in northwest Nevada and 1-4 mm/yr approximately north-south contraction near the California/Oregon border. The northward decreasing approximately east-west extension in northwest Nevada is consistent with the northern termination of Basin and Range deformation, faulting and characteristic topography. No significant extension is detected in the Oregon Basin and Range. The Oregon Cascade arc moves north at ???3.5 mm/yr and is possibly influenced by the approximately eastward motion of the Juan de Fuca plate. These results disagree with secular northwest trenchward motion of the Oregon forearc inferred from paleomagnetic rotations. South of latitude 43??, however, trenchward motion exists and is consistent with block rotations, approximately east-west Basin and Range extension, and northwest Sierra Nevada translation. Copyright 2005 by the American Geophysical Union.

Autotetraploids of Vicia cracca show a higher allelic richness in natural populations and a higher seed set after artificial selfing than diploids

PubMed Central

Eliášová, Anežka; Trávníček, Pavel; Mandák, Bohumil; Münzbergová, Zuzana

2014-01-01

Background and Aims Despite the great importance of autopolyploidy in the evolution of angiosperms, relatively little attention has been devoted to autopolyploids in natural polyploid systems. Several hypotheses have been proposed to explain why autopolyploids are so common and successful, for example increased genetic diversity and heterozygosity and the transition towards selfing. However, case studies on patterns of genetic diversity and on mating systems in autopolyploids are scarce. In this study allozymes were employed to investigate the origin, population genetic diversity and mating system in the contact zone between diploid and assumed autotetraploid cytotypes of Vicia cracca in Central Europe. Methods Four enzyme systems resolved in six putative loci were investigated in ten diploid, ten tetraploid and five mixed-ploidy populations. Genetic diversity and heterozygosity, partitioning of genetic diversity among populations and cytotypes, spatial genetic structure and fixed heterozygosity were analysed. These studies were supplemented by a pollination experiment and meiotic chromosome observation. Key Results and Conclusions Weak evidence of fixed heterozygosity, a low proportion of unique alleles and genetic variation between cytotypes similar to the variation among populations within cytotypes supported the autopolyploid origin of tetraploids, although no multivalent formation was observed. Tetraploids possessed more alleles than diploids and showed higher observed zygotic heterozygosity than diploids, but the observed gametic heterozygosity was similar to the value observed in diploids and smaller than expected under panmixis. Values of the inbreeding coefficient and differentiation among populations (ρST) suggested that the breeding system in both cytotypes of V. cracca is mixed mating with prevailing outcrossing. The reduction in seed production of tetraploids after selfing was less than that in diploids. An absence of correlation between genetic and

Isolation and characterization of 10 microsatellite loci in Callicarpa subpubescens (Verbenaceae), an endemic species of the Bonin Islands.

PubMed

Mori, K; Kaneko, S; Isagi, Y; Murakami, N; Kato, H

2008-11-01

Ten microsatellite loci were isolated and characterized for Callicarpa subpubescens (Verbenaceae), an endemic tree species of the Bonin Islands. The observed number of alleles at each locus ranged from two to eight with an average of 4.9, and the expected heterozygosity ranged from 0.238 to 0.690 with an average of 0.483. All 10 loci were screened in cross-amplification tests for two other endemic Callicarpa species that also inhabit the Bonin Islands. All loci were successfully amplified in these species. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Characterization of 13 microsatellite loci for the deep-sea coral, Lophelia pertusa (Linnaeus 1758), from the western North Atlantic Ocean and Gulf of Mexico

USGS Publications Warehouse

Morrison, C.L.; Eackles, M.S.; Johnson, Robin L.; King, T.L.

2008-01-01

A suite of 13 polymorphic tri- and tetranucleotide microsatellite loci were isolated from the ahermatypic deep-sea coral, Lophelia pertusa. Among 51 individuals collected from three disjunct oceanic regions, allelic diversity ranged from six to 38 alleles and averaged 9.1 alleles per locus. Observed heterozygosity ranged from 9.1 to 96.8% and averaged 62.3% in the Gulf of Mexico population. For some loci, amplification success varied among collections, suggesting regional variation in priming site sequences. Four loci showed departures from Hardy–Weinberg equilibrium in certain collections which may reflect nonrandom mating.

Characterization of polymorphic microsatellites for Tripterygium (Celastraceae), a monospecific genus of medicinal importance.

PubMed

Novy, Ari; Jones, Kenneth C

2011-10-01

Microsatellite markers were developed for the medicinal plant Tripterygium (Celastraceae) to assess its population structure and to facilitate source tracking of plant materials used for medicinal extracts. Ten microsatellite markers were isolated and characterized in T. wilfordii using an enriched genomic library. The number of alleles per locus ranged from five to 12. Observed and expected heterozygosity ranged from 0.166 to 0.630 and 0.392 to 0.562, respectively. These markers will be useful for a variety of applications including source tracking of plant materials, resolution of taxonomic issues, and population genetics studies.

Microsatellite primers for the endangered aquatic herb, Ottelia acuminata (Hydrocharitaceae).

PubMed

Xu, Chao; Du, Zhi-Yuan; Chen, Jin-Ming; Wang, Qing-Feng

2012-06-01

Microsatellite primers were developed in the endangered aquatic herb, Ottelia acuminata, to characterize its genetic diversity and understand its population structure. Eight polymorphic microsatellite markers were developed from two populations of O. acuminata in China. The number of alleles per locus ranged from one to 15; the observed and expected heterozygosities ranged from 0 to 0.885 and from 0 to 0.888, respectively, in the two populations. Selected loci also amplified successfully in O. sinensis. These microsatellite markers will facilitate further studies on the conservation genetics and evolutionary history of O. acuminata.

Emulsion chamber observations of primary cosmic-ray electrons in the energy range 30-1000 GeV

NASA Technical Reports Server (NTRS)

Nishimura, J.; Fujii, M.; Taira, T.; Aizu, E.; Hiraiwa, H.; Kobayashi, T.; Niu, K.; Ohta, I.; Golden, R. L.; Koss, T. A.

1980-01-01

The results of a series of emulsion exposures, beginning in Japan in 1968 and continued in the U.S. since 1975, which have yielded a total balloon-altitude exposure of 98,700 sq m sr s, are presented. The data are discussed in terms of several models of cosmic-ray propagation. Interpreted in terms of the energy-dependent leaky-box model, the spectrum results suggest a galactic electron residence time of 1.0(+2.0, -0.5) x 10 to the 7th yr, which is consistent with results from Be-10 observations. Finally, the possibility that departures from smooth power law behavior in the spectrum due to individual nearby sources will be observable in the energy range above 1 TeV is discussed.

Comparative Serum Fatty Acid Profiles of Captive and Free-Ranging Cheetahs (Acinonyx jubatus) in Namibia

PubMed Central

Wachter, Bettina; Heinrich, Sonja K.; Reyers, Fred; Mienie, Lodewyk J.

2016-01-01

Cheetahs (Acinonyx jubatus) are highly specialised large felids, currently listed as vulnerable on the IUCN red data list. In captivity, they are known to suffer from a range of chronic non-infectious diseases. Although low heterozygosity and the stress of captivity have been suggested as possible causal factors, recent studies have started to focus on the contribution of potential dietary factors in the pathogenesis of these diseases. Fatty acids are an important component of the diet, not only providing a source of metabolisable energy, but serving other important functions in hormone production, cellular signalling as well as providing structural components in biological membranes. To develop a better understanding of lipid metabolism in cheetahs, we compared the total serum fatty acid profiles of 35 captive cheetahs to those of 43 free-ranging individuals in Namibia using gas chromatography-mass spectrometry. The unsaturated fatty acid concentrations differed most remarkably between the groups, with all of the polyunsaturated and monounsaturated fatty acids, except arachidonic acid and hypogeic acid, detected at significantly lower concentrations in the serum of the free-ranging animals. The influence of age and sex on the individual fatty acid concentrations was less notable. This study represents the first evaluation of the serum fatty acids of free-ranging cheetahs, providing critical information on the normal fatty acid profiles of free-living, healthy individuals of this species. The results raise several important questions about the potential impact of dietary fatty acid composition on the health of cheetahs in captivity. PMID:27992457

Quasiperiodic modulations of energetic electron fluxes in the ULF range observed by the ERG satellite

NASA Astrophysics Data System (ADS)

Teramoto, M.; Hori, T.; Kurita, S.; Yoshizumi, M.; Saito, S.; Higashio, N.; Mitani, T.; Matsuoka, A.; Park, I.; Takashima, T.; Nomura, R.; Nose, M.; Fujimoto, A.; Tanaka, Y.; Shinohara, M.; Shinohara, I.

2017-12-01

Exploration of energization and Radiation in Geospace (ERG) satellite was successfully launched on December 20, 2016. The Extremely High-Energy Electron Experiment (XEP) and High-Energy Electron Experiments (HEP-L and HEP-H) are carried by the ERG satellite to observe energetic electrons. These instruments frequently observed quasiperiodic modulations of energetic electron fluxes with period of 100-600 sec. Continuous flux modulations with the period of 600 s appeared in the 700keV-3.6MeV energy range during the period 0920UT-1120UT on March 31, 2017 when the ERG satellite was located at L 5.5-6.1 and MLT 3-4 h. We compare these flux modulations with the magnetic field observed by the Magnetic Field Experiment (MGF) on the ERG satellite. It is found that these flux modulations are not accompanied by corresponding magnetic signatures. It indicates that these quasiperiodic flux modulations are not caused by drift-resonant interactions between ULF waves and energetic electrons, at least locally. In this study, we will show several events and discuss possible mechanism for quasiperiodic flux modulations of energetic electrons on XEP and HEP.

Single Nucleotide Polymorphism (SNP)-Based Loss of Heterozygosity (LOH) Testing by Real Time PCR in Patients Suspect of Myeloproliferative Disease

PubMed Central

Huijsmans, Cornelis J. J.; Poodt, Jeroen; Damen, Jan; van der Linden, Johannes C.; Savelkoul, Paul H. M.; Pruijt, Johannes F. M.; Hilbink, Mirrian; Hermans, Mirjam H. A.

2012-01-01

During tumor development, loss of heterozygosity (LOH) often occurs. When LOH is preceded by an oncogene activating mutation, the mutant allele may be further potentiated if the wild-type allele is lost or inactivated. In myeloproliferative neoplasms (MPN) somatic acquisition of JAK2V617F may be followed by LOH resulting in loss of the wild type allele. The occurrence of LOH in MPN and other proliferative diseases may lead to a further potentiating the mutant allele and thereby increasing morbidity. A real time PCR based SNP profiling assay was developed and validated for LOH detection of the JAK2 region (JAK2LOH). Blood of a cohort of 12 JAK2V617F-positive patients (n = 6 25–50% and n = 6>50% JAK2V617F) and a cohort of 81 patients suspected of MPN was stored with EDTA and subsequently used for validation. To generate germ-line profiles, non-neoplastic formalin-fixed paraffin-embedded tissue from each patient was analyzed. Results of the SNP assay were compared to those of an established Short Tandem Repeat (STR) assay. Both assays revealed JAK2LOH in 1/6 patients with 25–50% JAK2V617F. In patients with >50% JAK2V617F, JAK2LOH was detected in 6/6 by the SNP assay and 5/6 patients by the STR assay. Of the 81 patients suspected of MPN, 18 patients carried JAK2V617F. Both the SNP and STR assay demonstrated the occurrence of JAK2LOH in 5 of them. In the 63 JAK2V617F-negative patients, no JAK2LOH was observed by SNP and STR analyses. The presented SNP assay reliably detects JAK2LOH and is a fast and easy to perform alternative for STR analyses. We therefore anticipate the SNP approach as a proof of principle for the development of LOH SNP-assays for other clinically relevant LOH loci. PMID:22768290

Isolation and characterization of microsatellite loci in the whale shark (Rhincodon typus)

USGS Publications Warehouse

Ramirez-Macias, D.; Shaw, K.; Ward, R.; Galvan-Magana, F.; Vazquez-Juarez, R.

2009-01-01

In preparation for a study on population structure of the whale shark (Rhincodon typus), nine species-specific polymorphic microsatellite DNA markers were developed. An initial screening of 50 individuals from Holbox Island, Mexico found all nine loci to be polymorphic, with two to 17 alleles observed per locus. Observed and expected heterozygosity per locus ranged from 0.200 to 0.826 and from 0.213 to 0.857, respectively. Neither statistically significant deviations from Hardy–Weinberg expectations nor statistically significant linkage disequilibrium between loci were observed. These microsatellite loci appear suitable for examining population structure, kinship assessment and other applications.

THROES: a caTalogue of HeRschel Observations of Evolved Stars. I. PACS range spectroscopy

NASA Astrophysics Data System (ADS)

Ramos-Medina, J.; Sánchez Contreras, C.; García-Lario, P.; Rodrigo, C.; da Silva Santos, J.; Solano, E.

2018-03-01

This is the first of a series of papers presenting the THROES (A caTalogue of HeRschel Observations of Evolved Stars) project, intended to provide a comprehensive overview of the spectroscopic results obtained in the far-infrared (55-670 μm) with the Herschel space observatory on low-to-intermediate mass evolved stars in our Galaxy. Here we introduce the catalogue of interactively reprocessed Photoconductor Array Camera and Spectrometer (PACS) spectra covering the 55-200 μm range for 114 stars in this category for which PACS range spectroscopic data is available in the Herschel Science Archive (HSA). Our sample includes objects spanning a range of evolutionary stages, from the asymptotic giant branch to the planetary nebula phase, displaying a wide variety of chemical and physical properties. The THROES/PACS catalogue is accessible via a dedicated web-based interface and includes not only the science-ready Herschel spectroscopic data for each source, but also complementary photometric and spectroscopic data from other infrared observatories, namely IRAS, ISO, or AKARI, at overlapping wavelengths. Our goal is to create a legacy-value Herschel dataset that can be used by the scientific community in the future to deepen our knowledge and understanding of these latest stages of the evolution of low-to-intermediate mass stars. The THROES/PACS catalogue is accessible at http://https://throes.cab.inta-csic.es/

Critical configurations (determinantal loci) for range and range difference satellite networks

NASA Technical Reports Server (NTRS)

Tsimis, E.

1973-01-01

The observational modes of Geometric Satellite Geodesy are discussed. The geometrical analysis of the problem yielded a regression model for the adjustment of the observations along with a suitable and convenient metric for the least-squares criterion. The determinantal loci (critical configurations) for range networks are analyzed. An attempt is made to apply elements of the theory of variants for this purpose. The use of continuously measured range differences for loci determination is proposed.

Novel microsatellite development and characterization for Phacelia formosula (Hydrophyllaceae)1

PubMed Central

Schwabe, Anna L.; Neale, Jennifer Ramp

2017-01-01

Premise of the study: Microsatellite primers were developed to characterize genetic diversity and structuring in the genus Phacelia (Hydrophyllaceae) and to further conservation efforts for P. formosula. Methods and Results: Fifteen novel microsatellite primers were developed for P. formosula. These were characterized for genetic variation in three separate P. formosula populations. Two to nine alleles were found per locus. Overall observed heterozygosity and expected heterozygosity ranged from 0.000 to 0.800 and 0.000 to 0.840, respectively. Additionally, these loci were successfully amplified and showed polymorphism in P. gina-glenneae and a potential new Phacelia species. Conclusions: These microsatellite markers will be useful in assessing genetic diversity, structuring, and gene flow within and among populations of the rare P. formosula, in addition to related Phacelia species. These markers will provide important genetic data needed for appropriate conservation and management of these rare plants. PMID:28791208

Isolation and characterization of 10 microsatellite loci in Cneorum tricoccon (Cneoraceae), a Mediterranean relict plant.

PubMed

García-Fernández, Alfredo; Lázaro-Nogal, Ana; Traveset, Anna; Valladares, Fernando

2012-08-01

The main aim of this study was to isolate and characterize microsatellite loci in Cneorum tricoccon (Cneoraceae), a Mediterranean shrub relict of the early Tertiary, which inhabits western Mediterranean islands and coasts. Microsatellites will be useful for investigating biogeography and landscape genetics across the species distribution range, including current or past gene flow. Seventeen microsatellite loci were characterized, of which 10 were polymorphic and amplified for a total of 56 alleles in three populations of C. tricoccon. The markers revealed average coefficients of expected heterozygosity (H(e) = 0.425), observed heterozygosity (H(o) = 0.282), and inbreeding coefficient value per population (F(IS) = 0.408). These microsatellite primers will potentially be useful in the study of population and landscape genetics, conservation status of isolated populations, island-continental distribution, current or historical movements between populations, and in the investigation of the consequences of dispersal mechanisms of these plants.

The Effect and Relative Importance of Neutral Genetic Diversity for Predicting Parasitism Varies across Parasite Taxa

PubMed Central

Ruiz-López, María José; Monello, Ryan J.; Gompper, Matthew E.; Eggert, Lori S.

2012-01-01

Understanding factors that determine heterogeneity in levels of parasitism across individuals is a major challenge in disease ecology. It is known that genetic makeup plays an important role in infection likelihood, but the mechanism remains unclear as does its relative importance when compared to other factors. We analyzed relationships between genetic diversity and macroparasites in outbred, free-ranging populations of raccoons (Procyon lotor). We measured heterozygosity at 14 microsatellite loci and modeled the effects of both multi-locus and single-locus heterozygosity on parasitism using an information theoretic approach and including non-genetic factors that are known to influence the likelihood of parasitism. The association of genetic diversity and parasitism, as well as the relative importance of genetic diversity, differed by parasitic group. Endoparasite species richness was better predicted by a model that included genetic diversity, with the more heterozygous hosts harboring fewer endoparasite species. Genetic diversity was also important in predicting abundance of replete ticks (Dermacentor variabilis). This association fit a curvilinear trend, with hosts that had either high or low levels of heterozygosity harboring fewer parasites than those with intermediate levels. In contrast, genetic diversity was not important in predicting abundance of non-replete ticks and lice (Trichodectes octomaculatus). No strong single-locus effects were observed for either endoparasites or replete ticks. Our results suggest that in outbred populations multi-locus diversity might be important for coping with parasitism. The differences in the relationships between heterozygosity and parasitism for the different parasites suggest that the role of genetic diversity varies with parasite-mediated selective pressures. PMID:23049796

Improving Global Reanalyses and Short Range Forecast Using TRMM and SSM/I-Derived Precipitation and Moisture Observations

NASA Technical Reports Server (NTRS)

Hou, Arthur Y.; Zhang, Sara Q.; deSilva, Arlindo M.

2000-01-01

Global reanalyses currently contain significant errors in the primary fields of the hydrological cycle such as precipitation, evaporation, moisture, and the related cloud fields, especially in the tropics. The Data Assimilation Office (DAO) at the NASA Goddard Space Flight Center has been exploring the use of tropical rainfall and total precipitable water (TPW) observations from the TRMM Microwave Imager (TMI) and the Special Sensor Microwave/ Imager (SSM/I) instruments to improve short-range forecast and reanalyses. We describe a "1+1"D procedure for assimilating 6-hr averaged rainfall and TPW in the Goddard Earth Observing System (GEOS) Data Assimilation System (DAS). The algorithm is based on a 6-hr time integration of a column version of the GEOS DAS, hence the "1+1"D designation. The scheme minimizes the least-square differences between the observed TPW and rain rates and those produced by the column model over the 6-hr analysis window. This 1+lD scheme, in its generalization to four dimensions, is related to the standard 4D variational assimilation but uses analysis increments instead of the initial condition as the control variable. Results show that assimilating the TMI and SSM/I rainfall and TPW observations improves not only the precipitation and moisture fields but also key climate parameters such as clouds, the radiation, the upper-tropospheric moisture, and the large-scale circulation in the tropics. In particular, assimilating these data reduce the state-dependent systematic errors in the assimilated products. The improved analysis also provides better initial conditions for short-range forecasts, but the improvements in forecast are less than improvements in the time-averaged assimilation fields, indicating that using these data types is effective in correcting biases and other errors of the forecast model in data assimilation.

Improving Global Reanalyses and Short-Range Forecast Using TRMM and SSM/I-Derived Precipitation and Moisture Observations

NASA Technical Reports Server (NTRS)

Hou, Arthur Y.; Zhang, Sara Q.; daSilva, Arlindo M.

1999-01-01

Global reanalyses currently contain significant errors in the primary fields of the hydrological cycle such as precipitation, evaporation, moisture, and the related cloud fields, especially in the tropics. The Data Assimilation Office (DAO) at the NASA Goddard Space Flight Center has been exploring the use of tropical rainfall and total precipitable water (TPW) observations from the TRMM Microwave Imager (TMI) and the Special Sensor Microwave/ Imager (SSM/I) instruments to improve short-range forecast and reanalyses. We describe a 1+1D procedure for assimilating 6-hr averaged rainfall and TPW in the Goddard Earth Observing System (GEOS) Data Assimilation System (DAS). The algorithm is based on a 6-hr time integration of a column version of the GEOS DAS, hence the 1+1D designation. The scheme minimizes the least-square differences between the observed TPW and rain rates and those produced by the column model over the 6-hr analysis window. This 1+1D scheme, in its generalization to four dimensions, is related to the standard 4D variational assimilation but uses analysis increments instead of the initial condition as the control variable. Results show that assimilating the TMI and SSW rainfall and TPW observations improves not only the precipitation and moisture fields but also key climate parameters such as clouds, the radiation, the upper-tropospheric moisture, and the large-scale circulation in the tropics. In particular, assimilating these data reduce the state-dependent systematic errors in the assimilated products. The improved analysis also provides better initial conditions for short-range forecasts, but the improvements in forecast are less than improvements in the time-averaged assimilation fields, indicating that using these data types is effective in correcting biases and other errors of the forecast model in data assimilation.

Loss of heterozygosity on chromosome 9q22.3 in microdissected basal cell carcinomas around the Semipalatinsk Nuclear Testing Site, Kazakhstan.

PubMed

Iwata, Kenji; Takamura, Noboru; Nakashima, Masahiro; Alipov, Gabit; Mine, Mariko; Matsumoto, Naomichi; Yoshiura, Koichiro; Prouglo, Yuriy; Sekine, Ichiro; Katayama, Ichiro; Yamashita, Shunichi

2004-04-01

A high incidence of skin cancers has been noted around the Semipalatinsk Nuclear Testing Site (SNTS) in Kazakhstan. Recently, basal cell carcinoma (BCC) susceptibility genes, human homolog of the Drosophila pathed gene (PTCH), and the xeroderma pigmentosa group A-complementing gene (XPA), have been cloned and localized on chromosome 9q22.3. To clarify the effect of low-dose irradiation on the occurrence of BCC, we used microdissection and polymerase chain reaction to identify loss of heterozygosity (LOH) at 9q22.3 using BCC samples obtained from this region. Ten Japanese samples were analyzed as controls. LOH with at least 1 marker was identified in 5 of 14 cases from around SNTS, whereas only 1 case with 1 marker was identified among the 10 Nagasaki cases. The total number of LOH alleles from SNTS (8 of 45) was significantly higher than the number from Nagasaki (1 of 26) (P = 0.03). The higher incidence of LOH on 9q22.3 in BCC from around SNTS suggests involvement of chronic low-dose irradiation by fallout from the test site as a factor in the cancers.

New microsatellite loci isolated via next-generation sequencing for two endangered pronghorn from the Sonoran Desert

USGS Publications Warehouse

Munguia-Vega, Adrian; Klimova, Anastasia; Culver, Melanie

2013-01-01

We isolated 16 novel microsatellite loci in two subspecies of endangered desert pronghorns (Antilocapra americana sonoriensis and Antilocapra americana peninsularis) using a shotgun pyrosequencing approach. All and 87.5 % of the loci were polymorphic within each subspecies, respectively. The mean number of alleles per locus was 4.86 (range 2–8) and 2.5 alleles per locus (range 1–4 alleles), and observed heterozygosity ranged from 0.13 to 0.78 (mean 0.48) and 0.00 to 0.61 (mean 0.31), respectively. We did not find significant linkage disequilibrium among loci pairs and only one locus deviated significantly from Hardy–Weinberg equilibrium in peninsularis.

Types of propagation of radio waves of the decameter range, according to observations by the OBS method on Cuba--Soviet Union paths

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berdeyans, D.; Bocharov, V.I.; Lobachevskii, L.A.

Ionosphere observations by the OBS method were performed to study ionospheric conditions under which radio waves in the decameter range propagate on Cuba--Soviet Union paths. The results of observations in the summer of 1973 are reported. The distance--frequency and distance--time characteristics of back-scattered signals in the sounding direction for each day of observation are discussed. (JFP)

Historical, observed, and modeled wildfire severity in montane forests of the Colorado Front Range.

PubMed

Sherriff, Rosemary L; Platt, Rutherford V; Veblen, Thomas T; Schoennagel, Tania L; Gartner, Meredith H

2014-01-01

Large recent fires in the western U.S. have contributed to a perception that fire exclusion has caused an unprecedented occurrence of uncharacteristically severe fires, particularly in lower elevation dry pine forests. In the absence of long-term fire severity records, it is unknown how short-term trends compare to fire severity prior to 20th century fire exclusion. This study compares historical (i.e. pre-1920) fire severity with observed modern fire severity and modeled potential fire behavior across 564,413 ha of montane forests of the Colorado Front Range. We used forest structure and tree-ring fire history to characterize fire severity at 232 sites and then modeled historical fire-severity across the entire study area using biophysical variables. Eighteen (7.8%) sites were characterized by low-severity fires and 214 (92.2%) by mixed-severity fires (i.e. including moderate- or high-severity fires). Difference in area of historical versus observed low-severity fire within nine recent (post-1999) large fire perimeters was greatest in lower montane forests. Only 16% of the study area recorded a shift from historical low severity to a higher potential for crown fire today. An historical fire regime of more frequent and low-severity fires at low elevations (<2260 m) supports a convergence of management goals of ecological restoration and fire hazard mitigation in those habitats. In contrast, at higher elevations mixed-severity fires were predominant historically and continue to be so today. Thinning treatments at higher elevations of the montane zone will not return the fire regime to an historic low-severity regime, and are of questionable effectiveness in preventing severe wildfires. Based on present-day fuels, predicted fire behavior under extreme fire weather continues to indicate a mixed-severity fire regime throughout most of the montane forest zone. Recent large wildfires in the Front Range are not fundamentally different from similar events that occurred

Historical, Observed, and Modeled Wildfire Severity in Montane Forests of the Colorado Front Range

PubMed Central

Sherriff, Rosemary L.; Platt, Rutherford V.; Veblen, Thomas T.; Schoennagel, Tania L.; Gartner, Meredith H.

2014-01-01

Large recent fires in the western U.S. have contributed to a perception that fire exclusion has caused an unprecedented occurrence of uncharacteristically severe fires, particularly in lower elevation dry pine forests. In the absence of long-term fire severity records, it is unknown how short-term trends compare to fire severity prior to 20th century fire exclusion. This study compares historical (i.e. pre-1920) fire severity with observed modern fire severity and modeled potential fire behavior across 564,413 ha of montane forests of the Colorado Front Range. We used forest structure and tree-ring fire history to characterize fire severity at 232 sites and then modeled historical fire-severity across the entire study area using biophysical variables. Eighteen (7.8%) sites were characterized by low-severity fires and 214 (92.2%) by mixed-severity fires (i.e. including moderate- or high-severity fires). Difference in area of historical versus observed low-severity fire within nine recent (post-1999) large fire perimeters was greatest in lower montane forests. Only 16% of the study area recorded a shift from historical low severity to a higher potential for crown fire today. An historical fire regime of more frequent and low-severity fires at low elevations (<2260 m) supports a convergence of management goals of ecological restoration and fire hazard mitigation in those habitats. In contrast, at higher elevations mixed-severity fires were predominant historically and continue to be so today. Thinning treatments at higher elevations of the montane zone will not return the fire regime to an historic low-severity regime, and are of questionable effectiveness in preventing severe wildfires. Based on present-day fuels, predicted fire behavior under extreme fire weather continues to indicate a mixed-severity fire regime throughout most of the montane forest zone. Recent large wildfires in the Front Range are not fundamentally different from similar events that occurred

Testing for post-copulatory selection for major histocompatibility complex genotype in a semi-free-ranging primate population.

PubMed

Setchell, Joanna M; Abbott, Kristin M; Gonzalez, Jean-Paul; Knapp, Leslie A

2013-10-01

A large body of evidence suggests that major histocompatibility complex (MHC) genotype influences mate choice. However, few studies have investigated MHC-mediated post-copulatory mate choice under natural, or even semi-natural, conditions. We set out to explore this question in a large semi-free-ranging population of mandrills (Mandrillus sphinx) using MHC-DRB genotypes for 127 parent-offspring triads. First, we showed that offspring MHC heterozygosity correlates positively with parental MHC dissimilarity suggesting that mating among MHC dissimilar mates is efficient in increasing offspring MHC diversity. Second, we compared the haplotypes of the parental dyad with those of the offspring to test whether post-copulatory sexual selection favored offspring with two different MHC haplotypes, more diverse gamete combinations, or greater within-haplotype diversity. Limited statistical power meant that we could only detect medium or large effect sizes. Nevertheless, we found no evidence for selection for heterozygous offspring when parents share a haplotype (large effect size), genetic dissimilarity between parental haplotypes (we could detect an odds ratio of ≥1.86), or within-haplotype diversity (medium-large effect). These findings suggest that comparing parental and offspring haplotypes may be a useful approach to test for post-copulatory selection when matings cannot be observed, as is the case in many study systems. However, it will be extremely difficult to determine conclusively whether post-copulatory selection mechanisms for MHC genotype exist, particularly if the effect sizes are small, due to the difficulty in obtaining a sufficiently large sample. © 2013 Wiley Periodicals, Inc.

Possible observation of Griffith phase over large temperature range in plasma sintered La0.67Ca0.33MnO3

NASA Astrophysics Data System (ADS)

Mishra, D. K.; Roul, B. K.; Singh, S. K.; Srinivasu, V. V.

2018-02-01

We report on the possible observation of Griffith phase in a wide range of temperature (>272-378 K) in the 2.5 min plasma sintered La0.67Ca0.33MnO3 (LCMO) as deduced from careful electron spin resonance studies. This is 106 K higher than the paramagnetic to ferromagnetic transition (Curie transition ∼272 K) temperature. The indication of Griffith phase in such a wide range is not reported earlier by any group. We purposefully prepared LCMO samples by plasma sintering technique so as to create a disordered structure by rapid quenching which we believe, is the prime reason for the observation of Griffith Phase above the Curie transition temperature. The inverse susceptibility curve represents the existence of ferromagnetic cluster in paramagnetic region. The large resonance peak width (40-60 mT) within the temperature range 330-378 K confirms the sample magnetically inhomogeneity which is also established from our electron probe microstructure analysis (EPMA). EPMA establishes the presence of higher percentage of Mn3+ cluster in comparison to Mn4+. This is the reason for which Griffith state is enhanced largely to a higher range of temperature.

Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety 'Amrapali' (Mangifera indica L.).

PubMed

Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

2016-01-01

Mango (Mangifera indica L.) is called "king of fruits" due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties 'Neelam', 'Dashehari' and their hybrid 'Amrapali' using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.

WE-G-204-02: Utility of a Channelized Hotelling Model Observer Over a Large Range of Angiographic Exposure Levels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fetterly, K; Favazza, C

2015-06-15

Purpose: Mathematical model observers provide a figure of merit that simultaneously considers a test object and the contrast, noise, and spatial resolution properties of an imaging system. The purpose of this work was to investigate the utility of a channelized Hotelling model observer (CHO) to assess system performance over a large range of angiographic exposure conditions. Methods: A 4 mm diameter disk shaped, iodine contrast test object was placed on a 20 cm thick Lucite phantom and 1204 image frames were acquired using fixed x-ray beam quality and for several detector target dose (DTD) values in the range 6 tomore » 240 nGy. The CHO was implemented in the spatial domain utilizing 96 Gabor functions as channels. Detectability index (DI) estimates were calculated using the “resubstitution” and “holdout” methods to train the CHO. Also, DI values calculated using discrete subsets of the data were used to estimate a minimally biased DI as might be expected from an infinitely large dataset. The relationship between DI, independently measured CNR, and changes in results expected assuming a quantum limited detector were assessed over the DTD range. Results: CNR measurements demonstrated that the angiography system is not quantum limited due to relatively increasing contamination from electronic noise that reduces CNR for low DTD. Direct comparison of DI versus CNR indicates that the CHO relatively overestimates DI for low DTD and/or underestimates DI values for high DTD. The relative magnitude of the apparent bias error in the DI values was ∼20% over the 40x DTD range investigated. Conclusion: For the angiography system investigated, the CHO can provide a minimally biased figure of merit if implemented over a restricted exposure range. However, bias leads to overestimates of DI for low exposures. This work emphasizes the need to verify CHO model performance during real-world application.« less

Polymorphic microsatellite loci identified through development and cross-species amplification within shorebirds

USGS Publications Warehouse

Williams, I.; Guzzetti, B.M.; Gust, Judy R.; Sage, G.K.; Gill, Robert E.; Tibbitts, T.L.; Sonsthagen, S.A.; Talbot, S.L.

2012-01-01

We developed microsatellite loci for demographic assessments of shorebirds, a group with limited markers. First, we isolated five dinucleotide repeat microsatellite loci from the Black Oystercatcher (Haematopodidae: Haematopus bachmani), and three from the Bristle-thighed Curlew (Scolopacidae: Numenius tahitiensis); both species are of conservation concern. All eight loci were polymorphic in their respective target species. Hbaμ loci were characterized by two to three alleles with observed heterozygosity ranging from 0.07 to 0.33, and two to nine alleles were detected for Nut loci with observed heterozygosity ranging from 0.08 to 0.72. No linkage disequilibrium or departures from Hardy–Weinberg equilibrium were observed. The eight loci were also tested for cross-species amplification in 12 other species within Charadriidae and Scolopacidae, and the results demonstrated transferability across several genera. We further tested all 14 species at 12 additional microsatellite markers developed for other shorebirds: Dunlin (Calidris alpina; four loci) and Ruff (Philomachus pugnax; eight loci). Two markers (Hbaμ4 and Ruff6) were polymorphic in 13 species, while two (Calp6 and Ruff9) were monomorphic. The remaining eight markers revealed polymorphism in one to nine species each. Our results provide further evidence that locus Ruff10 is sex-linked, contrary to the initial description. These markers can be used to enhance our understanding of shorebird biology by, for example, helping to determine migratory connectivity among breeding and wintering populations and detecting relatedness among individuals.

Constraints on the Mass and Location of Planet 9 set by Range and VLBI Observations of Spacecraft at Saturn

NASA Astrophysics Data System (ADS)

Jacobson, Robert A.; Folkner, William M.; Park, Ryan S.; Williams, James G.

2017-06-01

Batygin and Brown, 2016 AJ, found that all Kuiper belt objects (KBOs) with well determined orbits having periods greater than 4000 years share nearly the same orbital plane and are apsidally aligned. They attribute this orbital clustering to the existence of a distant planet, Planet 9, well beyond Neptune, with a mass roughly ten times that of Earth. If such a planet exists, it would affect the motion of the known solar system planets, in particular Saturn, which is well observed with radiometric ranging from the Voyager and Cassini spacecraft and VLBI observations of Cassini. The current planetary ephemerides do not account for the postulated Planet 9, yet their fit to the observational data shows no obvious effect that could be attributed to neglecting that planet. However, it is possible that the effect could be absorbed by the estimated parameters used to determine the ephemerides. Those parameters include the planetary orbital elements, mass of the Sun, and the masses of the asteroids that perturb the Martian orbit. We recently updated the Voyager and Cassini data sets and extended the latter through 2017 March. We analyze the sensitivity of these data to the tidal perturbations caused by Planet 9 for a range of positions on the sky and tidal parameters (the ratio of the mass of Planet 9 to the cube of its distance from Saturn). We determine an upper bound on the tidal parameter and the most probable directions consistent with the observational data.

Serial Founder Effects During Range Expansion: A Spatial Analog of Genetic Drift

PubMed Central

Slatkin, Montgomery; Excoffier, Laurent

2012-01-01

Range expansions cause a series of founder events. We show that, in a one-dimensional habitat, these founder events are the spatial analog of genetic drift in a randomly mating population. The spatial series of allele frequencies created by successive founder events is equivalent to the time series of allele frequencies in a population of effective size ke, the effective number of founders. We derive an expression for ke in a discrete-population model that allows for local population growth and migration among established populations. If there is selection, the net effect is determined approximately by the product of the selection coefficients and the number of generations between successive founding events. We use the model of a single population to compute analytically several quantities for an allele present in the source population: (i) the probability that it survives the series of colonization events, (ii) the probability that it reaches a specified threshold frequency in the last population, and (iii) the mean and variance of the frequencies in each population. We show that the analytic theory provides a good approximation to simulation results. A consequence of our approximation is that the average heterozygosity of neutral alleles decreases by a factor of 1 – 1/(2ke) in each new population. Therefore, the population genetic consequences of surfing can be predicted approximately by the effective number of founders and the effective selection coefficients, even in the presence of migration among populations. We also show that our analytic results are applicable to a model of range expansion in a continuously distributed population. PMID:22367031

Serial founder effects during range expansion: a spatial analog of genetic drift.

PubMed

Slatkin, Montgomery; Excoffier, Laurent

2012-05-01

Range expansions cause a series of founder events. We show that, in a one-dimensional habitat, these founder events are the spatial analog of genetic drift in a randomly mating population. The spatial series of allele frequencies created by successive founder events is equivalent to the time series of allele frequencies in a population of effective size ke, the effective number of founders. We derive an expression for ke in a discrete-population model that allows for local population growth and migration among established populations. If there is selection, the net effect is determined approximately by the product of the selection coefficients and the number of generations between successive founding events. We use the model of a single population to compute analytically several quantities for an allele present in the source population: (i) the probability that it survives the series of colonization events, (ii) the probability that it reaches a specified threshold frequency in the last population, and (iii) the mean and variance of the frequencies in each population. We show that the analytic theory provides a good approximation to simulation results. A consequence of our approximation is that the average heterozygosity of neutral alleles decreases by a factor of 1-1/(2ke) in each new population. Therefore, the population genetic consequences of surfing can be predicted approximately by the effective number of founders and the effective selection coefficients, even in the presence of migration among populations. We also show that our analytic results are applicable to a model of range expansion in a continuously distributed population.

Polymorphic microsatellite loci for the sand pocket mouse Chaetodipus arenarius, an endemic from the Baja California Peninsula

USGS Publications Warehouse

Munguia-Vega, A.; Rodriguez-Estrella, R.; Nachman, M.; Culver, M.

2009-01-01

Fifteen polymorphic microsatellite loci were isolated from an enriched genomic library of the sand pocket mouse Chaetodipus arenarius. The mean number of alleles per locus was 11.53 (range five to 19) and the average observed heterozygosity was 0.764 (range 0.121 to 1.0). The markers will be used for detecting the impact of human-induced habitat fragmentation on patterns of gene flow, genetic structure, and extinction risk. In addition, these markers will be useful across the genus because most of the loci cross-amplified and were polymorphic in three other species of Chaetodipus. ?? 2008 The Authors.

Microsatellite markers in Rhodiola (Crassulaceae), a medicinal herb genus widely used in traditional Chinese medicine.

PubMed

You, Jianling; Liu, Wensheng; Zhao, Yao; Zhu, Yongqing; Zhang, Wenju; Wang, Yuguo; Lu, Fan; Song, Zhiping

2013-03-01

Microsatellite loci are described for Rhodiola, a medicinal herb genus widely used in traditional Chinese medicine. • A total of 17 polymorphic microsatellite primer pairs were developed using the combined biotin capture method. The number of alleles per locus ranged from one to 12 across 192 individuals from R. bupleuroides, R. crenulata, R. fastigiata, and R. sacra, and the mean observed and expected heterozygosities ranged from 0.177 to 0.412 and from 0.363 to 0.578, respectively. • The results demonstrate the potential use of this new set of microsatellite markers for genotyping individuals and estimating genetic diversity in Rhodiola.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alonso, S.; Castro, A.; Fernandez-Fernandez, I.

1997-02-01

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

Development of a Ranging System for the Forward Scattering Meteor Radio Echo Observation Using a GPS-Synchronized Multiple Receiving Stations

NASA Astrophysics Data System (ADS)

Usui, T.; Yoshida, H.; Miyamoto, H.; Yaguchi, N.; Terasawa, T.; Yoshikawa, I.

2012-05-01

We are developing an instrument for teaching purpose to determine the trajectory of a meteor with the Ham-band Radio Observations(HRO) . In this work, we describe newly developed ranging system with using Frequency Modulated signals and show some results.

Adaptive Blending of Model and Observations for Automated Short-Range Forecasting: Examples from the Vancouver 2010 Olympic and Paralympic Winter Games

NASA Astrophysics Data System (ADS)

Bailey, Monika E.; Isaac, George A.; Gultepe, Ismail; Heckman, Ivan; Reid, Janti

2014-01-01

An automated short-range forecasting system, adaptive blending of observations and model (ABOM), was tested in real time during the 2010 Vancouver Olympic and Paralympic Winter Games in British Columbia. Data at 1-min time resolution were available from a newly established, dense network of surface observation stations. Climatological data were not available at these new stations. This, combined with output from new high-resolution numerical models, provided a unique and exciting setting to test nowcasting systems in mountainous terrain during winter weather conditions. The ABOM method blends extrapolations in time of recent local observations with numerical weather predictions (NWP) model predictions to generate short-range point forecasts of surface variables out to 6 h. The relative weights of the model forecast and the observation extrapolation are based on performance over recent history. The average performance of ABOM nowcasts during February and March 2010 was evaluated using standard scores and thresholds important for Olympic events. Significant improvements over the model forecasts alone were obtained for continuous variables such as temperature, relative humidity and wind speed. The small improvements to forecasts of variables such as visibility and ceiling, subject to discontinuous changes, are attributed to the persistence component of ABOM.

Genetic variation and forensic efficiency of autosomal insertion/deletion polymorphisms in Chinese Bai ethnic group: phylogenetic analysis to other populations

PubMed Central

Yang, Chun-Hua; Yin, Cai-Yong; Shen, Chun-Mei; Guo, Yu-Xin; Dong, Qian; Yan, Jiang-Wei; Wang, Hong-Dan; Zhang, Yu-Dang; Meng, Hao-Tian; Jin, Rui

2017-01-01

Thirty insertion/deletion loci were utilized to study the genetic diversities of 125 bloodstain samples collected from Bai group in Yunnan Dali region, China. The observed heterozygosity and expected heterozygosity of the 30 loci ranged from 0.1520 to 0.5680, and 0.1927 to 0.4997, respectively. No deviations from Hardy-Weinberg equilibrium tests after Bonferroni correction were found at all 30 loci in Bai group. The cumulative probability of exclusion and combined discrimination power were 0.9859 and 0.9999999999887, respectively, which indicated the 30 loci could be used as complementary genetic markers for paternity testing and were qualified for personal identification in forensic cases. We found the studied Bai group had close relationships with Tibetan, Yi and Han groups from China by the population structure, principal component analysis, population differentiations, and phylogenetic reconstruction studies. Even so, for a better understanding of Bai ethnicity's genetic milieu, DNA genotyping at various genetic markers is necessary in future studies. PMID:28465476

Genetic variation and forensic efficiency of autosomal insertion/deletion polymorphisms in Chinese Bai ethnic group: phylogenetic analysis to other populations.

PubMed

Yang, Chun-Hua; Yin, Cai-Yong; Shen, Chun-Mei; Guo, Yu-Xin; Dong, Qian; Yan, Jiang-Wei; Wang, Hong-Dan; Zhang, Yu-Dang; Meng, Hao-Tian; Jin, Rui; Chen, Feng; Zhu, Bo-Feng

2017-06-13

Thirty insertion/deletion loci were utilized to study the genetic diversities of 125 bloodstain samples collected from Bai group in Yunnan Dali region, China. The observed heterozygosity and expected heterozygosity of the 30 loci ranged from 0.1520 to 0.5680, and 0.1927 to 0.4997, respectively. No deviations from Hardy-Weinberg equilibrium tests after Bonferroni correction were found at all 30 loci in Bai group. The cumulative probability of exclusion and combined discrimination power were 0.9859 and 0.9999999999887, respectively, which indicated the 30 loci could be used as complementary genetic markers for paternity testing and were qualified for personal identification in forensic cases. We found the studied Bai group had close relationships with Tibetan, Yi and Han groups from China by the population structure, principal component analysis, population differentiations, and phylogenetic reconstruction studies. Even so, for a better understanding of Bai ethnicity's genetic milieu, DNA genotyping at various genetic markers is necessary in future studies.

Development and characterization of EST-SSR markers for Artocarpus hypargyreus (Moraceae)1

PubMed Central

Liu, Haijun; Tan, Weizheng; Sun, Hongbin; Liu, Yu; Meng, Kaikai; Liao, Wenbo

2016-01-01

Premise of the study: Polymorphic microsatellite markers were developed for Artocarpus hypargyreus (Moraceae), a threatened species endemic to China, to investigate the genetic diversity and structure of the species. Methods and Results: Based on the transcriptome data of A. hypargyreus, 63 primer pairs were preliminarily designed and tested, of which 34 were successfully amplified and 10 displayed clear polymorphisms across the 67 individuals from four populations of A. hypargyreus. The results showed the number of alleles per locus ranged from three to 10, and the observed heterozygosity and expected heterozygosity per locus varied from 0.000 to 0.706 and from 0.328 to 0.807, respectively. Conclusions: These microsatellite markers will be useful in exploring genetic diversity and structure of A. hypargyreus. Furthermore, most loci were successfully cross-amplified in A. nitidus and A. heterophyllus, indicating that they will be of great value for genetic study across this genus. PMID:28101438

Loss of heterozygosity and methylation of multiple tumor suppressor genes on chromosome 3 in hepatocellular carcinoma.

PubMed

Zhang, Xiaoying; Li, Hiu Ming; Liu, Zhiyan; Zhou, Gengyin; Zhang, Qinghui; Zhang, Tingguo; Zhang, Jianping; Zhang, Cuijuan

2013-01-01

Genetic and epigenetic alterations are the two key mechanisms in the development of hepatocellular carcinoma (HCC). However, how they contribute to hepatocarcinogenesis and the correlation between them has not been fully elucidated. A total of 48 paired HCCs and noncancerous tissues were used to detect loss of heterozygosity (LOH) and the methylation profiles of five tumor suppressor genes (RASSF1A, BLU, FHIT, CRBP1, and HLTF) on chromosome 3 by using polymerase chain reaction (PCR) and methylation-specific PCR. Gene expression was analyzed by immunohistochemistry and reverse transcription (RT)-PCR. Sixteen of 48 (33.3 %) HCCs had LOH on at least one locus on chromosome 3, and two smallest common deleted regions (3p22.3-24.3 and 3p12.3-14.2) were identified. RASSF1A, BLU, and FHIT showed very high frequencies of methylation in HCCs (100, 81.3, and 64.6 %, respectively) and noncancerous tissues, but not in liver tissues from control patients. Well-differentiated HCCs showed high methylation frequencies of these genes but very low frequencies of LOH. Furthermore, BLU methylation was associated with an increased level of alpha-fetoprotein, and FHIT methylation was inversely correlated with HCC recurrence. In comparison, CRBP1 showed moderate frequencies of methylation, while HLTF showed low frequencies of methylation, and CRBP1 methylation occurred mainly in elderly patients. Treatment with 5-aza-2'-deoxycytidine demethylated at least one of these genes and restored their expression in a DNA methylation-dependent or -independent manner. Hypermethylation of RASSF1A, BLU, and FHIT is a common and very early event in hepatocarcinogenesis; CRBP1 methylation may also be involved in the later stage. Although LOH was not too frequent on chromosome 3, it may play a role as another mechanism in hepatocarcinogenesis.

Isolation and characterization of microsatellite loci in Alasmidonta heterodon (Bivalvia: Unionidae)

USGS Publications Warehouse

Shaw, K.M.; King, T.L.; Lellis, W.A.; Eackles, M.S.

2006-01-01

We developed 13 species-specific microsatellite markers for the federally endangered Atlantic slope unionid Alasmidonta heterodon. Four to 18 alleles per locus were observed among 30 individuals. Observed heterozygosity throughout the loci ranged from 26.9 to 86.2% and averaged 63.6%. Estimates of individual pairwise genetic distances indicated that levels of genetic diversity among loci were sufficient to produce unique multilocus genotypes for all animals surveyed. Randomization tests showed that genotypes for this collection were consistent with Hardy-Weinberg expectations, and no significant linkage disequilibrium was observed between loci. These loci therefore appear suitable for population surveys, kinship assessment and other such applications. ?? 2006 Blackwell Publishing Ltd.

Development of microsatellite primers of the largest seagrass, Enhalus acoroides (Hydrocharitaceae).

PubMed

Gao, Hui; Jiang, Kai; Geng, Yan; Chen, Xiao-Yong

2012-03-01

Microsatellite primers were developed for the seagrass Enhalus acoroides to investigate genetic variation and identify clonal structure. Four polymorphic loci and 32 monomorphic loci were developed in E. acoroides. Two to four alleles per locus were observed at the polymorphic loci across 60 individuals of two E. acoroides populations. The observed and expected heterozygosities within populations ranged from 0.100 to 0.5667 and from 0.0977 to 0.5079, respectively. Our study revealed very low polymorphism in E. acoroides, even at the polymorphic loci. Nevertheless, these primers are a useful tool to study genetic variation, clonal structure, and mating system.

Characterization of 12 polymorphic microsatellite markers for a facultatively eusocial sweat bee (Megalopta genalis).

PubMed

Kapheim, Karen M; Pollinger, John P; Wcislo, William T; Wayne, Robert K

2009-11-01

We developed a library of twelve polymorphic di- and tri-nucleotide microsatellite markers for Megalopta genalis, a facultatively eusocial sweat bee. We tested each locus in a panel of 23 unrelated females and found 7-20 alleles per locus. Observed and expected heterozygosities ranged from 0.65 to 0.96 and from 0.69 to 0.95 respectively. None of the loci deviated from Hardy-Weinberg equilibrium proportions or was found to be in gametic disequilibrium. © 2009 Blackwell Publishing Ltd.

Genetic structure and conservation of Mountain Lions in the South-Brazilian Atlantic Rain Forest.

PubMed

Castilho, Camila S; Marins-Sá, Luiz G; Benedet, Rodrigo C; Freitas, Thales R O

2012-01-01

The Brazilian Atlantic Rain Forest, one of the most endangered ecosystems worldwide, is also among the most important hotspots as regards biodiversity. Through intensive logging, the initial area has been reduced to around 12% of its original size. In this study we investigated the genetic variability and structure of the mountain lion, Puma concolor. Using 18 microsatellite loci we analyzed evidence of allele dropout, null alleles and stuttering, calculated the number of allele/locus, PIC, observed and expected heterozygosity, linkage disequilibrium, Hardy-Weinberg equilibrium, F(IS), effective population size and genetic structure (MICROCHECKER, CERVUS, GENEPOP, FSTAT, ARLEQUIN, ONESAMP, LDNe, PCAGEN, GENECLASS software), we also determine whether there was evidence of a bottleneck (HYBRIDLAB, BOTTLENECK software) that might influence the future viability of the population in south Brazil. 106 alleles were identified, with the number of alleles/locus ranging from 2 to 11. Mean observed heterozygosity, mean number of alleles and polymorphism information content were 0.609, 5.89, and 0.6255, respectively. This population presented evidence of a recent bottleneck and loss of genetic variation. Persistent regional poaching constitutes an increasing in the extinction risk.

Genetic structure and conservation of Mountain Lions in the South-Brazilian Atlantic Rain Forest

PubMed Central

Castilho, Camila S.; Marins-Sá, Luiz G.; Benedet, Rodrigo C.; Freitas, Thales R.O.

2012-01-01

The Brazilian Atlantic Rain Forest, one of the most endangered ecosystems worldwide, is also among the most important hotspots as regards biodiversity. Through intensive logging, the initial area has been reduced to around 12% of its original size. In this study we investigated the genetic variability and structure of the mountain lion, Puma concolor. Using 18 microsatellite loci we analyzed evidence of allele dropout, null alleles and stuttering, calculated the number of allele/locus, PIC, observed and expected heterozygosity, linkage disequilibrium, Hardy-Weinberg equilibrium, FIS, effective population size and genetic structure (MICROCHECKER, CERVUS, GENEPOP, FSTAT, ARLEQUIN, ONESAMP, LDNe, PCAGEN, GENECLASS software), we also determine whether there was evidence of a bottleneck (HYBRIDLAB, BOTTLENECK software) that might influence the future viability of the population in south Brazil. 106 alleles were identified, with the number of alleles/locus ranging from 2 to 11. Mean observed heterozygosity, mean number of alleles and polymorphism information content were 0.609, 5.89, and 0.6255, respectively. This population presented evidence of a recent bottleneck and loss of genetic variation. Persistent regional poaching constitutes an increasing in the extinction risk. PMID:22481876

Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (Mangifera indica L.)

PubMed Central

Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

2016-01-01

Mango (Mangifera indica L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango. PMID:27736892

Genetic diversity and reproductive success in mandrills (Mandrillus sphinx).

PubMed

Charpentier, M; Setchell, J M; Prugnolle, F; Knapp, L A; Wickings, E J; Peignot, P; Hossaert-McKey, M

2005-11-15

Recent studies of wild animal populations have shown that estimators of neutral genetic diversity, such as mean heterozygosity, are often correlated with various fitness traits, such as survival, disease susceptibility, or reproductive success. We used two estimators of genetic diversity to explore the relationship between heterozygosity and reproductive success in male and female mandrills (Mandrillus sphinx) living in a semifree ranging setting in Gabon. Because social rank is known to influence reproductive success in both sexes, we also examined the correlation between genetic diversity and social rank in females, and acquisition of alpha status in males, as well as length of alpha male tenure. We found that heterozygous individuals showed greater reproductive success, with both females and males producing more offspring. However, heterozygosity influenced reproductive success only in dominant males, not in subordinates. Neither the acquisition of alpha status in males, nor social rank in females, was significantly correlated with heterozygosity, although more heterozygous alpha males showed longer tenure than homozygous ones. We also tested whether the benefits of greater genetic diversity were due mainly to a genome-wide effect of inbreeding depression or to heterosis at one or a few loci. Multilocus effects best explained the correlation between heterozygosity and reproductive success and tenure, indicating the occurrence of inbreeding depression in this mandrill colony.

Genetic analysis of Black Tiger shrimp (Penaeus monodon) across its natural distribution range reveals more recent colonization of Fiji and other South Pacific islands.

PubMed

Waqairatu, Salote S; Dierens, Leanne; Cowley, Jeff A; Dixon, Tom J; Johnson, Karyn N; Barnes, Andrew C; Li, Yutao

2012-08-01

The Black Tiger shrimp (Penaeus monodon) has a natural distribution range from East Africa to the South Pacific Islands. Although previous studies of Indo-Pacific P. monodon have found populations from the Indian Ocean and Australasia to differ genetically, their relatedness to South Pacific shrimp remains unknown. To address this, polymorphisms at eight shared microsatellite loci and haplotypes in a 418-bp mtDNA-CR (control region) sequence were examined across 682 P. monodon from locations spread widely across its natural range, including the South Pacific islands of Fiji, Palau, and Papua New Guinea (PNG). Observed microsatellite heterozygosities of 0.82-0.91, allele richness of 6.85-9.69, and significant mtDNA-CR haplotype variation indicated high levels of genetic diversity among the South Pacific shrimp. Analysis of microsatellite genotypes using a Bayesian STRUCTURE method segregated Indo-Pacific P. monodon into eight distinct clades, with Palau and PNG shrimp clustering among others from Southeast Asia and eastern Australia, respectively, and Fiji shrimp clustering as a distinct group. Phylogenetic analyses of mtDNA-CR haplotypes delineated shrimp into three groupings, with shrimp from Fiji again being distinct by sharing no haplotypes with other populations. Depending on regional location, the genetic structures and substructures identified from the genotyping and mtDNA-CR haplotype phylogeny could be explained by Metapopulation and/or Member-Vagrant type evolutionary processes. Neutrality tests of mutation-drift equilibrium and estimation of the time since population expansion supported a hypothesis that South Pacific P. monodon were colonized from Southeast Asia and eastern Australia during the Pleistocene period over 60,000 years ago when land bridges were more expansive and linked these regions more closely.

Isolation and characterization of 108 novel microsatellite loci for Atlantic coastal killifish (Fundulus heteroclitus)

EPA Science Inventory

We characterized 108 polymorphic microsatellite loci for the mummichog (Fundulus heteroclitus), an Atlantic coastal killifish. Allelic diversity among 26 individuals ranged between 2 and 15 alleles per locus, while expected heterozygosity ranged from 0.075 to 0.904. Significant ...

Isolation and characterization of microsatellite loci for mountain mullet (Agonostomus monticola).

PubMed

Feldheim, Kevin A; Sanchez, Patrick J; Matamoros, Wilfredo A; Schaefer, Jacob F; Kreiser, Brian R

2009-11-01

We report on the isolation of 15 polymorphic microsatellite loci from mountain mullet (Agonostomus monticola). In the two populations sampled, loci exhibited two to 21 alleles and observed heterozygosity values ranged from 0.222 to 1.000. All loci conformed to Hardy-Weinberg equilibrium expectations, and none exhibited linkage disequilibrium. Although A. monticola is an important subsistence fishery in parts of its range, little is known about its ecology and many populations appear to be experiencing declines. These microsatellite loci should prove useful in the study of population structure of A. monticola and aid in other potential conservation efforts such as the management of hatchery broodstock. © 2009 Blackwell Publishing Ltd.

Development of microsatellite markers for Dimorphandra mollis (Leguminosae), a widespread tree from the Brazilian cerrado.

PubMed

Souza, Helena A V; Collevatti, Rosane G; Lemos-Filho, José P; Santos, Fabrício R; Lovato, Maria Bernadete

2012-03-01

Microsatellite markers were developed for Dimorphandra mollis (Leguminosae), a widespread tree in the Brazilian cerrado (a savanna-like vegetation). Microsatellite markers were developed from an enriched library. The analyses of polymorphism were based on 56 individuals from three populations. Nine microsatellite loci were polymorphic, with the number of alleles per locus ranging from three to 10 across populations. The observed and expected heterozygosities per locus and population ranged from 0.062 to 0.850 and from 0.062 to 0.832, respectively. These microsatellites provide an efficient tool for population genetics studies and will be used to assess the genetic diversity and spatial genetic structure of D. mollis.

An intriguing high performance liquid chromatogram of a double heterozygosity for Hb Q-India/Hb D-Punjab.

PubMed

Badyal, Rama Kumari; Chhabra, Sanjeev; Sharma, Prashant; Das, Reena

2014-01-01

Cation exchange high performance liquid chromatography (HPLC) is commonly utilized as the first method of screening for thalassemias and hemoglobinopathies worldwide. This method of diagnosis requires knowledge of the clinical background and complete blood counts as well as skill and experience in interpreting the sometimes complex results produced. An asymptomatic 27-year-old pregnant North Indian woman was found to have a highly unusual chromatographic pattern with multiple unexpected peaks during routine antenatal screening. Most concerning was a C-window peak as Hb C (HBB: c.19G>A) is rare in ethnic Asian Indian populations. Cellulose acetate electrophoresis at alkaline pH (8.6) and parental screening were performed. These revealed the correct diagnosis to be a double heterozygosity for Hb Q-India (HBA1: c.193G>C) (an uncommon asymptomatic α-globin chain variant) plus Hb D-Punjab (HBB: c.364G>C) (a β-globin chain variant that is common in this region and is asymptomatic in the heterozygous state). The unexpected C-window peak was the hybrid of the abnormal α-Q-India and β-D-Punjab globin chains. Another small peak was explained as a variant Hb A2 formed by the combination of α-Q-India and δ-globin chains. Hematopathologists should be cognizant of the complex pattern resulting from coinheritance of both α- and β-globin structural variants. Second-line testing and parental testing are invaluable in resolving unknown peaks, especially if rare or unexpected variants are being considered. Although both Hb Q-India and Hb D-Punjab are relatively common in northwestern India, to the best of our knowledge, only two recent reports describe a total of three cases of such diagnostically puzzling coinheritance.

Low temperature resistivity studies of SmB6: Observation of two-dimensional variable-range hopping conductivity

NASA Astrophysics Data System (ADS)

Batkova, Marianna; Batko, Ivan; Gabáni, Slavomír; Gažo, Emil; Konovalova, Elena; Filippov, Vladimir

2018-05-01

We studied electrical resistance of a single-crystalline SmB6 sample with a focus on the region of the "low-temperature resistivity plateau". Our observations did not show any true saturation of the electrical resistance at temperatures below 3 K down to 70 mK. According to our findings, temperature dependence of the electrical conduction in a certain temperature interval above 70 mK can be decomposed into a temperature-independent term and a temperature-activated term that can be described by variable-range hopping formula for two-dimensional systems, exp [ -(T0 / T) 1 / 3 ]. Thus, our results indicate importance of hopping type of electrical transport in the near-surface region of SmB6.

Population genetic characterization and family reconstruction in brood bank collections of the Indian major carp Labeo rohita (Cyprinidae:Cypriniformes).

PubMed

Ullah, Ashraf; Basak, Abhisak; Islam, Md Nazrul; Alam, Md Samsul

2015-01-01

The founder stock of a captive breeding program is prone to changes in genetic structure due to inbreeding and genetic drift. Genetic characterization of the founder population using suitable molecular markers may help monitor periodic changes in the genetic structure in future. To develop benchmark information about the genetic structure we analyzed six microsatellite loci in the Brodbank collections of rohu (Labeo rohita) originated from three major rivers-the Jamuna, the Padma and the Halda. A total of 28 alleles were detected in 90 individuals with an average of 4.6 alleles per locus. The average observed heterozygosity ranged from 0.655 to 0.705 and the expected heterozygosity ranged from 0.702 to 0.725. The mean F IS values were 0.103, 0.106 and 0.018 for the Jamuna, Padma and Halda fishes respectively. The population pair-wise F ST values ranged from 0.0057 to 0.0278. Structure analysis grouped the fishes of the three rivers into two clusters. The numbers of half-sib families were 5, 5 and 4 and the numbers of full-sib families were 12, 10 and 18 for the Halda, Jamuna and the Padma samples respectively. Bottleneck was detected in all the river samples. We recommend to collect more fish from different locations of the major rivers to broaden the genetic variability of the founder stocks of the Brood bank.

Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep.

PubMed

Al-Mamun, Hawlader Abdullah; Clark, Samuel A; Kwan, Paul; Gondro, Cedric

2015-11-24

Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (N e ), heterozygosity, fixation index (F ST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r (2) and D'), N e , heterozygosity, F ST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller N e than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest F ST = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection. This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This

Genetic Diversity in Nannotrigona testaceicornis (Hymenoptera: Apidae) Aggregations in Southeastern Brazil

PubMed Central

Fonseca, A. S.; Oliveira, E.J.F.; Freitas, G.S.; Assis, A.F.; Souza, C.C.M.; Contel, E.P.B.; Soares, A.E.E.

2017-01-01

The Meliponini, also known as stingless bees, are distributed in tropical and subtropical areas of the world and plays an essential role in pollinating many wild plants and crops These bees can build nests in cavities of trees or walls, underground or in associations with ants or termites; interestingly, these nests are sometimes found in aggregations. In order to assess the genetic diversity and structure in aggregates of Nannotrigona testaceicornis (Lepeletier), samples of this species were collected from six aggregations and genetically analyzed for eight specific microsatellite loci. We observed in this analysis that the mean genetic diversity value among aggregations was 0.354, and the mean expected and observed heterozygosity values was 0.414 and 0.283, respectively. The statistically significant Fis value indicated an observed heterozygosity lower than the expected heterozygosity in all loci studied resulting in high homozygosis level in these populations. In addition, the low number of private alleles observed reinforces the absence of structuring that is seen in the aggregates. These results can provide relevant information about genetic diversity in aggregations of N. testaceicornis and contribute to the management and conservation of these bees’ species that are critical for the pollination process. PMID:28130454

Clonal Evolution and Clinical Significance of Copy Number Neutral Loss of Heterozygosity of Chromosome Arm 6p in Acquired Aplastic Anemia

PubMed Central

Betensky, Marisol; Babushok, Daria; Roth, Jacquelyn J.; Mason, Philip J; Biegel, Jaclyn A.; Busse, Tracy M; Li, Yimei; Lind, Curt; Papazoglou, Anna; Monos, Dimitri; Podsakoff, Gregory; Bessler, Monica; Olson, Timothy S.

2015-01-01

Acquired aplastic anemia (aAA) results from the T cell-mediated autoimmune destruction of hematopoietic stem cells. Factors predicting response to immune suppression therapy (IST) or development of myelodysplastic syndrome (MDS) are beginning to be elucidated. Our recent data suggest most patients with aAA treated with IST develop clonal somatic genetic alterations in hematopoietic cells. One frequent acquired abnormality is copy-number neutral loss of heterozygosity on chromosome 6p (6p CN-LOH) involving the human leukocyte antigen (HLA) locus. We hypothesized that because 6p CN-LOH clones may arise from selective pressure to escape immune surveillance through deletion of HLA alleles, the development of 6p CN-LOH may affect response to IST. We used single nucleotide polymorphism array genotyping and targeted next-generation sequencing of HLA alleles to assess frequency of 6p CN-LOH, identity of HLA alleles lost through 6p CN-LOH, and impact of 6p CN-LOH on response to IST. 6p CN-LOH clones were present in 11.3% of patients, remained stable over time, and were not associated with development of MDS-defining cytogenetic abnormalities. Notably, no patient with 6p CN-LOH treated with IST achieved a complete response. In summary, clonal 6p CN-LOH in aAA defines a unique subgroup of patients that may provide insights into hematopoietic clonal evolution. PMID:26702937

Loss of heterozygosity at 11p13 and 11p15 in Wilms tumor: a study of 22 cases from India.

PubMed

Sigamani, Elanthenral; Wari, Mohammad Nahidul; Iyer, Venkateswaran K; Agarwala, Sandeep; Sharma, Arundhati; Bakhshi, Sameer; Dinda, Amit

2013-03-01

11p13 and 11p15 loss of heterozygosity (LOH) in Wilms tumor (WT), the commonest molecular pathogenetic event in WT, shows variation in different parts of the world. The present study looked for the presence of 11p13 and 11p15 LOH as well as nephrogenic rests in WT occurring in India. Twenty-two cases of WT were subjected to thorough pathological examination for presence of nephrogenic rests. Fresh frozen tissue was evaluated for LOH at 11p13 and 11p15, using PCR for microsatellite markers. Among twenty-two consecutive cases of WT, 20 were unilateral and 2 were bilateral. 6/22 showed LOH at 11p13 (27.7 %) and 1/22 showed LOH at 11p15 (4.54 %). 2/22 cases showed presence of nephrogenic rests. One of the cases with LOH at 11p13 had intralobar nephrogenic rest in the adjacent kidney. One specimen had perilobar nephrogenic rest in the adjacent kidney but did not show LOH for either 11p13 or 11p15 in the tumor. LOH at 11p13 is seen in 27.27 % of WT in India, which is similar to reports in the English language literature. LOH at 11p15 was seen in 4.54 % of WT, which is lower than that reported from Western subjects.

The risk of familial Mediterranean fever in MEFV heterozygotes: a statistical approach.

PubMed

Jéru, Isabelle; Hentgen, Véronique; Cochet, Emmanuelle; Duquesnoy, Philippe; Le Borgne, Gaëlle; Grimprel, Emmanuel; Stojanovic, Katia Stankovic; Karabina, Sonia; Grateau, Gilles; Amselem, Serge

2013-01-01

Familial Mediterranean fever (FMF) is an autosomal recessive autoinflammatory disorder due to MEFV mutations and one of the most frequent Mediterranean genetic diseases. The observation of many heterozygous patients in whom a second mutated allele was excluded led to the proposal that heterozygosity could be causal. However, heterozygosity might be coincidental in many patients due to the very high rate of mutations in Mediterranean populations. To better delineate the pathogenicity of heterozygosity in order to improve genetic counselling and disease management. Complementary statistical approaches were used: estimation of FMF prevalence at population levels, genotype comparison in siblings from 63 familial forms, and genotype study in 557 patients from four Mediterranean populations. At the population level, we did not observe any contribution of heterozygosity to disease prevalence. In affected siblings of patients carrying two MEFV mutations, 92% carry two mutated alleles, whereas 4% are heterozygous with typical FMF diagnosis. We demonstrated statistically that patients are more likely to be heterozygous than healthy individuals, as shown by the higher ratio heterozygous carriers/non carriers in patients (p<10(-7)-p<0.003). The risk for heterozygotes to develop FMF was estimated between 2.1 × 10(-3) and 5.8 × 10(-3) and the relative risk, as compared to non carriers, between 6.3 and 8.1. This is the first statistical demonstration that heterozygosity is not responsible for classical Mendelian FMF per se, but constitutes a susceptibility factor for clinically-similar multifactorial forms of the disease. We also provide a first estimate of the risk for heterozygotes to develop FMF.

Free range hens use the range more when the outdoor environment is enriched.

PubMed

Nagle, T A D; Glatz, P C

2012-04-01

To evaluate the role of using forage, shade and shelterbelts in attracting birds into the range, three trials were undertaken with free range layers both on a research facility and on commercial farms. Each of the trials on the free range research facility in South Australia used a total of 120 laying hens (Hyline Brown). Birds were housed in an eco-shelter which had 6 internal pens of equal size with a free range area adjoining the shelter. The on-farm trials were undertaken on commercial free range layer farms in the Darling Downs in Southeast Queensland with bird numbers on farms ranging from 2,000-6,800 hens. The first research trial examined the role of shaded areas in the range; the second trial examined the role of forage and the third trial examined the influence of shelterbelts in the range. These treatments were compared to a free range area with no enrichment. Aggressive feather pecking was only observed on a few occasions in all of the trials due to the low bird numbers housed. Enriching the free range environment attracted more birds into the range. Shaded areas were used by 18% of the hens with a tendency (p = 0.07) for more hens to be in the paddock. When forage was provided in paddocks more control birds (55%) were observed in the range in morning than in the afternoon (30%) while for the forage treatments 45% of the birds were in the range both during the morning and afternoon. When shelterbelts were provided there was a significantly (p<0.05) higher % of birds in the range (43% vs. 24%) and greater numbers of birds were observed in areas further away from the poultry house. The results from the on-farm trials mirrored the research trials. Overall 3 times more hens used the shaded areas than the non shaded areas, with slightly more using the shade in the morning than in the afternoon. As the environmental temperature increased the number of birds using the outdoor shade also increased. Overall 17 times more hens used the shelterbelt areas than the

Ranging Behaviour of Commercial Free-Range Laying Hens

PubMed Central

Chielo, Leonard Ikenna; Pike, Tom; Cooper, Jonathan

2016-01-01

Simple Summary Commercial free-range production has become a significant sector of the fresh egg market due to legislation banning conventional cages and consumer preference for products perceived as welfare friendly, as access to outdoor range can lead to welfare benefits such as greater freedom of movement and enhanced behavioural opportunities. This study investigated dispersal patterns, feather condition and activity of laying hens in three distinct zones of the range area; the apron area near shed; enriched zone 10–50 m from shed; and outer range beyond 50 m, in six flocks of laying hens under commercial free-range conditions varying in size between 4000 and 24,000 hens. Each flock was visited for four days to record number of hens in each zone, their behaviour, feather condition and nearest neighbour distances (NND), as well as record temperature and relative humidity during the visit. Temperature and relative humidity varied across the study period in line with seasonal variations and influenced the use of range with fewer hens out of shed as temperature fell or relative humidity rose. On average, 12.5% of the hens were observed on the range and most of these hens were recorded in the apron zone as hen density decreased rapidly with increasing distance from the shed. Larger flocks appeared to have a lower proportion of hens on range. The hens used the range more in the early morning followed by a progressive decrease through to early afternoon. The NND was greatest in the outer range and decreased towards the shed. Feather condition was generally good and hens observed in the outer range had the best overall feather condition. Standing, pecking, walking and foraging were the most commonly recorded behaviours and of these, standing occurred most in the apron whereas walking and foraging behaviours were recorded most in the outer range. This study supported the findings of previous studies that reported few hens in the range and greater use of areas closer

The fitness consequences of multiple-locus heterozygosity: the relationship between heterozygosity and growth rate in pitch pine (Pinus rigida Mill.)

Treesearch

Robin M. Bush; Peter E. Smouse; F. Thomas Ledig

1987-01-01

Positive correlations between measures of "fitness" and the number of electrophoretic loci for which an individual is heterozygous have been observed in many species. Two major hypotheses have been proposed to explain this phenomenon: inbreeding depression and overdominance. Until recently, there has been no way to distinguish between these hypotheses. The...

PERMANENT GENETIC RESOURCES: Isolation and characterization of polymorphic microsatellite loci in common evening primrose (Oenothera biennis).

PubMed

Larson, E L; Bogdanowicz, S M; Agrawal, A A; Johnson, M T J; Harrison, R G

2008-03-01

We developed nine polymorphic microsatellite loci for evening primrose (Oenothera biennis). These loci have two to 18 alleles per locus and observed heterozygosities ranging from 0 to 0.879 in a sample of 34 individuals. In a pattern consistent with the functionally asexual reproductive system of this species, 17/36 pairs of loci revealed significant linkage disequilibrium and three loci showed significant deviations from Hardy-Weinberg equilibrium. The loci will be informative in identifying genotypes in multigenerational field studies to assess changes in genotype frequencies. © 2007 The Authors.

Development and characterization of novel microsatellite loci for Lusitanian toadfish, Halobatrachus didactylus

PubMed Central

Fonseca, Paulo J.; Amorim, Maria Clara P.

2015-01-01

The Lusitanian toadfish Halobatrachus didactylus is an eastern Atlantic polygynous species showing male paternal care. In this paper we describe 5 novel microsatellite loci obtained by 454 GS-FLX Titanium pyrosequencing of a microsatellite-enriched library. The number of alleles per polymorphic locus varied between 2 and 4, and the observed heterozygosity ranged from 0.082 to 0.600. No significant deviation from Hardy–Weinberg equilibrium was found and there was no evidence for linkage disequilibrium. These markers will be of great value for paternity studies and population genetics of this species. PMID:25653909

Observation of seafloor crustal movement using the seafloor acoustic ranging on Kumano-nada

NASA Astrophysics Data System (ADS)

Osada, Y.; Kido, M.; Fujimoto, H.

2010-12-01

Along the Nankai Trough, where the Philippine Sea plate subducts under southeastern Japan with a convergence rate of about 65 mm/yr, large interplate thrust earthquakes of magnitude 8 class have occurred repeatedly with recurrence intervals of 100-200 years. About 60 years have passed since the last earthquakes happened in 1944 and 1946. Therefore it is important to monitor the tectonic activities in the Nankai Trough. Since most of the source region of the earthquakes is located beneath the ocean, an observation system is necessary in the offshore source region. We developed a seafloor acoustic ranging system to continuously monitor the seafloor crustal movement. We aim to monitor the activity in the splay faults in the rupture area of the Tonankai earthquake in the Nankai subduction zone. Slips along the active splay faults may be an important mechanism that the elastic strain caused by relative plate motion. We carried out two experiments, a short-term (one day) and a long-term (four month) experiments, to estimate the repeatability of acoustic measurements of this system. We deployed four PXPs (precision acoustic transponders) with about 600 m (M2-S1 baseline) and 920 m (M2-S2 base line) spacing in the long-term experiment. The standard deviation in acoustic measurements was about 1 cm on each baseline. In September 2008 we carried out an observation to monitor an active splay faults on Kumano-Nada prism slope. We deployed three PXPs with about 925 m (M1-S2 baseline) and 725 m (M1-S2 base line) spacing at the depth of some 2880 m. We recovered them in August 2010 to get data of acoustic measurements for 6 month and pressure measurements for 18 month. The round trip travel time shows a variation with peak-to-peak amplitude of about 1msec. We preliminarily collected the time series of round trip travel times using sound speed, which was estimated from measured temperature and pressure, and attitude data. We discuss the result of a variation of distance.

Genetic analysis of Black Tiger shrimp (Penaeus monodon) across its natural distribution range reveals more recent colonization of Fiji and other South Pacific islands

PubMed Central

Waqairatu, Salote S; Dierens, Leanne; Cowley, Jeff A; Dixon, Tom J; Johnson, Karyn N; Barnes, Andrew C; Li, Yutao

2012-01-01

The Black Tiger shrimp (Penaeus monodon) has a natural distribution range from East Africa to the South Pacific Islands. Although previous studies of Indo-Pacific P. monodon have found populations from the Indian Ocean and Australasia to differ genetically, their relatedness to South Pacific shrimp remains unknown. To address this, polymorphisms at eight shared microsatellite loci and haplotypes in a 418-bp mtDNA-CR (control region) sequence were examined across 682 P. monodon from locations spread widely across its natural range, including the South Pacific islands of Fiji, Palau, and Papua New Guinea (PNG). Observed microsatellite heterozygosities of 0.82–0.91, allele richness of 6.85–9.69, and significant mtDNA-CR haplotype variation indicated high levels of genetic diversity among the South Pacific shrimp. Analysis of microsatellite genotypes using a Bayesian STRUCTURE method segregated Indo-Pacific P. monodon into eight distinct clades, with Palau and PNG shrimp clustering among others from Southeast Asia and eastern Australia, respectively, and Fiji shrimp clustering as a distinct group. Phylogenetic analyses of mtDNA-CR haplotypes delineated shrimp into three groupings, with shrimp from Fiji again being distinct by sharing no haplotypes with other populations. Depending on regional location, the genetic structures and substructures identified from the genotyping and mtDNA-CR haplotype phylogeny could be explained by Metapopulation and/or Member–Vagrant type evolutionary processes. Neutrality tests of mutation-drift equilibrium and estimation of the time since population expansion supported a hypothesis that South Pacific P. monodon were colonized from Southeast Asia and eastern Australia during the Pleistocene period over 60,000 years ago when land bridges were more expansive and linked these regions more closely. PMID:22957205

Tetranucleotide microsatellite loci from the black bear (Ursus americanus)

USGS Publications Warehouse

Sanderlin, J.S.; Faircloth, B.C.; Shamblin, B.; Conroy, M.J.

2009-01-01

We describe primers and polymerase chain reaction conditions to amplify 21 tetranucleotide microsatellite DNA loci in black bears (Ursus americanus). We tested primers using individuals from two populations, one each in Georgia and Florida. Among individuals from Georgia (n = 29), primer pairs yielded an average of 2.9 alleles (range, one to four) and an average observed heterozygosity (HO) of 0.50 (range, 0.00 to 0.79). Among individuals from Florida (n = 19), primer pairs yielded an average of 5.7 alleles (range, one to 14) and an HO of 0.55 (range, 0.00 to 1.00). A comparison of previously developed markers with individuals from Georgia suggests that bear populations in Georgia and Florida have reduced allelic diversity relative to other populations. ?? 2008 The Authors.

Molecular Genetic Diversity of the Gyeongju Donggyeong Dog in Korea

PubMed Central

LEE, Eun-Woo; CHOI, Seong-Kyoon; CHO, Gil-Jae

2014-01-01

ABSTRACT The present study was conducted to analyze the genetic characteristics of the Donggyeong dog and establish parentage conservation systems for it by using 10 microsatellite markers recommended by the International Society for Animal Genetics (ISAG). A total of 369 dogs from 12 dog breeds including the Donggyeong dog were genotyped using 10 microsatellite loci. The number of alleles per locus varied from 5 to 10 with a mean value of 7.6 in the Donggyeong dog. The observed heterozygosity and expected heterozygosity ranged from 0.4706 to 0.9020 (mean 0.7657) and from 0.4303 to 0.8394 (mean 0.7266), respectively. The total exclusion probability of 10 microsatellite loci was 0.99955. Of the 10 microsatellite markers, the AHT121, AHTh260 and CXX279 markers had relatively high PIC values (≥0.7). This study found that there were specific alleles, 116 allele at AHT121 in the Donggyeong dog when compared with other dog breeds. Also, the results showed two (Korean native dogs and the foreign dog breeds) distinct clusters. The closest distance (0.1184) was observed between the Donggyeong dog and Jindo dog, and the longest distance (0.3435) was observed between the Donggyeong dog and Bulgae. The Korean native dog breeds have comparatively near genetic distances between each other. PMID:25030603

Internal roosting location is associated with differential use of the outdoor range by free-range laying hens.

PubMed

Pettersson, I C; Weeks, C A; Norman, K I; Knowles, T G; Nicol, C J

2018-04-01

1. In commercial free-range systems for laying hens, popholes to the outdoor range are often installed on one side of the house only. In multi-tier systems, it is possible that some individuals fail to access the range due to internal barriers to movement. 2. Five commercial multi-tier flocks from different units were studied. For each flock, two different colour markers were used to distinguish 200 birds roosting near the popholes (NP-Roost) and 200 birds roosting far from the popholes (FP-Roost) at night. The following day, counts of marked birds on the range and inside the house were performed. 3. Significantly more NP-Roost birds were observed in all areas of the outdoor range than FP-Roost birds the next day. Distance of FP area from the popholes was very strongly positively correlated with effect size in the adjacent range area. 4. Additionally, in the indoor area far from the popholes (FP) more FP-Roost birds were observed the next day than NP-Roost birds. In the indoor area near to the popholes (NP) more NP-Roost birds were observed the next day than FP-Roost birds. 5. These results suggest that roosting location is associated with differential range use when popholes are only available on one side of the shed as birds that roosted far from the popholes used the range less.

Receiver performance of laser ranging measurements between the Lunar Observer and a subsatellite for lunar gravity studies

NASA Technical Reports Server (NTRS)

Davidson, Frederic M.; Sun, Xiaoli

1992-01-01

The optimal receiver for a direct detection laser ranging system for slow Doppler frequency shift measurement is shown to consist of a phase tracking loop which can be implemented approximately as a phase lock loop with a 2nd or 3rd order loop filter. The laser transmitter consists of an AlGaAs laser diode at a wavelength of about 800 nm and is intensity modulated by a sinewave. The receiver performance is shown to be limited mainly by the preamplifier thermal noise when a silicon avalanche photodiode is used. A high speed microchannel plate photomultiplier tube is shown to outperform a silicon APD despite its relatively low quantum efficiency at wavelengths near 800 nm. The maximum range between the Lunar Observer and the subsatellite for lunar gravity studies is shown to be about 620 km when using a state-of-the-art silicon APD and about 1000 km when using a microchannel plate photomultiplier tube in order to achieve a relative velocity measurement accuracy of 1 millimeter per second. Other parameters such as the receiver time base jitter and drift also limit performance and have to be considered in the design of an actual system.

A General Model of Negative Frequency Dependent Selection Explains Global Patterns of Human ABO Polymorphism

PubMed Central

Villanea, Fernando A.; Safi, Kristin N.; Busch, Jeremiah W.

2015-01-01

The ABO locus in humans is characterized by elevated heterozygosity and very similar allele frequencies among populations scattered across the globe. Using knowledge of ABO protein function, we generated a simple model of asymmetric negative frequency dependent selection and genetic drift to explain the maintenance of ABO polymorphism and its loss in human populations. In our models, regardless of the strength of selection, models with large effective population sizes result in ABO allele frequencies that closely match those observed in most continental populations. Populations must be moderately small to fall out of equilibrium and lose either the A or B allele (Ne ≤ 50) and much smaller (N e ≤ 25) for the complete loss of diversity, which nearly always involved the fixation of the O allele. A pattern of low heterozygosity at the ABO locus where loss of polymorphism occurs in our model is consistent with small populations, such as Native American populations. This study provides a general evolutionary model to explain the observed global patterns of polymorphism at the ABO locus and the pattern of allele loss in small populations. Moreover, these results inform the range of population sizes associated with the recent human colonization of the Americas. PMID:25946124

Reaction of the high-latitude lower ionosphere to solar proton events from observations in the ELF range

NASA Astrophysics Data System (ADS)

Lebed', O. M.; Larchenko, A. V.; Pil'gaev, S. V.; Fedorenko, Yu. V.

2017-01-01

The reaction of the lower ionosphere to the solar proton events that occurred in 2011-2012 is studied in this paper based on the results of measurements of the propagation velocity and the E z / H τ ratio of the low-frequency electromagnetic pulses (atmospherics) in the ELF range at the high-latitude observatories Lovozero and Barentsburg. With numerical modeling methods, it is shown that horizontal local irregularities of the lower ionosphere conductivity profile could be a cause of the splashes in the E z / H τ ratio observed in the experiment during the solar proton event of March 7, 2012, which was a unique event in both the proton flux value and energy.

Development and characterization of microsatellite markers for Berberis thunbergii (Berberidaceae).

PubMed

Allen, Jenica M; Obae, Samuel G; Brand, Mark H; Silander, John A; Jones, Kenneth L; Nunziata, Schyler O; Lance, Stacey L

2012-05-01

Microsatellite markers were isolated and characterized in Berberis thunbergii, an invasive and ornamental shrub in the eastern United States, to assess genetic diversity among populations and potentially identify horticultural cultivars. A total of 12 loci were identified for the species. Eight of the loci were polymorphic and were screened in 24 individuals from two native (Tochigi and Ibaraki prefectures, Japan) and one invasive (Connecticut, USA) population and 21 horticultural cultivars. The number of alleles per locus ranged from three to seven, and observed heterozygosity ranged from 0.048 to 0.636. These new markers will provide tools for examining genetic relatedness of B. thunbergii plants in the native and invasive range, including phylogeographic studies and assessment of rapid evolution in the invasive range. These markers may also provide tools for examining hybridization with other related species in the invasive range.

Clonal evolution and clinical significance of copy number neutral loss of heterozygosity of chromosome arm 6p in acquired aplastic anemia.

PubMed

Betensky, Marisol; Babushok, Daria; Roth, Jacquelyn J; Mason, Philip J; Biegel, Jaclyn A; Busse, Tracy M; Li, Yimei; Lind, Curt; Papazoglou, Anna; Monos, Dimitri; Podsakoff, Gregory; Bessler, Monica; Olson, Timothy S

2016-01-01

Acquired aplastic anemia (aAA) results from the T cell-mediated autoimmune destruction of hematopoietic stem cells. Factors predicting response to immune suppression therapy (IST) or development of myelodysplastic syndrome (MDS) are beginning to be elucidated. Our recent data suggest most patients with aAA treated with IST develop clonal somatic genetic alterations in hematopoietic cells. One frequent acquired abnormality is copy-number neutral loss of heterozygosity on chromosome 6p (6p CN-LOH) involving the human leukocyte antigen (HLA) locus. We hypothesized that because 6p CN-LOH clones may arise from selective pressure to escape immune surveillance through deletion of HLA alleles, the development of 6p CN-LOH may affect response to IST. We used single nucleotide polymorphism array genotyping and targeted next-generation sequencing of HLA alleles to assess frequency of 6p CN-LOH, identity of HLA alleles lost through 6p CN-LOH, and impact of 6p CN-LOH on response to IST. 6p CN-LOH clones were present in 11.3% of patients, remained stable over time, and were not associated with development of MDS-defining cytogenetic abnormalities. Notably, no patient with 6p CN-LOH treated with IST achieved a complete response. In summary, clonal 6p CN-LOH in aAA defines a unique subgroup of patients that may provide insights into hematopoietic clonal evolution. Copyright © 2016 Elsevier Inc. All rights reserved.

Remote Sensing of Climate-Driven Range Shifts of Vegetation across North American Mountain Ranges

NASA Astrophysics Data System (ADS)

Kendrick, J. A.; Sax, D. F.; Kellner, J. R.

2015-12-01

Global climate change is driving shifts in local environmental conditions, and many organisms are projected to become poorly adapted to their current ranges. Some species may respond by gradually shifting their range limits to track environmental change. This adaptation strategy is expected to be most feasible in regions with sharp climatic gradients, such as mountain ranges. However, the extent to which this process is taking place is poorly understood, and some evidence suggests that shifts upwards in elevation might be more difficult than expected. Direct empirical evidence of range shifts in response to recent climate change could inform models and conservation strategies. Here we used Monte Carlo spectral unmixing of Landsat surface reflectance data to characterize changes in vegetation cover across major North American mountain ranges over the past 30 years. This approach allows us to observe changes in photosynthetic and nonphotosynthetic vegetation as well as absolute change in vegetation cover. We found evidence of a gradual increase in total vegetation cover at increasing elevations, but this pattern varied in its strength both within and among mountain ranges. We also observed more dramatic changes in vegetation type which differed strongly between regions with different climates. Our analysis shows that upslope range shift is a possible climate response in many cases, but that this process does not occur uniformly.

Spatiotemporal patterns of precipitation inferred from streamflow observations across the Sierra Nevada mountain range

NASA Astrophysics Data System (ADS)

Henn, Brian; Clark, Martyn P.; Kavetski, Dmitri; Newman, Andrew J.; Hughes, Mimi; McGurk, Bruce; Lundquist, Jessica D.

2018-01-01

Given uncertainty in precipitation gauge-based gridded datasets over complex terrain, we use multiple streamflow observations as an additional source of information about precipitation, in order to identify spatial and temporal differences between a gridded precipitation dataset and precipitation inferred from streamflow. We test whether gridded datasets capture across-crest and regional spatial patterns of variability, as well as year-to-year variability and trends in precipitation, in comparison to precipitation inferred from streamflow. We use a Bayesian model calibration routine with multiple lumped hydrologic model structures to infer the most likely basin-mean, water-year total precipitation for 56 basins with long-term (>30 year) streamflow records in the Sierra Nevada mountain range of California. We compare basin-mean precipitation derived from this approach with basin-mean precipitation from a precipitation gauge-based, 1/16° gridded dataset that has been used to simulate and evaluate trends in Western United States streamflow and snowpack over the 20th century. We find that the long-term average spatial patterns differ: in particular, there is less precipitation in the gridded dataset in higher-elevation basins whose aspect faces prevailing cool-season winds, as compared to precipitation inferred from streamflow. In a few years and basins, there is less gridded precipitation than there is observed streamflow. Lower-elevation, southern, and east-of-crest basins show better agreement between gridded and inferred precipitation. Implied actual evapotranspiration (calculated as precipitation minus streamflow) then also varies between the streamflow-based estimates and the gridded dataset. Absolute uncertainty in precipitation inferred from streamflow is substantial, but the signal of basin-to-basin and year-to-year differences are likely more robust. The findings suggest that considering streamflow when spatially distributing precipitation in complex terrain

Western diet enhances intestinal tumorigenesis in Min/+ mice, associating with mucosal metabolic and inflammatory stress and loss of Apc heterozygosity.

PubMed

Niku, Mikael; Pajari, Anne-Maria; Sarantaus, Laura; Päivärinta, Essi; Storvik, Markus; Heiman-Lindh, Anu; Suokas, Santeri; Nyström, Minna; Mutanen, Marja

2017-01-01

Western-type diet (WD) is a risk factor for colorectal cancer, but the underlying mechanisms are poorly understood. We investigated the interaction of WD and heterozygous mutation in the Apc gene on adenoma formation and metabolic and immunological changes in the histologically normal intestinal mucosa of Apc Min/+ (Min/+) mice. The diet used was high in saturated fat and low in calcium, vitamin D, fiber and folate. The number of adenomas was twofold higher in the WD mice compared to controls, but adenoma size, proliferation or apoptosis did not differ. The ratio of the Min to wild-type allele was higher in the WD mice, indicating accelerated loss of Apc heterozygosity (LOH). Densities of intraepithelial CD3ε + T lymphocytes and of mucosal FoxP3 + regulatory T cells were higher in the WD mice, implying inflammatory changes. Western blot analyses from the mucosa of the WD mice showed suppressed activation of the ERK and AKT pathways and a tendency for reduced activation of the mTOR pathway as measured in phosphoS6/S6 levels. The expression of pyruvate dehydrogenase kinase 4 was up-regulated in both mRNA and protein levels. Gene expression analyses showed changes in oxidation/reduction, fatty acid and monosaccharide metabolic pathways, tissue organization, cell fate and regulation of apoptosis. Together, our results suggest that the high-risk Western diet primes the intestine to tumorigenesis through synergistic effects in energy metabolism, inflammation and oxidative stress, which culminate in the acceleration of LOH of the Apc gene. Copyright © 2016 Elsevier Inc. All rights reserved.

Microsatellite loci for the stingless bee Melipona rufiventris (Hymenoptera: Apidae).

PubMed

Lopes, Denilce Meneses; D Silva, Filipe Oliveira; Fernandes Salomão, Tânia Maria; Campos, Lúcio Antônio D Oliveira; Tavares, Mara Garcia

2009-05-01

Eight microsatellite primers were developed from ISSR (intersimple sequence repeats) markers for the stingless bee Melipona rufiventris. These primers were tested in 20 M. rufiventris workers, representing a single population from Minas Gerais state. The number of alleles per locus ranged from 2 to 5 (mean = 2.63) and the observed and expected heterozygosity values ranged from 0.00 to 0.44 (mean = 0.20) and from 0.05 to 0.68 (mean = 0.31), respectively. Several loci were also polymorphic in M. quadrifasciata, M. bicolor, M. mandacaia and Partamona helleri and should prove useful in population studies of other stingless bees. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Development of eight polymorphic microsatellites for a Zn/Cd hyperaccumulator Sedum alfredii Hance (Crassulaceae).

PubMed

Huang, Hui-Run; Shu, Wen-Sheng; Mao, Zhi-Bin; Ge, Xue-Jun

2008-09-01

Sedum alfredii is a Zn/Cd hyperaccumulator distributed in East Asia. A total of eight polymorphic microsatellite markers were developed. These loci were screened in 25 individuals from one heavy metal-tolerant population and one nontolerant population, respectively. The average allele number of these markers was 5.25 per locus, ranging from two to nine. Population-specific alleles were found at each locus. The observed and expected heterozygosities ranged from 0.000 to 0.640 and from 0.451 to 0.819. Significant deviation from Hardy-Weinberg equilibrium was detected at both the species and the population level. No significant linkage disequilibrium was detected at population level. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Observations of Acyl Peroxy Nitrates During the Front Range Air Pollution and Photochemistry Éxperiment (FRAPPÉ)

NASA Astrophysics Data System (ADS)

Zaragoza, Jake; Callahan, Sara; McDuffie, Erin E.; Kirkland, Jeffrey; Brophy, Patrick; Durrett, Lindsi; Farmer, Delphine K.; Zhou, Yong; Sive, Barkley; Flocke, Frank; Pfister, Gabriele; Knote, Christoph; Tevlin, Alex; Murphy, Jennifer; Fischer, Emily V.

2017-11-01

We report on measurements of acyl peroxy nitrates (APNs) obtained from two ground sites and the NSF/National Center for Atmospheric Research C-130 aircraft during the 2014 Front Range Air Pollution and Photochemistry Éxperiment (FRAPPÉ). The relative abundance of the APNs observed at the Boulder Atmospheric Observatory (BAO) indicates that anthropogenic emissions of volatile organic compounds (VOCs) are the dominant drivers of photochemistry during days with the most elevated peroxyacetyl nitrate (PAN). Reduced major axis regression between propionyl peroxynitrate (PPN) and PAN observed at BAO and from the C-130 produced a slope of 0.21 (R2 = 0.92). Periods of lower PPN/PAN ratios ( 0.10) were associated with cleaner background air characterized by lower ammonia and formic acid abundances. The abundance of methacryloyl peroxynitrate relative to PAN only exceeded 0.05 at BAO when PAN mixing ratios were <300 parts per trillion by volume, implying low influence of isoprene oxidation during periods with substantial local PAN production. We show an example of a day (19 July) where high O3 was not accompanied by enhanced local PAN production. The contribution of biogenic VOCs to local O3 production on the other days in July with elevated O3 (22, 23, 28, and 29 July 2014) was small; evidence is provided in the high abundance of PPN to PAN (slopes between 0.18 and 0.26). The PAN chemistry observed from surface and aircraft platforms during FRAPPÉ implies that anthropogenic VOCs played a dominant role in PAN production during periods with the most O3 and that the relative importance of biogenic hydrocarbon chemistry decreased with increasing O3 production during FRAPPÉ.

DSS range delay calibrations: Current performance level

NASA Technical Reports Server (NTRS)

Spradlin, G. L.

1976-01-01

A means for evaluating Deep Space Station (DSS) range delay calibration performance was developed. Inconsistencies frequently noted in these data are resolved. Development of the DSS range delay data base is described. The data base is presented with comments regarding apparent discontinuities. Data regarding the exciter frequency dependence of the delay values are presented. The improvement observed in the consistency of current DSS range delay calibration data over the performance previously observed is noted.

The Clark Phase-able Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS

NASA Astrophysics Data System (ADS)

Halldórsson, Bjarni V.; Aguiar, Derek; Tarpine, Ryan; Istrail, Sorin

A phase transition is taking place today. The amount of data generated by genome resequencing technologies is so large that in some cases it is now less expensive to repeat the experiment than to store the information generated by the experiment. In the next few years it is quite possible that millions of Americans will have been genotyped. The question then arises of how to make the best use of this information and jointly estimate the haplotypes of all these individuals. The premise of the paper is that long shared genomic regions (or tracts) are unlikely unless the haplotypes are identical by descent (IBD), in contrast to short shared tracts which may be identical by state (IBS). Here we estimate for populations, using the US as a model, what sample size of genotyped individuals would be necessary to have sufficiently long shared haplotype regions (tracts) that are identical by descent (IBD), at a statistically significant level. These tracts can then be used as input for a Clark-like phasing method to obtain a complete phasing solution of the sample. We estimate in this paper that for a population like the US and about 1% of the people genotyped (approximately 2 million), tracts of about 200 SNPs long are shared between pairs of individuals IBD with high probability which assures the Clark method phasing success. We show on simulated data that the algorithm will get an almost perfect solution if the number of individuals being SNP arrayed is large enough and the correctness of the algorithm grows with the number of individuals being genotyped.

New progress of ranging technology at Wuhan Satellite Laser Ranging Station

NASA Technical Reports Server (NTRS)

Xia, Zhiz-Hong; Ye, Wen-Wei; Cai, Qing-Fu

1993-01-01

A satellite laser ranging system with an accuracy of the level of centimeter has been successfully developed at the Institute of Seismology, State Seismological Bureau with the cooperation of the Institute of Geodesy and Geophysics, Chinese Academy of Science. With significant improvements on the base of the second generation SLR system developed in 1985, ranging accuracy of the new system has been upgraded from 15 cm to 3-4 cm. Measuring range has also been expanded, so that the ETALON satellite with an orbit height of 20,000 km launched by the former U.S.S.R. can now be tracked. Compared with the 2nd generation SLR system, the newly developed system has the following improvements. A Q modulated laser is replaced by a mode-locked YAG laser. The new device has a pulse width of 150 ps and a repetition rate of 1-4 pps. A quick response photomultiplier has been adopted as the receiver for echo; for example, the adoption of the MCP tube has obviously reduced the jitter error of the transit time and has improved the ranging accuracy. The whole system is controlled by an IBM PC/XT Computer to guide automatic tracking and measurement. It can carry out these functions for satellite orbit calculation, real-time tracking and adjusting, data acquisition and the preprocessed of observing data, etc. The automatization level and reliability of the observation have obviously improved.

Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

PubMed Central

Liu, Jian-Bin; Wang, Fan; Lang, Xia; Zha, Xi; Sun, Xiao-Ping; Yue, Yao-Jing; Feng, Rui-Lin; Yang, Bo-Hui; Guo, Jian

2013-01-01

This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright’s F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding. PMID:25049794

Founder effects and the genetic structure of coulter pine

Treesearch

F. Thomas Ledig

2000-01-01

Mean expected heterozygosity at 33 isozyme loci decreased with latitude from 0.193 near the southern extreme of Coulter pine's range to 0.107 at its northern extreme. This decrease was paralleled by a loss of alleles north of the Peninsular Ranges of southern California. Fiftenn alleles dropped out along the roughly linear range, at points coincident with large...

Isolation and Characterization of Microsatellite Loci for Cotesia plutellae (Hymenoptera: Braconidae)

PubMed Central

Liu, Tiansheng; Ke, Fushi; You, Shijun; Chen, Wenbin; He, Weiyi; You, Minsheng

2017-01-01

Fourteen polymorphic microsatellite loci were isolated in this transcriptome-based data analysis for Cotesia plutellae, which is an important larval parasitoid of the worldwide pest Plutella xylostella. A subsequent test was performed for a wild C. plutellae population (N = 32) from Fuzhou, Fujian, southeastern China, to verify the effectiveness of the 14 microsatellite loci in future studies on C. plutellae genetic diversity. The observed number of alleles ranged from two to six. The expected and observed heterozygosity ranged from 0.123 to 0.316 and from 0.141 to 0.281, respectively. The polymorphism information content (PIC) value ranged from 0.272 to 0.622. Potentially due to the substructure of the sampled population, three of the 14 microsatellite loci deviated from Hardy—Weinberg equilibrium (HWE). Further, loci C6, C22, and C31 could be amplified in Cocobius fulvus and Encarsia japonica, suggesting the transferability of these three polymorphic loci to other species of Hymenoptera. PMID:28632152

Isolation of microsatellite loci for Rhodiola alsia (Crassulaceae), an important ethno-medicinal herb endemic to the Qinghai-Tibetan plateau.

PubMed

Zhang, F Q; Lei, S Y; Gao, Q B; Khan, G; Xing, R; Yang, H L; Chen, S L

2015-05-18

Rhodiola alsia, which has been used widely in traditional Chinese medicine for a considerable time, grows on moist habitats at high altitude near the snow line. Microsatellite loci were developed for R. alsia to investigate its population genetics. In total, 17 polymorphic microsatellites were developed based on ESTs from the Illumina HiSeq(TM) 2000 platform. The microsatellite loci were checked for variability using 80 individuals of R. alsia sampled from four locations on the Qinghai-Tibet Plateau. The total number of alleles per locus ranged from 10 to 20, and the observed heterozygosity ranged from 0.000 to 1.000. The null allele frequency ranged from 0.000 to 0.324. These microsatellites are expected to be helpful in future studies of population genetics in R. alsia and related species.

Development of microsatellite markers using next-generation sequencing for the columnar cactus Echinopsis chiloensis (Cactaceae).

PubMed

Ossa, Carmen G; Larridon, Isabel; Peralta, Gioconda; Asselman, Pieter; Pérez, Fernanda

2016-12-01

The aim of this study was to develop microsatellite markers as a tool to study population structure, genetic diversity and effective population size of Echinopsis chiloensis, an endemic cactus from arid and semiarid regions of Central Chile. We developed 12 polymorphic microsatellite markers for E. chiloensis using next-generation sequencing and tested them in 60 individuals from six sites, covering all the latitudinal range of this species. The number of alleles per locus ranged from 3 to 8, while the observed (Ho) and expected (He) heterozygosity ranged from 0.0 to 0.80 and from 0.10 to 0.76, respectively. We also detected significant differences between sites, with F ST values ranging from 0.05 to 0.29. Microsatellite markers will enable us to estimate genetic diversity and population structure of E. chiloensis in future ecological and phylogeographic studies.

Tetranucleotide microsatellite loci from the black bear (Ursus americanus).

PubMed

Sanderlin, Jamie Skvarla; Faircloth, Brant C; Shamblin, Brian; Conroy, Michael J

2009-01-01

We describe primers and polymerase chain reaction conditions to amplify 21 tetranucleotide microsatellite DNA loci in black bears (Ursus americanus). We tested primers using individuals from two populations, one each in Georgia and Florida. Among individuals from Georgia (n = 29), primer pairs yielded an average of 2.9 alleles (range, one to four) and an average observed heterozygosity (H(O) ) of 0.50 (range, 0.00 to 0.79). Among individuals from Florida (n = 19), primer pairs yielded an average of 5.7 alleles (range, one to 14) and an H(O) of 0.55 (range, 0.00 to 1.00). A comparison of previously developed markers with individuals from Georgia suggests that bear populations in Georgia and Florida have reduced allelic diversity relative to other populations. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Frequent loss of heterozygosity in two distinct regions, 8p23.1 and 8p22, in hepatocellular carcinoma

PubMed Central

Lu, Tomoe; Hano, Hiroshi; Meng, Chenxi; Nagatsuma, Keisuke; Chiba, Satoru; Ikegami, Masahiro

2007-01-01

AIM: To identify the precise location of putative tumor suppressor genes (TSGs) on the short arm of chromosome 8 in patients with hepatocellular carcinoma (HCC). METHODS: We used 16 microsatellite markers informative in Japanese patients, which were selected from 61 published markers, on 8p, to analyze the frequency of loss of heterozygosity (LOH) in each region in 33 cases (56 lesions) of HCC. RESULTS: The frequency of LOH at 8p23.2-21 with at least one marker was 63% (20/32) in the informative cases. More specifically, the frequency of LOH at 8p23.2, 8p23.1, 8p22, and 8p21 was 6%, 52%, 47%, and 13% in HCC cases. The LOH was significantly more frequent at 8p23.1 and 8p22 than the average (52% vs 22%, P = 0.0008; and 47% vs 22%, P = 0.004, respectively) or others sites, such as 8p23.2 (52% vs 6%, P = 0.003; 47% vs 22%, P = 0.004) and 8p21 (52% vs 13%, P = 0.001; 47% vs 13%, P = 0.005) in liver cancer on the basis of cases. Notably, LOH frequency was significantly higher at D8S277, D8S503, D8S1130, D8S552, D8S254 and D8S258 than at the other sites. However, no allelic loss was detected at any marker on 8p in the lesions of nontumor liver tissues. CONCLUSION: Deletion of 8p, especially the loss of 8p23.1-22, is an important event in the initiation or promotion of HCC. Our results should be useful in identifying critical genes that might lie at 8p23.1-22. PMID:17373745

Observations of Solar Energetic Particles from 3He-rich Events over a Wide Range of Heliographic Longitude

NASA Astrophysics Data System (ADS)

Wiedenbeck, M. E.; Mason, G. M.; Cohen, C. M. S.; Nitta, N. V.; Gómez-Herrero, R.; Haggerty, D. K.

2013-01-01

A prevailing model for the origin of 3He-rich solar energetic particle (SEP) events attributes particle acceleration to processes associated with the reconnection between closed magnetic field lines in an active region and neighboring open field lines. The open field from the small reconnection volume then provides a path along which accelerated particles escape into a relatively narrow range of angles in the heliosphere. The narrow width (standard deviation <20°) of the distribution of X-ray flare longitudes found to be associated with 3He-rich SEP events detected at a single spacecraft at 1 AU supports this model. We report multispacecraft observations of individual 3He-rich SEP events that occurred during the solar minimum time period from 2007 January through 2011 January using instrumentation carried by the two Solar Terrestrial Relations Observatory spacecraft and the Advanced Composition Explorer. We find that detections of 3He-rich events at pairs of spacecraft are not uncommon, even when their longitudinal separation is >60°. We present the observations of the 3He-rich event of 2010 February 7, which was detected at all three spacecraft when they spanned 136° in heliographic longitude. Measured fluences of 3He in this event were found to have a strong dependence on longitude which is well fit by a Gaussian with standard deviation ~48° centered at the longitude that is connected to the source region by a nominal Parker spiral magnetic field. We discuss several mechanisms for distributing flare-accelerated particles over a wide range of heliographic longitudes including interplanetary diffusion perpendicular to the magnetic field, spreading of a compact cluster of open field lines between the active region and the source surface where the field becomes radial and opens out into the heliosphere, and distortion of the interplanetary field by a preceding coronal mass ejection. Statistical studies of additional 3He-rich events detected at multiple spacecraft

High-Resolution Chromosome 3p Allelotyping of Breast Carcinomas and Precursor Lesions Demonstrates Frequent Loss of Heterozygosity and a Discontinuous Pattern of Allele Loss

PubMed Central

Maitra, Anirban; Wistuba, Ignacio I.; Washington, Constance; Virmani, Arvind K.; Ashfaq, Raheela; Milchgrub, Sara; Gazdar, Adi F.; Minna, John D.

2001-01-01

We performed high-resolution allelotyping for loss of heterozygosity (LOH) analysis on microdissected samples from 45 primary breast cancers, 47 mammary preneoplastic epithelial foci, and 18 breast cancer cell lines, using a panel of 27 polymorphic chromosome 3p markers. Allele loss in some regions of chromosome 3p was detected in 39 of 45 (87%) primary breast tumors. The 3p21.3 region had the highest frequency of LOH (69%), followed by 3p22-24 (61%), 3p21.2-21.3 (58%), 3p25 (48%), 3p14.2 (45%), 3p14.3 (41%), and 3p12 (35%). Analysis of all of the data revealed at least nine discrete intervals showing frequent allele loss: D3S1511-D3S1284 (U2020/DUTT1 region centered on D3S1274 with a homozygous deletion), D3S1300-D3S1234 [fragile histidine triad (FHIT)/FRA3B region centered on D3S1300 with a homozygous deletion], D3S1076-D3S1573, D3S4624/Luca2.1-D3S4597/P1.5, D3S1478-D3S1029, D3S1029 (with a homozygous deletion), D3S1612-D3S1537, D3S1293-D3S1597, and D3S1597-telomere; it is more than likely that additional localized regions of LOH not examined in this study also exist on chromosome 3p. In multiple cases, there was discontinuous allele loss at several 3p sites in the same tumor. Twenty-one of 47 (45%) preneoplastic lesions demonstrated 3p LOH, including 12 of 13 (92%) ductal carcinoma in situ, 2 of 7 (29%) apocrine metaplasia, and 7 of 25 (28%) usual epithelial hyperplasia. The 3p21.3 region had the highest frequency of LOH in preneoplastic breast epithelium (36%), followed by 3p21.2-21.3 (20%), 3p14.2/FHIT region (11%), 3p25 (10%), and 3p22-24 (5%). In 39 3p loci showing LOH in both the tumor and accompanying preneoplasia, 34 (87%) showed loss of the same parental allele (P = 1.2 × 10−6, cumulative binomial test). In addition, when 21 preneoplastic samples showing LOH were compared to their accompanying cancers, 67% were clonally related, 20% were potentially clonally related but were divergent, and 13% were clonally unrelated. Overall this demonstrated the

Prognostic value of loss of heterozygosity and sub-cellular localization of SMAD4 varies with tumor stage in colorectal cancer.

PubMed

Jia, Xu; Shanmugam, Chandrakumar; Paluri, Ravi K; Jhala, Nirag C; Behring, Michael P; Katkoori, Venkat R; Sugandha, Shajan P; Bae, Sejong; Samuel, Temesgen; Manne, Upender

2017-03-21

Although loss of heterozygosity (LOH) at chromosome location 18q21 and decreased expression of SMAD4 in invasive colorectal cancers (CRCs) correlate with poor patient survival, the prognostic value of LOH at 18q21 and sub-cellular localization of SMAD4 have not been evaluated in relation to tumor stage. Genomic DNA samples from 209 formalin-fixed, paraffin-embedded sporadic CRC tissues and their matching controls were analyzed for 18q21 LOH, and corresponding tissue sections were evaluated by immunohistochemistry for expression of SMAD4 and assessed for its sub-cellular localization (nuclear vs. cytoplasmic). In addition, 53 frozen CRCs and their matching control tissues were analyzed for their mutational status and mRNA expression of SMAD4. The phenotypic expression pattern and LOH status were evaluated for correlation with patient survival by the use of Kaplan-Meier and Cox regression models. LOH of 18q21 was detected in 61% of the informative cases. In 8% of the cases, missense point mutations were detected in Smad4. In CRCs, relative to controls, there was increased SMAD4 staining in the cytoplasm (74%) and decreased staining in the nuclei (37%). LOH of 18q21 and high cytoplasmic localization of SMAD4 were associated with shortened overall survival of Stage II patients, whereas low nuclear expression of SMAD4 was associated with worse survival, but only for patients with Stage III CRCs. LOH of 18q21 and high cytoplasmic localization of SMAD4 in Stage II CRCs and low nuclear SMAD4 in Stage III CRCs are predictors of shortened patient survival.

Prognostic value of loss of heterozygosity and sub-cellular localization of SMAD4 varies with tumor stage in colorectal cancer

PubMed Central

Jia, Xu; Shanmugam, Chandrakumar; Paluri, Ravi K.; Jhala, Nirag C.; Behring, Michael P.; Katkoori, Venkat R.; Sugandha, Shajan P.; Bae, Sejong; Samuel, Temesgen; Manne, Upender

2017-01-01

Background Although loss of heterozygosity (LOH) at chromosome location 18q21 and decreased expression of SMAD4 in invasive colorectal cancers (CRCs) correlate with poor patient survival, the prognostic value of LOH at 18q21 and sub-cellular localization of SMAD4 have not been evaluated in relation to tumor stage. Methods Genomic DNA samples from 209 formalin-fixed, paraffin-embedded sporadic CRC tissues and their matching controls were analyzed for 18q21 LOH, and corresponding tissue sections were evaluated by immunohistochemistry for expression of SMAD4 and assessed for its sub-cellular localization (nuclear vs. cytoplasmic). In addition, 53 frozen CRCs and their matching control tissues were analyzed for their mutational status and mRNA expression of SMAD4. The phenotypic expression pattern and LOH status were evaluated for correlation with patient survival by the use of Kaplan-Meier and Cox regression models. Results LOH of 18q21 was detected in 61% of the informative cases. In 8% of the cases, missense point mutations were detected in Smad4. In CRCs, relative to controls, there was increased SMAD4 staining in the cytoplasm (74%) and decreased staining in the nuclei (37%). LOH of 18q21 and high cytoplasmic localization of SMAD4 were associated with shortened overall survival of Stage II patients, whereas low nuclear expression of SMAD4 was associated with worse survival, but only for patients with Stage III CRCs. Conclusions LOH of 18q21 and high cytoplasmic localization of SMAD4 in Stage II CRCs and low nuclear SMAD4 in Stage III CRCs are predictors of shortened patient survival. PMID:28423626

Genetic diversity and differentiation of five Cuban cattle breeds using 30 microsatellite loci.

PubMed

Acosta, A C; Uffo, O; Sanz, A; Ronda, R; Osta, R; Rodellar, C; Martin-Burriel, I; Zaragoza, P

2013-02-01

Conservation and improvement strategies in farm animals should be based on a combination of genetic and phenotypic characteristics. Genotype data from 30 microsatellites were used to assess the genetic diversity and relationships among five Cuban cattle breeds (Siboney de Cuba, Criollo Cubano, Cebú Cubano, Mambí de Cuba and Taíno de Cuba). All microsatellite markers were highly polymorphic in all the breeds. The expected heterozygosity ranged from 0.67 ± 0.02 in the Taíno de Cuba breed to 0.75 ± 0.02 in the Mambí de Cuba breed, and the observed heterozygosity ranged from 0.66 ± 0.03 in the Cebú Cubano breed to 0.73 ± 0.02 in the Siboney de Cuba breed. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (F(ST)). The exact test for Hardy-Weinberg equilibrium within breeds showed a significant deviation in each breed (p < 0.0003) for one or more loci. The genetic distance and structure analysis showed that a significant amount of genetic variation is maintained in the local cattle population and that all breeds studied could be considered genetically distinct. The Siboney de Cuba and Mambí de Cuba breeds seem to be the most genetically related among the studied five breeds. © 2012 Blackwell Verlag GmbH.

Genetic diversity of the forage peanut in the Jequitinhonha, São Francisco, and Paranã River valleys of Brazil.

PubMed

Azêvedo, H S F S; Sousa, A C B; Martins, K; Oliveira, J C; Yomura, R B T; Silva, L M; Valls, J F M; Assis, G M L; Campos, T

2016-09-09

Arachis pintoi and A. repens are legumes with a high forage value that are used to feed ruminants in consortium systems. Not only do they increase the persistence and quality of pastures, they are also used for ornamental and green cover. The objective of this study was to analyze microsatellite markers in order to access the genetic diversity of 65 forage peanut germplasm accessions in the section Caulorrhizae of the genus Arachis in the Jequitinhonha, São Francisco and Paranã River valleys of Brazil. Fifty-seven accessions of A. pintoi and eight of A. repens were analyzed using 17 microsatellites, and the observed heterozygosity (H O ), expected heterozygosity (H E ), number of alleles per locus, discriminatory power, and polymorphism information content were all estimated. Ten loci (58.8%) were polymorphic, and 125 alleles were found in total. The H E ranged from 0.30 to 0.94, and H O values ranged from 0.03 to 0.88. By using Bayesian analysis, the accessions were genetically differentiated into three gene pools. Neither the unweighted pair group method with arithmetic mean nor a neighbor-joining analysis clustered samples into species, origin, or collection area. These results reveal a very weak genetic structure that does not form defined clusters, and that there is a high degree of similarity between the two species.

Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

NASA Astrophysics Data System (ADS)

Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

2014-08-01

Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

Isolation and characterization of eight novel microsatellite loci in the double-crested cormorant (Phalacrocorax auritus)

USGS Publications Warehouse

Mercer, Dacey; Haig, Susan; Mullins, Thomas

2010-01-01

We describe the isolation and characterization of eight microsatellite loci from the double-crested cormorant (Phalacrocorax auritus). Genetic variability was assessed using 60 individuals from three populations. All loci were variable with the number of alleles ranging from two to 17 per locus, and observed heterozygosity varying from 0.05 to 0.89. No loci showed signs of linkage disequilibrium and all loci conformed to Hardy–Weinberg equilibrium frequencies. Further, all loci amplified and were polymorphic in two related Phalacrocorax species. These loci should prove useful for population genetic studies of the double-crested cormorant and other pelecaniform species.

Isolation and characterization of microsatellite loci for alligator gar (Atractosteus spatula) and their variability in two other species (Lepisosteus oculatus and L. osseus) of Lepisosteidae

USGS Publications Warehouse

Moyer, G.R.; Sloss, Brian L.; Kreiser, B.R.; Feldheim, K.A.

2009-01-01

We report on the isolation of 17 polymorphic microsatellite loci from alligator gar (Atractosteus spatula), a large-bodied species that has experienced population declines across much of its range. These loci possessed 2-19 alleles and observed heterozygosities of 0-0.974. All loci conformed to Hardy-Weinberg equilibrium expectations, and none exhibited linkage disequilibrium. Nine and eight of these loci were found to be polymorphic in the related species Lepisosteus oculatus and L. osseus, respectively. These microsatellite loci should prove useful in conservation efforts of A. spatula through the study of population structure and hatchery broodstock management. ?? 2009 Blackwell Publishing Ltd.

Isolation and characterization of polymorphic microsatellite loci in the green leafhopper Empoasca vitis Goethe (Homoptera).

PubMed

Papura, D; Giresse, X; Chauvin, B; Caron, H; Delmotte, F; VAN Helden, M

2009-05-01

Eight dinucleotide microsatellite loci were isolated and characterized within the green leafhopper Empoasca vitis (Goethe) using an enrichment cloning procedure. Primers were tested on 171 individuals collected in the southwest of France from the vine plants. The identified loci were polymorphic, with allelic diversity ranging from two to 18 alleles per locus. Observed heterozygosities were from 0.021 to 0.760. These microsatellite markers should prove to be a useful tool for estimating the population genetic structure, host-plant specialization and migration capacity of this insect. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Evaluation of Gravitational Field Models Based on the Laser Range Observation of Low Earth Orbit Satellites

NASA Astrophysics Data System (ADS)

Hong-bo, Wang; Chang-yin, Zhao; Wei, Zhang; Jin-wei, Zhan; Sheng-xian, Yu

2016-07-01

The Earth gravitational field model is one of the most important dynamic models in satellite orbit computation. Several space gravity missions made great successes in recent years, prompting the publishing of several gravitational filed models. In this paper, two classical (JGM3, EGM96) and four latest (EIGEN-CHAMP05S, GGM03S, GOCE02S, EGM2008) models are evaluated by employing them in the precision orbit determination (POD) and prediction. These calculations are performed based on the laser ranging observation of four Low Earth Orbit (LEO) satellites, including CHAMP, GFZ-1, GRACE-A, and SWARM-A. The residual error of observation in POD is adopted to describe the accuracy of six gravitational field models. The main results we obtained are as follows. (1) For the POD of LEOs, the accuracies of 4 latest models are at the same level, and better than those of 2 classical models; (2) Taking JGM3 as reference, EGM96 model's accuracy is better in most situations, and the accuracies of the 4 latest models are improved by 12%-47% in POD and 63% in prediction, respectively. We also confirm that the model's accuracy in POD is enhanced with the increasing degree and order if they are smaller than 70, and when they exceed 70, the accuracy keeps constant, implying that the model's degree and order truncated to 70 are sufficient to meet the requirement of LEO computation of centimeter precision.

The SEASAT altimeter wet tropospheric range correction revisited

NASA Technical Reports Server (NTRS)

Tapley, D. B.; Lundberg, J. B.; Born, G. H.

1984-01-01

An expanded set of radiosonde observations was used to calculate the wet tropospheric range correction for the brightness temperature measurements of the SEASAT scanning multichannel microwave radiometer (SMMR). The accuracy of the conventional algorithm for wet tropospheric range correction was evaluated. On the basis of the expanded observational data set, the algorithm was found to have a bias of about 1.0 cm, and a standard deviation 2.8 cm. In order to improve the algorithm, the exact linear, quadratic and logarithmic relationships between brightness temperatures and range corrections were determined. Various combinations of measurement parameters were used to reduce the standard deviation between SEASAT SMMR and radiosonde observations to about 2.1 cm. The performance of various range correction formulas is compared in a table.

Are fish outside their usual ranges early indicators of climate-driven range shifts?

PubMed

Fogarty, Hannah E; Burrows, Michael T; Pecl, Gretta T; Robinson, Lucy M; Poloczanska, Elvira S

2017-05-01

Shifts in species ranges are a global phenomenon, well known to occur in response to a changing climate. New species arriving in an area may become pest species, modify ecosystem structure, or represent challenges or opportunities for fisheries and recreation. Early detection of range shifts and prompt implementation of any appropriate management strategies is therefore crucial. This study investigates whether 'first sightings' of marine species outside their normal ranges could provide an early warning of impending climate-driven range shifts. We examine the relationships between first sightings and marine regions defined by patterns of local climate velocities (calculated on a 50-year timescale), while also considering the distribution of observational effort (i.e. number of sampling days recorded with biological observations in global databases). The marine trajectory regions include climate 'source' regions (areas lacking connections to warmer areas), 'corridor' regions (areas where moving isotherms converge), and 'sink' regions (areas where isotherms locally disappear). Additionally, we investigate the latitudinal band in which first sightings were recorded, and species' thermal affiliations. We found that first sightings are more likely to occur in climate sink and 'divergent' regions (areas where many rapid and diverging climate trajectories pass through) indicating a role of temperature in driving changes in marine species distributions. The majority of our fish first sightings appear to be tropical and subtropical species moving towards high latitudes, as would be expected in climate warming. Our results indicate that first sightings are likely related to longer-term climatic processes, and therefore have potential use to indicate likely climate-driven range shifts. The development of an approach to detect impending range shifts at an early stage will allow resource managers and researchers to better manage opportunities resulting from range

Hardware test program for evaluation of baseline range/range rate sensor concept

NASA Technical Reports Server (NTRS)

Pernic, E.

1985-01-01

The test program Phase II effort provides additional design information in terms of range and range rate (R/R) sensor performance when observing and tracking a typical spacecraft target. The target used in the test program was a one-third scale model of the Hubble Space Telescope (HST) available at the MSFC test site where the tests were performed. A modified Bendix millimeter wave radar served as the R/R sensor test bed for evaluation of range and range rate tracking performance, and generation of radar signature characteristics of the spacecraft target. A summary of program test results and conclusions are presented along with detailed description of the Bendix test bed radar with accompaning instrumentation. The MSFC test site and facilities are described. The test procedures used to establish background levels, and the calibration procedures used in the range accuracy tests and RCS (radar cross section) signature measurements, are presented and a condensed version of the daily log kept during the 5 September through 17 September test period is also presented. The test program results are given starting with the RCS signature measurements, then continuing with range measurement accuracy test results and finally the range and range rate tracking accuracy test results.

GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays

PubMed Central

Li, Ao; Liu, Zongzhi; Lezon-Geyda, Kimberly; Sarkar, Sudipa; Lannin, Donald; Schulz, Vincent; Krop, Ian; Winer, Eric; Harris, Lyndsay; Tuck, David

2011-01-01

There is an increasing interest in using single nucleotide polymorphism (SNP) genotyping arrays for profiling chromosomal rearrangements in tumors, as they allow simultaneous detection of copy number and loss of heterozygosity with high resolution. Critical issues such as signal baseline shift due to aneuploidy, normal cell contamination, and the presence of GC content bias have been reported to dramatically alter SNP array signals and complicate accurate identification of aberrations in cancer genomes. To address these issues, we propose a novel Global Parameter Hidden Markov Model (GPHMM) to unravel tangled genotyping data generated from tumor samples. In contrast to other HMM methods, a distinct feature of GPHMM is that the issues mentioned above are quantitatively modeled by global parameters and integrated within the statistical framework. We developed an efficient EM algorithm for parameter estimation. We evaluated performance on three data sets and show that GPHMM can correctly identify chromosomal aberrations in tumor samples containing as few as 10% cancer cells. Furthermore, we demonstrated that the estimation of global parameters in GPHMM provides information about the biological characteristics of tumor samples and the quality of genotyping signal from SNP array experiments, which is helpful for data quality control and outlier detection in cohort studies. PMID:21398628

No evidence for effects of infection with the amphibian chytrid fungus on populations of yellow-bellied toads.

PubMed

Wagner, Norman; Neubeck, Claus; Guicking, Daniela; Finke, Lennart; Wittich, Martin; Weising, Kurt; Geske, Christian; Veith, Michael

2017-02-08

The parasitic chytrid fungus Batrachochytrium dendrobatidis (Bd) can cause the lethal disease chytridiomycosis in amphibians and therefore may play a role in population declines. The yellow-bellied toad Bombina variegata suffered strong declines throughout western and northwestern parts of its range and is therefore listed as highly endangered for Germany and the federal state of Hesse. Whether chytridiomycosis may play a role in the observed local declines of this strictly protected anuran species has never been tested. We investigated 19 Hessian yellow-bellied toad populations for Bd infection rates, conducted capture-mark-recapture studies in 4 of them over 2 to 3 yr, examined survival histories of recaptured infected individuals, and tested whether multi-locus heterozygosity of individuals as well as expected heterozygosity and different environmental variables of populations affect probabilities of Bd infection. Our results show high prevalence of Bd infection in Hessian yellow-bellied toad populations, but although significant decreases in 2 populations could be observed, no causative link to Bd as the reason for this can be established. Mass mortalities or obvious signs of disease in individuals were not observed. Conversely, we show that growth of Bd-infected populations is possible under favorable habitat conditions and that most infected individuals could be recaptured with improved body indices. Neither genetic diversity nor environmental variables appeared to affect Bd infection probabilities. Hence, genetically diverse amphibian specimens and populations may not automatically be less susceptible for Bd infection.

Loss of genetic diversity and inbreeding in Kashmir red deer (Cervus elaphus hanglu) of Dachigam National Park, Jammu & Kashmir, India

PubMed Central

2013-01-01

Background Hangul (Cervus elaphus hanglu), the eastern most subspecies of red deer, is now confined only to the mountains in the Kashmir region of Jammu & Kashmir State of India. It is of great conservation significance as this is the last and only hope for Asiatic survivor of the red deer species in India. Wild population of free ranging hangul deer inhabiting in and around Dachigam National Park was genetically assessed in order to account for constitutive genetic attributes of hangul population using microsatellite markers. Results In a pool of 36 multi-locus genotypes, 30 unique individuals were identified based on six microsatellite loci. The estimated cumulative probability of identity assuming all individuals were siblings (PID sibs) was 0.009 (9 in 1000). Altogether, 49 different alleles were observed with mean (± s.e.) allelic number of 8.17 ± 1.05, ranging from 5 to 11 per locus. The observed heterozygosity ranged between 0.08 and 0.83, with mean 0.40 ± 0.11 and the inbreeding coefficient ranged between −0.04 and 0.87 with mean 0.38 ± 0.15. Majority of loci (5/6) were found to be informative (PIC value > 0.5). All loci deviated from Hardy-Weinberg equilibrium except Ca-38 (P > 0.05) and none of the pairs of loci showed significant linkage disequilibrium except the single pair of Ca-30 and Ca-43 (P < 0.05). Conclusions The preliminary findings revealed that hangul population is significantly inbred and exhibited a low genetic diversity in comparison to other deer populations of the world. We suggest prioritizing the potential individuals retaining high heterozygosity for ex situ conservation and genetic monitoring of the hangul population should be initiated covering the entire distribution range to ensure the long term survival of hangul. We speculate further ignoring genetics attributes may lead to a detrimental effect which can negatively influence the reproductive fitness and survivorship of the hangul population in the

Isolation and Characterization of 21 Microsatellite Loci in Cardiocrinum giganteum var. yunnanense (Liliaceae), an Important Economic Plant in China

PubMed Central

Li, Rong; Yang, Jie; Yang, Junbo; Dao, Zhiling

2012-01-01

Twenty-one microsatellite markers from the genome of Cardiocrinum giganteum var. yunnanense, an important economic plant in China, were developed with a fast isolation protocol by amplified fragment length polymorphism of sequences containing repeats (FIASCO). Polymorphism within each locus was assessed in 24 wild individuals from Gaoligong Mountains in western Yunnan Province, China. The number of alleles per locus ranged from 2 to 4 with a mean of 2.9. The expected and observed levels of heterozygosity ranged from 0.042 to 0.726 and from 0.000 to 1.000, with averages of 0.44 and 0.31, respectively. These polymorphic microsatellite markers should prove useful in population genetics studies and assessments of genetic variation to develop conservation and management strategies for this species. PMID:22408400

Isolation and characterization of polymorphic microsatellite markers in the black spiny tailed iguana (Ctenosaura pectinata) and their cross-utility in other Ctenosaura.

PubMed

Zarza, Eugenia; Pereyra, Ricardo T; Reynoso, Victor H; Emerson, Brent C

2009-01-01

We isolated and characterized 10 polymorphic microsatellite loci from the Mexican black iguana (Ctenosaura pectinata) and assessed levels of polymorphism in sampling sites located in the northern areas of the species' distribution range. Two to 19 alleles per locus and observed heterozygosity ranging from 0.15 to 0.96 were detected. These markers will be useful to describe population genetic structure, the extent of gene flow in contact zones, to study the mating system of the species and to address conservation genetics issues. Additionally, we evaluated the potential utility of these markers for studies of other species within the genus Ctenosaura (i.e. C. hemilopha, C. similis and C. oaxacana). © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Novel microsatellite loci for studies of Thamnophis Gartersnake genetic identity and hybridization

USGS Publications Warehouse

Sloss, Brian L.; Schuurman, Gregor W.; Paloski, Rori A.; Boyle, Owen D.; Kapfer, Joshua M.

2012-01-01

Butler’s Gartersnakes (BGS; Thamnophis butleri) are confined to open and semi-open canopy wetlands and adjacent uplands, habitats under threat of development in Wisconsin. To address issues of species identity and putative hybridization with congeneric snakes, a suite of 18 microsatellite loci capable of cross-species amplification of Plains Gartersnakes (T. radix) and Common Gartersnakes (T. sirtalis) was developed. All loci were polymorphic in BGS with mean number of alleles per locus of 16.11 (range = 3–41) and mean observed heterozygosity of 0.659 (range = 0.311–0.978). Loci amplified efficiently in the congeneric species with high levels of intra- and inter-specific variation. These loci will aid ongoing efforts to effectively identify and manage BGS in Wisconsin.

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

PubMed Central

Hane, James K.; Anderson, Jonathan P.; Williams, Angela H.; Sperschneider, Jana; Singh, Karam B.

2014-01-01

Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA. We also observed SNP-level “hypermutation” of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the

Identification and characterization of the highly polymorphic locus D14S739 in the Han Chinese population

PubMed Central

Shao, Chengchen; Zhang, Yaqi; Zhou, Yueqin; Zhu, Wei; Xu, Hongmei; Liu, Zhiping; Tang, Qiqun; Shen, Yiwen; Xie, Jianhui

2015-01-01

Aim To systemically select and evaluate short tandem repeats (STRs) on the chromosome 14 and obtain new STR loci as expanded genotyping markers for forensic application. Methods STRs on the chromosome 14 were filtered from Tandem Repeats Database and further selected based on their positions on the chromosome, repeat patterns of the core sequences, sequence homology of the flanking regions, and suitability of flanking regions in primer design. The STR locus with the highest heterozygosity and polymorphism information content (PIC) was selected for further analysis of genetic polymorphism, forensic parameters, and the core sequence. Results Among 26 STR loci selected as candidates, D14S739 had the highest heterozygosity (0.8691) and PIC (0.8432), and showed no deviation from the Hardy-Weinberg equilibrium. 14 alleles were observed, ranging in size from 21 to 34 tetranucleotide units in the core region of (GATA)9-18 (GACA)7-12 GACG (GACA)2 GATA. Paternity testing showed no mutations. Conclusion D14S739 is a highly informative STR locus and could be a suitable genetic marker for forensic applications in the Han Chinese population. PMID:26526885

Development and characterization of microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla

PubMed Central

Byers, James E.; Greig, Thomas W.; Strand, Allan E.; Weinberger, Florian

2015-01-01

Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid–diploid primary producer. PMID:26339541

Development and characterization of EST-SSR markers for Begonia luzhaiensis (Begoniaceae)1

PubMed Central

Tseng, Yu-Hsin; Huang, Han-Yau; Xu, Wei-Bin; Yang, Hsun-An; Liu, Yan; Peng, Ching-I; Chung, Kuo-Fang

2017-01-01

Premise of the study: Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure. Methods and Results: Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.804 with averages of 0.370 and 0.404, respectively. Five loci could be successfully amplified in B. leprosa. Conclusions: The expressed sequence tag–simple sequence repeat markers are the first specifically developed for B. luzhaiensis and the first developed in Begonia sect. Coelocentrum. These markers will be useful for future studies of the genetic structure and phylogeography of B. luzhaiensis. PMID:28529834

Genetic variability in the Florida manatee (Trichechus manatus)

USGS Publications Warehouse

McClenaghan, Leroy R.; O'Shea, Thomas J.

1988-01-01

Tissue was obtained from 59 manatee (Trichechus manatus) carcasses salvaged from 20 counties in Florida. Allozyme phenotypes at 24 structural loci were determined by gel electrophoresis. Averages for the proportion of polymorphic loci and mean heterozygosity were 0.300 (range, 0.167-0.417) and 0.050 (range, 0.028-0.063), respectively. These estimates are equivalent to or higher than those generally reported for other species of marine mammals and do not support the hypothesis that body size and heterozygosity in mammals are related inversely. Among-region gene diversity accounted for only 4% of the total diversity. High rates of gene flow probably account for genetic homogeneity across regions. An F-statistic analysis revealed a general tendency toward excess homozygosity within regions. Management efforts to prevent future reductions in population size that would erode existing genic diversity should continue.

First Experiences Using Small Unmanned Aerial Vehicles for Volcano Observation in the Visible Range

NASA Astrophysics Data System (ADS)

Buschmann, M.; Krüger, L.; Bange, J.

2007-05-01

Many of the most active volcanoes in the world are located in Middle and South America. While permanently installed sensors for seismicity give reliable supervision of volcanic activities, they lack the possibility to determine occurrence and extent of surface activities. Both from the point of science and civil protection, visible documentation of activities is of great interest. While satellites and manned aircraft already offer many possibilities, they also have disadvantages like delayed or poor image data availability or high costs. The Institute of Aerospace Systems of the Technical University of Braunschweig, in collaboration with the spin-off company Mavionics, developed a family of extremely small and lightweight Unmanned Aerial Vehicles (UAV), with the smallest aircraft weighting only 550~g (19~ounces) at a wing span of 50 cm (20~inch). These aircraft are operating completely automatically, controlled by a highly miniaturized autopilot system. Flight mission is defined by a list of GPS waypoints using a conventional notebook. While in radio range, current position and status of the aircraft is displayed on the notebook and waypoints can easily be changed by the user. However, when radio connection is not available, the aircraft operates on its on, completing the flight mission automatically. This greatly increases the operating range of the system. Especially for the purpose of volcano observation in South America, the aircraft Carolo~P330 was developed, weighting 5~kg (11~pounds) at a wing span of 3.3~m ( 11~ft). The whole system can be easily carried by car and the electric propulsion system avoids handling of flammable liquids. The batteries can be recharged in the field. Carolo~P330 has an endurance of up to 90~minutes at a flight speed of 25~m/s, giving it a maximum range of 67 km (41~miles). It was especially designed to operate under harsh conditions. The payload is a digital still camera, which delivers aerial images with a resolution of up to 8

Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity.

PubMed

Leisner, Courtney P; Hamilton, John P; Crisovan, Emily; Manrique-Carpintero, Norma C; Marand, Alexandre P; Newton, Linsey; Pham, Gina M; Jiang, Jiming; Douches, David S; Jansky, Shelley H; Buell, C Robin

2018-05-01

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825 767 562 bp in 8260 scaffolds with an N50 scaffold size of 713 602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49 124 high-confidence gene models representing 37 740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158 367 Solanaceae genes and 1897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

[Early loss of heterozygosity on chromosome arm 16q in flat epithelial atypia of the breast. Detection by microsatellite analyses].

PubMed

Schmidt, H; Dahrenmöller, C; Agelepoulos, K; Hungermann, D; Böcker, W

2008-11-01

With the improvement of breast carcinoma screening, pre-malignant cell lesions such as flat epithelial atypia (FEA) are detected more frequently. Several studies have demonstrated that FEA show features of a ductal neoplasia, but is it really a precursor lesion? We have started a comparative genetic analysis of a panel of nine microsatellite markers on six different chromosomal regions to investigate whether FEAs show the same characteristic genetic alterations as ductal carcinomas in situ (DCISs) and invasive carcinoma of the breast. FEAs, DCISs and invasive carcinomas of the same patients were microdissected using PALM micro laser technology. DNA was isolated using the QIAamp DNA Micro Kit (QIAGEN). We have investigated a set of the polymorphic microsatellite markers D7S522, D8S522, NEFL, D10S541 (PTEN), D13S153 (RB1), D16S400, D16S402, D16S422 and D17S855 (BRCA1) using multiplex PCR for the detection of allelic imbalances. Most of the investigated FEAs showed a lower frequency of loss of heterozygosity than associated DCISs or invasive carcinomas. However, we were able to detect the same alterations in FEAs as in DCISs or invasive carcinomas in a number of cases. Notably, the microsatellite marker on 16q showed more prevalent allelic imbalances in FEAs than the other investigated markers. One of the hallmarks in the pathogenesis of a large subgroup of invasive breast carcinomas is the early loss of chromosome arm 16q. In this study, we were able to detect frequent genetic alterations on chromosome 16q in FEAs, associated DCISs and invasive carcinomas. This suggests that FEA is a precursor lesion in the low-grade pathway.

A Maximum-Likelihood Method to Correct for Allelic Dropout in Microsatellite Data with No Replicate Genotypes

PubMed Central

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

2012-01-01

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

Range contraction in large pelagic predators

PubMed Central

Worm, Boris; Tittensor, Derek P.

2011-01-01

Large reductions in the abundance of exploited land predators have led to significant range contractions for those species. This pattern can be formalized as the range–abundance relationship, a general macroecological pattern that has important implications for the conservation of threatened species. Here we ask whether similar responses may have occurred in highly mobile pelagic predators, specifically 13 species of tuna and billfish. We analyzed two multidecadal global data sets on the spatial distribution of catches and fishing effort targeting these species and compared these with available abundance time series from stock assessments. We calculated the effort needed to reliably detect the presence of a species and then computed observed range sizes in each decade from 1960 to 2000. Results suggest significant range contractions in 9 of the 13 species considered here (between 2% and 46% loss of observed range) and significant range expansions in two species (11–29% increase). Species that have undergone the largest declines in abundance and are of particular conservation concern tended to show the largest range contractions. These include all three species of bluefin tuna and several marlin species. In contrast, skipjack tuna, which may have increased its abundance in the Pacific, has also expanded its range size. These results mirror patterns described for many land predators, despite considerable differences in habitat, mobility, and dispersal, and imply ecological extirpation of heavily exploited species across parts of their range. PMID:21693644

Genetic variation at microsatellite loci in the tropical herb Aphelandra aurantiaca (Acanthaceae).

PubMed

Suárez-Montes, Pilar; Tapia-López, Rosalinda; Núñez-Farfán, Juan

2015-11-01

To assess the effect of forest fragmentation on genetic variation and population structure of Aphelandra aurantiaca (Acanthaceae), a tropical and ornamental herbaceous perennial plant, we developed the first microsatellite primers for the species. Fourteen microsatellite markers were isolated and characterized from A. aurantiaca genomic libraries enriched for di-, tri-, and tetranucleotide repeat motifs. Polymorphism was evaluated in 107 individuals from four natural populations. Twelve out of 14 genetic markers were polymorphic. The number of alleles per locus ranged from two to 12, and the observed and expected heterozygosities ranged from 0.22 to 0.96 and from 0.20 to 0.87, respectively. Fixation indices ranged from -0.41 to 0.44. These newly developed microsatellite markers for A. aurantiaca will be useful for future population genetic studies, specifically to detect the possible loss of genetic diversity due to habitat fragmentation.

Characterization of 21 microsatellite markers from cogongrass, Imperata cylindrica (Poaceae), a weed species distributed worldwide.

PubMed

Chiang, Yu-Chung; Tsai, Chi-Chu; Hsu, Tsai-Wen; Chou, Chang-Hung

2012-11-01

Microsatellite loci were developed from Imperata cylindrica, a traditional medicinal herb in Asia and among the top 10 worst invasive weeds in the world, to aid in the identification of the limits of asexual clonal individuals. A total of 21 microsatellite markers, including 18 polymorphic and three monomorphic loci, were developed from I. cylindrica using a magnetic bead enrichment protocol. The primers amplified dinucleotide, trinucleotide, and complex repeats. The number of alleles ranged from one to 19 per locus, with an observed heterozygosity ranging from 0.09 to 1.00. Several loci deviated significantly from the within-population Hardy-Weinberg equilibrium as a result of asexual clonal reproduction. These polymorphic markers should be useful tools in further studies on the identification of the range of clonal reproduction units and the selection and classification of the medicinal cultivar.

The effect of entrainment through atmospheric boundary layer growth on observed and modeled surface ozone in the Colorado Front Range

NASA Astrophysics Data System (ADS)

Kaser, L.; Patton, E. G.; Pfister, G. G.; Weinheimer, A. J.; Montzka, D. D.; Flocke, F.; Thompson, A. M.; Stauffer, R. M.; Halliday, H. S.

2017-06-01

Ozone concentrations at the Earth's surface are controlled by meteorological and chemical processes and are a function of advection, entrainment, deposition, and net chemical production/loss. The relative contributions of these processes vary in time and space. Understanding the relative importance of these processes controlling surface ozone concentrations is an essential component for designing effective regulatory strategies. Here we focus on the diurnal cycle of entrainment through atmospheric boundary layer (ABL) growth in the Colorado Front Range. Aircraft soundings and surface observations collected in July/August 2014 during the DISCOVER-AQ/FRAPPÉ (Deriving Information on Surface conditions from Column and Vertically Resolved Observations Relevant to Air Quality/Front Range Air Pollution and Photochemistry Éxperiment) campaigns and equivalent data simulated by a regional chemical transport model are analyzed. Entrainment through ABL growth is most important in the early morning, fumigating the surface at a rate of 5 ppbv/h. The fumigation effect weakens near noon and changes sign to become a small dilution effect in the afternoon on the order of -1 ppbv/h. The chemical transport model WRF-Chem (Weather Research and Forecasting Model with chemistry) underestimates ozone at all altitudes during this study on the order of 10-15 ppbv. The entrainment through ABL growth is overestimated by the model in the order of 0.6-0.8 ppbv/h. This results from differences in boundary layer growth in the morning and ozone concentration jump across the ABL top in the afternoon. This implicates stronger modeled fumigation in the morning and weaker modeled dilution after 11:00 LT.

The Long-Range Impact of Television.

ERIC Educational Resources Information Center

Comstock, George

Long range effects may be of three varieties: those which are observable in the immediate period subsequent to exposure but are long range because of their continuing repetitive accumulation with each exposure; those which represent the cumulative or delayed impact on individuals of exposure to television; or those which represent the immediate…

Evaluation of Gravitational Field Models Based on the Laser Range Observation of Low Earth Orbit Satellites

NASA Astrophysics Data System (ADS)

Wang, H. B.; Zhao, C. Y.; Zhang, W.; Zhan, J. W.; Yu, S. X.

2015-09-01

The Earth gravitational filed model is a kind of important dynamic model in satellite orbit computation. In recent years, several space gravity missions have obtained great success, prompting a lot of gravitational filed models to be published. In this paper, 2 classical models (JGM3, EGM96) and 4 latest models, including EIGEN-CHAMP05S, GGM03S, GOCE02S, and EGM2008 are evaluated by being employed in the precision orbit determination (POD) and prediction, based on the laser range observation of four low earth orbit (LEO) satellites, including CHAMP, GFZ-1, GRACE-A, and SWARM-A. The residual error of observation in POD is adopted to describe the accuracy of six gravitational field models. We show the main results as follows: (1) for LEO POD, the accuracies of 4 latest models (EIGEN-CHAMP05S, GGM03S, GOCE02S, and EGM2008) are at the same level, and better than those of 2 classical models (JGM3, EGM96); (2) If taking JGM3 as reference, EGM96 model's accuracy is better in most situations, and the accuracies of the 4 latest models are improved by 12%-47% in POD and 63% in prediction, respectively. We also confirm that the model's accuracy in POD is enhanced with the increasing degree and order if they are smaller than 70, and when they exceed 70 the accuracy keeps stable, and is unrelated with the increasing degree, meaning that the model's degree and order truncated to 70 are sufficient to meet the requirement of LEO orbit computation with centimeter level precision.

High-Level Genetic Diversity and Complex Population Structure of Siberian Apricot (Prunus sibirica L.) in China as Revealed by Nuclear SSR Markers

PubMed Central

Wang, Zhe; Kang, Ming; Liu, Huabo; Gao, Jiao; Zhang, Zhengdong; Li, Yingyue; Wu, Rongling; Pang, Xiaoming

2014-01-01

Siberian apricot (Prunus sibirica L.), an ecologically and economically important tree species with a high degree of tolerance to a variety of extreme environmental conditions, is widely distributed across the mountains of northeastern and northern China, eastern and southeastern regions of Mongolia, Eastern Siberia, and the Maritime Territory of Russia. However, few studies have examined the genetic diversity and population structure of this species. Using 31 nuclear microsatellites, we investigated the level of genetic diversity and population structure of Siberian apricot sampled from 22 populations across China. The number of alleles per locus ranged from 5 to 33, with an average of 19.323 alleles. The observed heterozygosity and expected heterozygosity ranged from 0.037 to 0.874 and 0.040 to 0.924 with average values of 0.639 and 0.774, respectively. A STRUCTURE-based analysis clustered all of the populations into four genetic clusters. Significant genetic differentiation was observed between all population pairs. A hierarchical analysis of molecular variance attributed about 94% of the variation to within populations. No significant difference was detected between the wild and semi-wild groups, indicating that recent cultivation practices have had little impact on the genetic diversity of Siberian apricot. The Mantel test showed that the genetic distance among the populations was not significantly correlated with geographic distance (r = 0.4651, p = 0.9940). Our study represents the most comprehensive investigation of the genetic diversity and population structure of Siberian apricot in China to date, and it provides valuable information for the collection of genetic resources for the breeding of Siberian apricot and related species. PMID:24516551

[Study of genetic variation in Yakutian cattle (Bos taurus L.) using the prolactin bPRL, growth hormone bGH, and transcription factor bPit-1 genes].

PubMed

Lazebnaia, I V; Lazebnyĭ, O E; Sulimova, G E

2010-03-01

The genetic structure of the Yakutian cattle breed was studied using the following genes: bPRL (RsaI site in exon 3), bGH (AluI site in exon 5), and bPit-1 (HinfI site in exon 6). The values of observed heterozygosity were 0.36 for bPRL, 0.29 for bGH, and 0.16 for bPit-1. These values are within the range of values for this parameter established for a number of Bos taurus breeds. The results obtained show that genetic variation is preserved in this aboriginal Russian breed, despite a catastrophic reduction of the number of animals.

Isolation and characterization of microsatellite markers in Oligoryzomys longicaudatus (Muridae, Sigmodontinae, Oryzomini), the natural reservoir of genotype Andes hantavirus.

PubMed

González-Ittig, Raúl E; Salazar-Bravo, Jorge; Polop, Jaime J; Gardenal, Cristina N

2008-11-01

The rodent Oligoryzomys longicaudatus or long-tailed pygmy rice rat is the reservoir of the aetiological agent of the hantavirus pulmonary syndrome in southern Argentina and Chile. We characterize 11 polymorphic microsatellite loci which would be useful for studies on microgeographical population structure in the species. Amplification of these loci in 42 individuals from four natural populations revealed four to 21 alleles per locus, and values of observed heterozygosities ranging from 0.371 to 0.896. Cross-species amplifications showed that some of the primers designed may be useful for other species of the genus Oligoryzomys. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Isolation and characterization of microsatellite markers from the great hornbill, Buceros bicornis.

PubMed

Chamutpong, Siriphatr; Saito, Daichi S; Viseshakul, Nareerat; Nishiumi, Isao; Poonswad, Pilai; Ponglikitmongkol, Mathurose

2009-03-01

Thirteen polymorphic microsatellite markers were isolated and characterized from the great hornbill, Buceros bicornis. In analyses of 20 individuals, the numbers of alleles per locus varied from two to 11. The expected and observed heterozygosities ranged from 0.22 to 0.88 and from 0.20 to 1.00, respectively. The mean polymorphic information content was 0.62. Among these, three loci deviated from the Hardy-Weinberg equilibrium. However, no significant genotypic disequilibrium was detected between any pair of loci. These microsatellite markers are useful for the population genetic study of the great hornbill. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Characterization of Mauritius parakeet (Psittacula eques) microsatellite loci and their cross-utility in other parrots (Psittacidae, Aves).

PubMed

Raisin, Claire; Dawson, Deborah A; Greenwood, Andrew G; Jones, Carl G; Groombridge, Jim J

2009-07-01

We characterized 21 polymorphic microsatellite loci in the endangered Mauritius parakeet (Psittacula eques). Loci were isolated from a Mauritius parakeet genomic library that had been enriched separately for eight different repeat motifs. Loci were characterized in up to 43 putatively unrelated Mauritius parakeets from a single population inhabiting the Black River Gorges National Park, Mauritius. Each locus displayed between three and nine alleles, with the observed heterozygosity ranging between 0.39 and 0.96. All loci were tested in 10 other parrot species. Despite testing few individuals, between seven and 21 loci were polymorphic in each of seven species tested. © 2009 Blackwell Publishing Ltd.

Isolation and characterization of 10 polymorphic microsatellite loci for the endangered Galapagos-endemic whitespotted sandbass (Paralabrax albomaculatus).

PubMed

Bertolotti, Alicia C; Griffiths, Sarah M; Truelove, Nathan K; Box, Stephen J; Preziosi, Richard F; Salinas de Leon, Pelayo

2015-01-01

The white-spotted sandbass (Paralabrax albomaculatus) is a commercially important species in the Galapagos Marine Reserve, but is classified as endangered in the IUCN Red List. For this study, 10 microsatellite loci were isolated and characterized using Illumina paired-end sequencing. These loci can be used for genetic studies of population structure and connectivity to aid in the management of the white-spotted sandbass and other closely-related species. The 10 characterized loci were polymorphic, with 11-49 alleles per locus, and observed heterozygosity ranged from 0.575 to 0.964. This set of markers is the first to be developed for this species.

Out of Africa: modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa.

PubMed

DeGiorgio, Michael; Jakobsson, Mattias; Rosenberg, Noah A

2009-09-22

Studies of worldwide human variation have discovered three trends in summary statistics as a function of increasing geographic distance from East Africa: a decrease in heterozygosity, an increase in linkage disequilibrium (LD), and a decrease in the slope of the ancestral allele frequency spectrum. Forward simulations of unlinked loci have shown that the decline in heterozygosity can be described by a serial founder model, in which populations migrate outward from Africa through a process where each of a series of populations is formed from a subset of the previous population in the outward expansion. Here, we extend this approach by developing a retrospective coalescent-based serial founder model that incorporates linked loci. Our model both recovers the observed decline in heterozygosity with increasing distance from Africa and produces the patterns observed in LD and the ancestral allele frequency spectrum. Surprisingly, although migration between neighboring populations and limited admixture between modern and archaic humans can be accommodated in the model while continuing to explain the three trends, a competing model in which a wave of outward modern human migration expands into a series of preexisting archaic populations produces nearly opposite patterns to those observed in the data. We conclude by developing a simpler model to illustrate that the feature that permits the serial founder model but not the archaic persistence model to explain the three trends observed with increasing distance from Africa is its incorporation of a cumulative effect of genetic drift as humans colonized the world.

High dynamic range subjective testing

NASA Astrophysics Data System (ADS)

Allan, Brahim; Nilsson, Mike

2016-09-01

This paper describes of a set of subjective tests that the authors have carried out to assess the end user perception of video encoded with High Dynamic Range technology when viewed in a typical home environment. Viewers scored individual single clips of content, presented in High Definition (HD) and Ultra High Definition (UHD), in Standard Dynamic Range (SDR), and in High Dynamic Range (HDR) using both the Perceptual Quantizer (PQ) and Hybrid Log Gamma (HLG) transfer characteristics, and presented in SDR as the backwards compatible rendering of the HLG representation. The quality of SDR HD was improved by approximately equal amounts by either increasing the dynamic range or increasing the resolution to UHD. A further smaller increase in quality was observed in the Mean Opinion Scores of the viewers by increasing both the dynamic range and the resolution, but this was not quite statistically significant.

Observation of Quantum Beating in rb at 2.1 THz and 18.2 THz: Long-Range Rb^{*}-Rb Interactions.

NASA Astrophysics Data System (ADS)

Goldshlag, William; Ricconi, Brian J.; Eden, J. Gary

2017-06-01

The interaction of Rb 7s ^{2}S_{1/2}, 5d ^{2}D_{3/2,5/2} and 5p ^{2}P_{3/2} atoms with the background species at long range (100-1000Å) has been observed by pump-probe ultrafast laser spectroscopy. Parametric four-wave mixing in Rb vapor with pairs of 50-70 fs pulses produces coherent Rb 6P-5S emission at 420 nm that is modulated by Rb quantum beating. The two dominant beating frequencies are 18.2 THz and 2.07 THz, corresponding to quantum beating between 7S and 5D states and to the (5D-5P_{3/2})-(5P_{3/2}-5S) defect, respectively. Analysis of Rabi oscillations in these pump-probe experiments allows for the mean interaction energy at long range to be determined. The figure shows Fourier transform spectra of representative Rabi oscillation waveforms. The waveform and spectrum at left illustrate quantum beating in Rb at 2.1 THz. The spectrum at right is dominated by the 18.2 THz frequency component generated by 7S-5D beating in Rb. Insets show respective temporal behaviors of the 6P-5S line near the coherent transient (zero interpulse delay).

Allele frequencies for 13 STRs loci in a Western Anatolia population and their forensic evaluation.

PubMed

Baransel Isir, Aysun; Ozkorkmaz, Abdulmuttalip; Pehlivan, Sacide

2015-01-01

Numerous studies demonstrated that STRs have become powerful tools in forensic case work. To profile DNA samples from 104 Turkish males for 13 autosomal, STR markers intended for human identification purposes and to estimate the allele frequency distribution in forensic cases in a Turkish population. Thirteen autosomal STR loci, namely D3S1358, D2S1338, D16S539, D8S1179, D21S11, D18S51, TH01, D13S317, D7S820, CSF1PO, TPOX, D5S818 and FGA, were analysed in a sample of 104 healthy and unrelated Turkish individuals who have been living in the city of İzmir. All loci were amplified by using AmpFlSTR Identifier Kit. Genetic analysis was carried out on an ABI PRISM 310 Genetic Analyser. For each locus, 6-15 alleles were found with frequencies ranging from 0.005-0.514 and heterozygosities ranging from 0.686-0.868. The PIC value was highly significant (0.999). The 13 STR loci in the AmpFlSTR Identifier Kit are suitable for forensic identification and paternity tests due to high heterozygosity. The observed PD value is sufficiently high for human identification purposes. In conclusion, the 13 STR loci seem to be useful markers for personal identification and forensic case work in the Turkish population. The results also demonstrate the importance of region-specific studies.

Isolation and characterization of polymorphic microsatellite markers for blue fox (Alopex lagopus).

PubMed

Li, Y M; Guo, P C; Lu, J Y; Bai, C Y; Zhao, Z H; Yan, S Q

2016-06-03

The blue fox, belonging to the family Canidae, is a coat color variant of the native arctic fox (Alopex lagopus). To date, microsatellite loci in blue fox are typically amplified using canine simple sequence repeat primers. In the present study, we constructed an (AC)n enrichment library, and isolated and identified 17 polymorphic microsatellite markers for blue fox. The number of alleles per locus is from two to seven based on 24 examined individuals. The expected and observed heterozygosities were in the range of 0.3112 to 0.8236 and 0.2917 to 0.8750, respectively. The polymorphic information content per locus ranged from 0.2583 to 0.8022. These polymorphic markers can be useful for future population genetic studies of both farmed blue foxes and wild arctic foxes.

Isolation and characterization of microsatellite markers of sea cucumber Stichopus horrens.

PubMed

Li, Z B; Dai, G; Shangguan, J B; Ning, Y F; Li, Y Y; Chen, R B; Yuan, Y; Huang, Y S

2015-07-28

Curry fish (Stichopus horrens) is a tropical holothurian species and is widely distributed in the India-West Pacific. In the present study, 9 polymorphic microsatellite loci were isolated and characterized for S. horrens. These loci were tested in 30 individuals from Hainan Island in China. The number of alleles ranged from 2 to 5. The polymorphism information content ranged from 0.348-0.584. The levels of observed and expected heterozygosities varied from 0.1500-0.8000 and from 0.2014-0.5000, respectively. Most loci were in Hardy-Weinberg equilibrium, except HCS1-27 and HCS2-7, after sequential Bonferroni's correction, and no significant linkage disequilibrium was detected for any pairwise combination of loci. These polymorphic microsatellite loci will be useful for studying population structure and conservation strategy design for S. horrens.

PERMANENT GENETIC RESOURCES: Eighteen new polymorphic microsatellite markers for the endangered Florida manatee, Trichechus manatus latirostris.

PubMed

Tringali, Michael D; Seyoum, Seifu; Carney, Susan L; Davis, Michelle C; Rodriguez-Lopez, Marta A; Reynolds Iii, John E; Haubold, Elsa

2008-03-01

Here we describe 18 polymorphic microsatellite loci for Trichechus manatus latirostris (Florida manatee), isolated using a polymerase chain reaction-based technique. The number of alleles at each locus ranged from two to four (mean = 2.5) in specimens from southwest (n = 58) and northeast (n = 58) Florida. Expected and observed heterozygosities ranged from 0.11 to 0.67 (mean = 0.35) and from 0.02 to 0.78 (mean = 0.34), respectively. Departures from Hardy-Weinberg equilibrium occurred at two loci. There was no evidence of genotypic disequilibrium for any pair of loci. For individual identification, mean random-mating and θ-corrected match probabilities were 9.36 × 10(-7) and 1.95 × 10(-6) , respectively. © 2007 The Authors.

Jupiter before Juno: State of the atmosphere at cloud level in 2016 from PlanetCam observations in the 0.4-1.7 microns wavelength range and amateur observations in the visible

NASA Astrophysics Data System (ADS)

Hueso, Ricardo; Sanchez-Lavega, Agustin; Perez-Hoyos, Santiago; Rojas, Jose Felix; Iñurrigarro, Peio; Mendikoa, Iñigo; Go, Christopher; PVOL-IOPW Team

2016-10-01

The arrival of Juno to Jupiter provides a unique opportunity to link findings of the inner structure of the planet with astronomical observations of its meteorology at cloud level. Long time base observations of Jupiter's atmosphere before and during the Juno mission are critical in providing context to Junocam observations and may benefit the interpretation of the MWR data on the lower atmosphere structure as well as Juno data on the depth of the zonal winds. We have performed a long campaign of observations in the visible with the PlanetCam lucky imaging instrument in the 2.2m telescope at Calar Alto Observatory in Spain with observations obtained in December 2015 and in March, May, June and July 2016. In observations under good atmospheric seeing, the instrument allows to obtain images with a spatial resolution of 0.05'' in the visible and 0.1'' from 1.0 to 1.7 microns. The later is an interesting range of wavelengths for observing Jupiter because of the existence of several strong and weak methane absorption bands not generally used in high-resolution ground-based observations of the planet. A combination of images using narrow filters centered in methane absorption bands and their adjacent continuum allows studying the vertical structure of the clouds at horizontal spatial scales of 350-1000 km over the planet depending on the atmospheric seeing and filter used. The best images can be further processed showing features at spatial resolutions of about 150 km. We have also monitored the state of the atmosphere with images obtained by amateur astronomers contributing to the Planetary Virtual Observatory Laboratory database (http://pvol.ehu.eus). Based on both datasets we present zonal winds from -70 to +75 deg with an accuracy of 10 m/s in the low latitudes and 25 m/s in subpolar latitudes. Relative altitude maps of features observed in bands J, H and others with different methane absorption will be presented.

Analyses of the long-range transport of nitrogeneous species through the atmosphere from the Asian continent using observational data at Cape Hedo, Okinawa, and CMAQ postanalyses

NASA Astrophysics Data System (ADS)

Sadanaga, Y.; Bandow, H.; Uno, I.; Sera, T.; Yuba, A.; Takenaka, N.; Takami, A.; Kurokawa, J.; Hatakeyama, S.

2010-12-01

The long-term monitoring of air quality has been continuing at the Cape Hedo Atmosphere and Aerosol Monitoring Station (CHAAMS) in Okinawa, Japan in terms of assessing the environmental impact and biogeochemical effect to the marine-surface activities by the economic growth of Asian continent. Among the monitoring data, total odd nitrogen oxides (NOy), HNO3, particulate nitrate (NO3-(p)), NH3, NH4+ and SO42- were analyzed for the period from 16 March to 13 April 2008 as well as the postanalyses of those species by the Community Muti-scale Air Quality model (CMAQ) of those species. NOy and total nitrate (TN = HNO3 + NO3-(p)) concentrations from China (CH) air mass origin were high during the observational period in both observed and model-calculated result. The long-range transport of odd nitrogen species from the Asian continent is supported with respect to both the CMAQ postanalyses and the observations. HNO3 and NO3-(p) concentrations from CH air mass origin were also high during the observational period. However, the HNO3 diurnal variation with daytime peak and nighttime lows suggests that HNO3 around the CHAAMS forms photochemically in situ or in areas relatively close to the CHAAMS. The maximum and minimum concentrations of NH3 were observed at Pacific Ocean (PO) and Middle China air mass origins, respectively, and the observed NH3 concentrations from PO air mass origin were highest. NH3 concentration calculated by the CMAQ failed to reproduce observed variation, this is because the horizontal resolution of CMAQ (-20km) is not sufficient to allocate the land surface/vegetation base NH3 emission. NH4+ and SO42- concentrations from CH air mass origin were high during the observational period for both the observation and the CMAQ calculation. As well as the case of NOy and TN, the long-range transport of ammonium and sulfur compounds from the Asian continent is also supported in terms of both the CMAQ postanalyses and the observations.

Further characterization of loss of heterozygosity enhanced by p53 abrogation in human lymphoblastoid TK6 cells: disappearance of endpoint hotspots.

PubMed

Yatagai, Fumio; Morimoto, Shigeko; Kato, Takesi; Honma, Masamitsu

2004-06-13

Loss of heterozygosity (LOH) is the predominant mechanism of spontaneous mutagenesis at the heterozygous thymindine kinase locus (tk) in TK6 cells. LOH events detected in spontaneous TK(-) mutants (110 clones from p53 wild-type cells TK6-20C and 117 clones from p53-abrogated cells TK6-E6) were analyzed using 13 microsatellite markers spanning the whole of chromosome 17. Our analysis indicated an approximately 60-fold higher frequency of terminal deletions in p53-abrogated cells TK6-E6 compared to p53 wild-type cells TK6-20C whereas frequencies of point mutations (non-LOH events), interstitial deletions, and crossing over events were found to increase only less than twofold by such p53 abrogation. We then made use of an additional 17 microsatellite markers which provided an average map-interval of 1.6Mb to map various LOH endpoints on the 45Mb portion of chromosome 17q corresponding to the maximum length of LOH tracts (i.e. from the distal marker D17S932 to the terminal end). There appeared to be four prominent peaks (I-IV) in the distribution of LOH endpoints/Mb of Tk6-20C cells that were not evident in p53-abrogated cells TK6-E6, where they appeared to be rather broadly distributed along the 15-20Mb length (D17S1807 to D17S1607) surrounding two of the peaks that we detected in TK6-20C cells (peaks II and III). We suggest that the chromosomal instability that is so evident in TK6-E6 cells may be due to DNA double-strand break repair occurring through non homologous end-joining rather than allelic recombination.

Mandibular movement range in children.

PubMed

Machado, Barbara Cristina Zanandréa; Medeiros, Ana Paula Magalhães; Felício, Cláudia Maria de

2009-01-01

identification of the mandibular movement range is an important procedure in the evaluation of the stomatognathic system. However, there are few studies in children that focus on normal parameters or abnormalities. to determine the average range of mandibular movements in Brazilian children aged 6 to 12 years; to verify the difference between genders, in each age group, and between the different age groups: 6-8 years; 8.1-10 years; and 10.1-12 years. participants of the study were 240 healthy children selected among regular students from local schools of São Paulo State. The maximum mandibular opening, lateral excursion and protrusive movements, and deviation of the medium line, if present, were measured using a digital caliper. Student T test, Analysis of variance and Tukey test were considered significant for p < 0.05. the mean values observed in the studied sample were: 44.51mm for maximum mandibular opening; 7.71mm for lateral excursion to the right; 7.92mm for lateral excursion to the left; 7.45mm for protrusive movements. No statistical difference was observed between genders. There was a gradual increase in the range of mandibular movements, with significant differences mainly between the ages of 6-8 years and 10.1-12 years. during childhood the range of mandibular movements increases. Age should be considered in this analysis for a greater precision in the diagnosis.

Development and characterization of microsatellite markers for rice leaffolder, Cnaphalocrocis medinalis (Guenée) and cross-species amplification in other Pyralididae.

PubMed

An, Baoguang; Deng, Xiaolong; Shi, Huiyun; Ding, Meng; Lan, Jie; Yang, Jing; Li, Yangsheng

2014-02-01

Rice leaffolder, Cnaphalocrocis medinalis (Guenée), is a destructive and widespread pest on rice. In this study, 20 microsatellite markers were isolated and characterized from C. medinalis partial genomic libraries using the method of fast isolation by AFLP of sequence containing repeats. Of these markers, 18 markers displayed polymorphisms. Polymorphisms were evaluated in 48 individuals from two natural populations. The number of alleles per locus ranged from 2 to 15, and the expected and observed heterozygosities ranged from 0.324 to 0.934 and from 0.304 to 0.917, respectively. Cross-species amplification was also performed to test the transferability of the 20 microsatellite markers and a moderate level of cross amplication was observed across the three species of Pyralididae (26.67 %). These microsatellite loci would facilitate the future study on population genetics and molecular genetics of rice leaffolder and would also be useful for study in Chilo suppressalis, Scirpophaga incertulas and Pyrausta nubilalis.

Development and Characterization of Polymorphic Microsatellite Markers for Sedum sarmentosum (Crassulaceae) and Their Cross-Species Transferability.

PubMed

Xu, Jing; Hou, Fu-Yuan; Wan, Ding-Rong; Wang, Sha; Xu, Dong-Mei; Yang, Guang-Zhong

2015-11-05

Sedum sarmentosum is an important Chinese medicinal herb that exhibits anti-inflammatory, anti-angiogenic and anti-nociceptive properties. However, little is known about its genetic background. The first set of 14 microsatellite markers were isolated and characterized for S. sarmentosum using an SSR-enriched library. Fourteen polymorphic microsatellite markers were acquired with satisfactory amplifications and a polymorphic pattern in 48 S. sarmentosum individuals. The number of alleles ranged from 3 to 15. The observed and expected heterozygosities varied from 0.0833 to 0.8750 and 0.2168 to 0.9063, respectively. Two loci showed significant departure from the Hardy-Weinberg equilibrium. Cross-species amplification was carried out in other Sedum species. High rates of cross-species amplification were observed. The transferability value ranged from 85.7% in S. lineare to 64.3% in S. ellacombianum. These markers will be valuable for studying the genetic variation, population structure and germplasm characterization of S. sarmentosum and related Sedum species.

Isolation and characterization of new microsatellite markers in red tail prawn, Fenneropenaeus penicillatus, an endangered species in China.

PubMed

Yuan, Y; Shangguan, J B; Li, Z B; Ning, Y F; Huang, Y S; Li, B B; Mao, X Q

2015-11-30

Until recently, Fenneropenaeus penicillatus was considered a commercial shrimp species. However, in 2005, it was included on the Red List as an endangered species by the Chinese government. In this study, 19 new microsatellite markers in F. penicillatus were developed and tested in samples of 32 wild individuals from Nanao, China. Twelve loci were polymorphic and 7 were monomorphic. Of the 12 polymorphic loci, the number of alleles per locus ranged from 3 to 6, with an average of 4.42 alleles per locus. The polymorphism information content ranged from 0.302 to 0.670, with a mean of 0.4817. The observed and expected heterozygosities ranged from 0.2250 to 0.8889 and from 0.1111 to 0.7750, respectively. Significant deviations from Hardy-Weinberg equilibrium (HWE, adjusted P < 0.0042) after a Bonferroni correction were observed in 3 loci (NA-9, NA-57, and NA-64), whereas the other 9 loci were in HWE. These new microsatellite markers will be useful in further research on the population genetic structure of F. penicillatus.

Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome.

PubMed

Syring, John V; Tennessen, Jacob A; Jennings, Tara N; Wegrzyn, Jill; Scelfo-Dalbey, Camille; Cronn, Richard

2016-01-01

Whitebark pine (Pinus albicaulis) inhabits an expansive range in western North America, and it is a keystone species of subalpine environments. Whitebark is susceptible to multiple threats - climate change, white pine blister rust, mountain pine beetle, and fire exclusion - and it is suffering significant mortality range-wide, prompting the tree to be listed as 'globally endangered' by the International Union for Conservation of Nature and 'endangered' by the Canadian government. Conservation collections (in situ and ex situ) are being initiated to preserve the genetic legacy of the species. Reliable, transferrable, and highly variable genetic markers are essential for quantifying the genetic profiles of seed collections relative to natural stands, and ensuring the completeness of conservation collections. We evaluated the use of hybridization-based target capture to enrich specific genomic regions from the 27 GB genome of whitebark pine, and to evaluate genetic variation across loci, trees, and geography. Probes were designed to capture 7,849 distinct genes, and screening was performed on 48 trees. Despite the inclusion of repetitive elements in the probe pool, the resulting dataset provided information on 4,452 genes and 32% of targeted positions (528,873 bp), and we were able to identify 12,390 segregating sites from 47 trees. Variations reveal strong geographic trends in heterozygosity and allelic richness, with trees from the southern Cascade and Sierra Range showing the greatest distinctiveness and differentiation. Our results show that even under non-optimal conditions (low enrichment efficiency; inclusion of repetitive elements in baits), targeted enrichment produces high quality, codominant genotypes from large genomes. The resulting data can be readily integrated into management and gene conservation activities for whitebark pine, and have the potential to be applied to other members of 5-needle pine group (Pinus subsect. Quinquefolia) due to their

Comparative study on the use of specific and heterologous microsatellite primers in the stingless bees Melipona rufiventris and M. mondury (Hymenoptera, Apidae).

PubMed

Lopes, Denilce Meneses; de Oliveira Campos, Lúcio Antônio; Salomão, Tânia Maria Fernandes; Tavares, Mara Garcia

2010-04-01

Due to their high degree of polymorphism, microsatellites are considered useful tools for studying population genetics. Nevertheless, studies of genetic diversity in stingless bees by means of these primers have revealed a low level of polymorphism, possibly the consequence of the heterologous primers used, since in most cases these were not specifically designed for the species under consideration. Herein we compared the number of polymorphic loci and alleles per locus, as well as observed heterozygosity in Melipona rufiventris and M. mondury populations, using specific and heterologous primers. The use of specific primers placed in evidence the greater frequency of polymorphic loci and alleles per locus, besides an expressive increase in observed heterozygosity in M. rufiventris and M. mondury, thereby reinforcing the idea that populational studies should be undertaken by preferably using species-specific microsatellite primers.

Ambient seismic noise interferometry in Hawai'i reveals long-range observability of volcanic tremor

USGS Publications Warehouse

Ballmer, Silke; Wolfe, Cecily; Okubo, Paul G.; Haney, Matt; Thurber, Clifford H.

2013-01-01

The use of seismic noise interferometry to retrieve Green's functions and the analysis of volcanic tremor are both useful in studying volcano dynamics. Whereas seismic noise interferometry allows long-range extraction of interpretable signals from a relatively weak noise wavefield, the characterization of volcanic tremor often requires a dense seismic array close to the source. We here show that standard processing of seismic noise interferometry yields volcanic tremor signals observable over large distances exceeding 50 km. Our study comprises 2.5 yr of data from the U.S. Geological Survey Hawaiian Volcano Observatory short period seismic network. Examining more than 700 station pairs, we find anomalous and temporally coherent signals that obscure the Green's functions. The time windows and frequency bands of these anomalous signals correspond well with the characteristics of previously studied volcanic tremor sources at Pu'u 'Ō'ō and Halema'uma'u craters. We use the derived noise cross-correlation functions to perform a grid-search for source location, confirming that these signals are surface waves originating from the known tremor sources. A grid-search with only distant stations verifies that useful tremor signals can indeed be recovered far from the source. Our results suggest that the specific data processing in seismic noise interferometry—typically used for Green's function retrieval—can aid in the study of both the wavefield and source location of volcanic tremor over large distances. In view of using the derived Green's functions to image heterogeneity and study temporal velocity changes at volcanic regions, however, our results illustrate how care should be taken when contamination by tremor may be present.

The Geoscience Laser Altimetry/Ranging System (GLARS)

NASA Technical Reports Server (NTRS)

Cohen, S. C.; Degnan, J. J.; Bufton, J. L.; Garvin, J. B.; Abshire, J. B.

1986-01-01

The Geoscience Laser Altimetry Ranging System (GLARS) is a highly precise distance measurement system to be used for making extremely accurate geodetic observations from a space platform. It combines the attributes of a pointable laser ranging system making observations to cube corner retroreflectors placed on the ground with those of a nadir looking laser altimeter making height observations to ground, ice sheet, and oceanic surfaces. In the ranging mode, centimeter-level precise baseline and station coordinate determinations will be made on grids consisting of 100 to 200 targets separated by distances from a few tens of kilometers to about 1000 km. These measurements will be used for studies of seismic zone crustal deformations and tectonic plate motions. Ranging measurements will also be made to a coarser, but globally distributed array of retroreflectors for both precise geodetic and orbit determination applications. In the altimetric mode, relative height determinations will be obtained with approximately decimeter vertical precision and 70 to 100 meter horizontal resolution. The height data will be used to study surface topography and roughness, ice sheet and lava flow thickness, and ocean dynamics. Waveform digitization will provide a measure of the vertical extent of topography within each footprint. The planned Earth Observing System is an attractive candidate platform for GLARS since the GLAR data can be used both for direct analyses and for highly precise orbit determination needed in the reduction of data from other sensors on the multi-instrument platform. (1064, 532, and 355 nm)Nd:YAG laser meets the performance specifications for the system.

Ground-based observations of the corona in the visible and NIR spectral ranges

NASA Technical Reports Server (NTRS)

Epple, Alexander; Schwenn, Rainer

1995-01-01

Since late 1993 we have been using a mirror coronagraph on Pic du Midi (PICO) to observe the solar emission corona in several spectral lines of (FE-X), (FE-XIII), and (FE-XIV). For good meteorological conditions the diffuse corona and coronal holes in between can be seen out to 1.2 solar mass for sun center. Active regions can be mapped to bond 1.5 solar mass in the green and infrared lines. Recent observations of PICO are presented.

Short-Range Nucleon-Nucleon Correlations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Douglas Higinbotham

2011-10-01

Valence-shell nucleon knock-out experiments, such as 12C(e,e'p)11B, measure less strength then is predicted by independent particle shell model calculations. The theoretical solution to this problem is to include the correlations between the nucleons in the nucleus in the calculations. Motivated by these results, many electron scattering experiments have tried to directly observe these correlations in order to gain new insight into the short-range part of the nucleon-nucleon potential. Unfortunately, many competing mechanisms can cause the same observable final-state as an initial-state correlation, making truly isolating the signal extremely challenging. This paper reviews the recent experimental evidence for short-range correlations, asmore » well as explores the possibility that such correlations are responsible for the EMC effect in the 0.3 < xB < 0.7 deep inelastic scattering ratios.« less

Testing mate choice and overdominance at MH in natural families of Atlantic salmon Salmo salar.

PubMed

Tentelier, C; Barroso-Gomila, O; Lepais, O; Manicki, A; Romero-Garmendia, I; Jugo, B M

2017-04-01

This study aimed to test mate choice and selection during early life stages on major histocompatibility (MH) genotype in natural families of Atlantic salmon Salmo salar spawners and juveniles, using nine microsatellites to reconstruct families, one microsatellite linked to an MH class I gene and one minisatellite linked to an MH class II gene. MH-based mate choice was only detected for the class I locus on the first year, with lower expected heterozygosity in the offspring of actually mated pairs than predicted under random mating. The genotype frequencies of MH-linked loci observed in the juveniles were compared with frequencies expected from Mendelian inheritance of parental alleles to detect selection during early life stages. No selection was detected on the locus linked to class I gene. For the locus linked to class II gene, observed heterozygosity was higher than expected in the first year and lower in the second year, suggesting overdominance and underdominance, respectively. Within family, juveniles' body size was linked to heterozygosity at the same locus, with longer heterozygotes in the first year and longer homozygotes in the second year. Selection therefore seems to differ from one locus to the other and from year to year. © 2017 The Fisheries Society of the British Isles.

Macrogeographic and microgeographic genetic structure of the Chagas' disease vector Triatoma infestans (Hemiptera: Reduviidae) from Catamarca, Argentina.

PubMed

Pérez de Rosas, Alicia R; Segura, Elsa L; Fichera, Laura; García, Beatriz Alicia

2008-07-01

The genetic structure in populations of the Chagas' disease vector Triatoma infestans from six localities belonging to areas under the same insecticide treatment conditions of Catamarca province (Argentina) was examined at macrogeographical and microgeographical scales. A total of 238 insects were typed for 10 polymorphic microsatellite loci. The average observed and expected heterozygosities ranged from 0.319 to 0.549 and from 0.389 to 0.689, respectively. The present results confirm that populations of T. infestans are highly structured. Spatial genetic structure was detectable at macrogeographical and microgeographical levels. Comparisons of the levels of genetic variability between two temporal samples were carried out to assess the impact of the insecticide treatment. The genetic diversity of the population was not significantly affected after insecticide use since different genetic parameters (allele number, observed and expected heterozygosities) remained stable. However, loss of low frequency alleles and not previously found alleles were detected. The effective population size (N(e)) estimated was substantially lower in the second temporal sample than in the first; nevertheless, it is possible that the size of the remnant population after insecticide treatment was still large enough to retain the genetic diversity. Very few individuals did not belong to the local T. infestans populations as determined by assignment analyses, suggesting a low level of immigration in the population. The results of the assignment and first-generation migrant tests suggest male-biased dispersal at microgeographical level.

Concurrence of B-lymphoblastic leukemia and myeloproliferative neoplasm with copy neutral loss of heterozygosity at chromosome 1p harboring a MPL W515S mutation.

PubMed

Tao, Jiangchuan; Zhang, Xiaohui; Lancet, Jeffrey; Bennett, John M; Cai, Li; Papenhausen, Peter; Moscinski, Lynn; Zhang, Ling

2014-01-01

B-lymphoblastic leukemia (B-ALL) is a neoplasm of precursors committed to B-cell lineage, whereas myeloproliferative neoplasm (MPN) is a clonal proliferation derived from myeloid stem cells. Concurrent B-ALL with MPN is uncommon except in the presence of abnormalities of the PDGFRA, PDGFRB, or FGFR1 genes or the BCR-ABL1 fusion gene. Herein, we describe a rare concurrence, B-ALL with MPN without the aforementioned genetic aberrations, in a 64-year-old male patient. The patient was initially diagnosed with B-ALL with normal karyotype and responded well to aggressive chemotherapy but had sustained leukocytosis and splenomegaly. The posttreatment restaging bone marrow was free of B-ALL but remained hypercellular with myeloid predominance. Using a single nucleotide polymorphism microarray study, we identified a copy neutral loss of heterozygosity at the terminus of 1p in the bone marrow samples taken at diagnosis and again at remission, 49% and 100%, respectively. Several additional genetic abnormalities were present in the initial marrow sample but not in the remission marrow samples. Retrospective molecular studies detected a MPL W515S homozygous mutation in both the initial and remission marrows for B-ALL, at 30-40% and 80% dosage effect, respectively. In summary, we present a case of concurrent B-ALL and MPN and demonstrate a stepwise cytogenetic and molecular approach to the final diagnosis. Copyright © 2014 Elsevier Inc. All rights reserved.

High-Resolution Genome-Wide Analysis of Irradiated (UV and γ-Rays) Diploid Yeast Cells Reveals a High Frequency of Genomic Loss of Heterozygosity (LOH) Events

PubMed Central

St. Charles, Jordan; Hazkani-Covo, Einat; Yin, Yi; Andersen, Sabrina L.; Dietrich, Fred S.; Greenwell, Patricia W.; Malc, Ewa; Mieczkowski, Piotr; Petes, Thomas D.

2012-01-01

In diploid eukaryotes, repair of double-stranded DNA breaks by homologous recombination often leads to loss of heterozygosity (LOH). Most previous studies of mitotic recombination in Saccharomyces cerevisiae have focused on a single chromosome or a single region of one chromosome at which LOH events can be selected. In this study, we used two techniques (single-nucleotide polymorphism microarrays and high-throughput DNA sequencing) to examine genome-wide LOH in a diploid yeast strain at a resolution averaging 1 kb. We examined both selected LOH events on chromosome V and unselected events throughout the genome in untreated cells and in cells treated with either γ-radiation or ultraviolet (UV) radiation. Our analysis shows the following: (1) spontaneous and damage-induced mitotic gene conversion tracts are more than three times larger than meiotic conversion tracts, and conversion tracts associated with crossovers are usually longer and more complex than those unassociated with crossovers; (2) most of the crossovers and conversions reflect the repair of two sister chromatids broken at the same position; and (3) both UV and γ-radiation efficiently induce LOH at doses of radiation that cause no significant loss of viability. Using high-throughput DNA sequencing, we also detected new mutations induced by γ-rays and UV. To our knowledge, our study represents the first high-resolution genome-wide analysis of DNA damage-induced LOH events performed in any eukaryote. PMID:22267500

Hookworm infection, anaemia and genetic variability of the New Zealand sea lion.

PubMed

Acevedo-Whitehouse, Karina; Petetti, Laura; Duignan, Padraig; Castinel, Aurelie

2009-10-07

Hookworms are intestinal blood-feeding nematodes that parasitize and cause high levels of mortality in a wide range of mammals, including otariid pinnipeds. Recently, an empirical study showed that inbreeding (assessed by individual measures of multi-locus heterozygosity) is associated with hookworm-related mortality of California sea lions. If inbreeding increases susceptibility to hookworms, effects would expectedly be stronger in small, fragmented populations. We tested this assumption in the New Zealand sea lion, a threatened otariid that has low levels of genetic variability and high hookworm infection rates. Using a panel of 22 microsatellites, we found that average allelic diversity (5.9) and mean heterozygosity (0.72) were higher than expected for a small population with restricted breeding, and we found no evidence of an association between genetic variability and hookworm resistance. However, similar to what was observed for the California sea lion, homozygosity at a single locus explained the occurrence of anaemia and thrombocytopenia in hookworm-infected pups (generalized linear model, F = 11.81, p < 0.001) and the effect was apparently driven by a particular allele (odds ratio = 34.95%; CI: 7.12-162.41; p < 0.00001). Our study offers further evidence that these haematophagus parasites exert selective pressure on otariid blood-clotting processes.

Hookworm infection, anaemia and genetic variability of the New Zealand sea lion

PubMed Central

Acevedo-Whitehouse, Karina; Petetti, Laura; Duignan, Padraig; Castinel, Aurelie

2009-01-01

Hookworms are intestinal blood-feeding nematodes that parasitize and cause high levels of mortality in a wide range of mammals, including otariid pinnipeds. Recently, an empirical study showed that inbreeding (assessed by individual measures of multi-locus heterozygosity) is associated with hookworm-related mortality of California sea lions. If inbreeding increases susceptibility to hookworms, effects would expectedly be stronger in small, fragmented populations. We tested this assumption in the New Zealand sea lion, a threatened otariid that has low levels of genetic variability and high hookworm infection rates. Using a panel of 22 microsatellites, we found that average allelic diversity (5.9) and mean heterozygosity (0.72) were higher than expected for a small population with restricted breeding, and we found no evidence of an association between genetic variability and hookworm resistance. However, similar to what was observed for the California sea lion, homozygosity at a single locus explained the occurrence of anaemia and thrombocytopenia in hookworm-infected pups (generalized linear model, F = 11.81, p < 0.001) and the effect was apparently driven by a particular allele (odds ratio = 34.95%; CI: 7.12–162.41; p < 0.00001). Our study offers further evidence that these haematophagus parasites exert selective pressure on otariid blood-clotting processes. PMID:19605394

Short-range photoassociation of LiRb

NASA Astrophysics Data System (ADS)

Blasing, David; Stevenson, Ian; Pérez-Ríos, Jesús; Elliott, Daniel; Chen, Yong

2017-04-01

We have observed short-range photoassociation of 7Li85Rb to the two lowest vibrational states of the d3 Π potential. We have also observed several a3Σ+ vibrational levels with generation rates between 102 and 103 molecules per second, resulting from the spontaneous decay of these d3 Π molecules. This is the first observation of many of these a3Σ+ levels. We observe an alternation of the peak heights in the rotational photoassociation spectrum that depends on the parity of the excited molecular state. Franck-Condon overlap calculations predict that photoassociation to higher vibrational levels of the d3 Π , in particular the sixth vibrational level, should populate the lowest vibrational level of the a3Σ+ state with a rate as high as 104 molecules per second. This work also motivates an experimental search for short-range photoassociation to other bound molecules, such as the c3Σ+ or b3 Π , as prospects for preparing ground-state molecules. The experimental work was funded by the Purdue Office of the Vice President for Research AMO Incentive Grant 206732 and J.P.-R. acknowledges support from NSF Grant No. PHY-130690.

Large-Range Movements of Neotropical Orchid Bees Observed via Radio Telemetry

PubMed Central

Wikelski, Martin; Moxley, Jerry; Eaton-Mordas, Alexander; López-Uribe, Margarita M.; Holland, Richard; Moskowitz, David; Roubik, David W.; Kays, Roland

2010-01-01

Neotropical orchid bees (Euglossini) are often cited as classic examples of trapline-foragers with potentially extensive foraging ranges. If long-distance movements are habitual, rare plants in widely scattered locations may benefit from euglossine pollination services. Here we report the first successful use of micro radio telemetry to track the movement of an insect pollinator in a complex and forested environment. Our results indicate that individual male orchid bees (Exaerete frontalis) habitually use large rainforest areas (at least 42–115 ha) on a daily basis. Aerial telemetry located individuals up to 5 km away from their core areas, and bees were often stationary, for variable periods, between flights to successive localities. These data suggest a higher degree of site fidelity than what may be expected in a free living male bee, and has implications for our understanding of biological activity patterns and the evolution of forest pollinators. PMID:20520813

A detail enhancement and dynamic range adjustment algorithm for high dynamic range images

NASA Astrophysics Data System (ADS)

Xu, Bo; Wang, Huachuang; Liang, Mingtao; Yu, Cong; Hu, Jinlong; Cheng, Hua

2014-08-01

Although high dynamic range (HDR) images contain large amounts of information, they have weak texture and low contrast. What's more, these images are difficult to be reproduced on low dynamic range displaying mediums. If much more information is to be acquired when these images are displayed on PCs, some specific transforms, such as compressing the dynamic range, enhancing the portions of little difference in original contrast and highlighting the texture details on the premise of keeping the parts of large contrast, are needed. To this ends, a multi-scale guided filter enhancement algorithm which derives from the single-scale guided filter based on the analysis of non-physical model is proposed in this paper. Firstly, this algorithm decomposes the original HDR images into base image and detail images of different scales, and then it adaptively selects a transform function which acts on the enhanced detail images and original images. By comparing the treatment effects of HDR images and low dynamic range (LDR) images of different scene features, it proves that this algorithm, on the basis of maintaining the hierarchy and texture details of images, not only improves the contrast and enhances the details of images, but also adjusts the dynamic range well. Thus, it is much suitable for human observation or analytical processing of machines.

Expression and functional analysis of menin in a multiple endocrine neoplasia type 1 (MEN1) patient with somatic loss of heterozygosity in chromosome 11q13 and unidentified germline mutation of the MEN1 gene.

PubMed

Naito, Junko; Kaji, Hiroshi; Sowa, Hideaki; Kitazawa, Riko; Kitazawa, Sohei; Tsukada, Toshihiko; Hendy, Geoffrey N; Sugimoto, Toshitsugu; Chihara, Kazuo

2006-06-01

In some patients with multiple endocrine neoplasia type 1 (MEN1) it is not possible to identify a germline mutation in the MEN1 gene. We sought to document the loss of expression and function of the MEN1 gene product, menin, in the tumors of such a patient. The proband is an elderly female patient with primary hyperparathyroidism, pancreatic islet tumor, and breast cancer. Her son has primary hyperparathyroidism. No germline MEN1 mutation was identified in the proband or her son. However, loss of heterozygosity at the MEN1 locus and complete lack of menin expression were demonstrated in the proband's tumor tissue. The proband's cultured parathyroid cells lacked the normal reduction in proliferation and parathyroid hormone secretion in response to transforming growth factor- beta. This assessment provided insight into the molecular pathogenesis of the patient and provides evidence for a critical requirement for menin in the antiproliferative action of transforming growth factor-beta.

Copy number of the Adenomatous Polyposis Coli gene is not always neutral in sporadic colorectal cancers with loss of heterozygosity for the gene.

PubMed

Zauber, Peter; Marotta, Stephen; Sabbath-Solitare, Marlene

2016-03-12

Changes in the number of alleles of a chromosome may have an impact upon gene expression. Loss of heterozygosity (LOH) indicates that one allele of a gene has been lost, and knowing the exact copy number of the gene would indicate whether duplication of the remaining allele has occurred. We were interested to determine the copy number of the Adenomatous Polyposis Coli (APC) gene in sporadic colorectal cancers with LOH. We selected 38 carcinomas with LOH for the APC gene region of chromosome 5, as determined by amplification of the CA repeat region within the D5S346 loci. The copy number status of APC was ascertained using the SALSA® MLPA® P043-B1 APC Kit. LOH for the DCC gene, KRAS gene mutation, and microsatellite instability were also evaluated for each tumor, utilizing standard polymerase chain reaction methods. No tumor demonstrated microsatellite instability. LOH of the DCC gene was also present in 33 of 36 (91.7%) informative tumors. A KRAS gene mutation was present in 16 of the 38 (42.1%) tumors. Twenty-four (63.2%) of the tumors were copy number neutral, 10 (26.3%) tumors demonstrated major loss, while two (5.3%) showed partial loss. Two tumors (5.3%) had copy number gain. Results of APC and DCC LOH, KRAS and microsatellite instability indicate our colorectal cancer cases were typical of sporadic cancers following the 'chromosomal instability' pathway. The majority of our colorectal carcinomas with LOH for APC gene are copy number neutral. However, one-third of our cases showed copy number loss, suggesting that duplication of the remaining allele is not required for the development of a colorectal carcinoma.

Sequential occurrence of preneoplastic lesions and accumulation of loss of heterozygosity in patients with gallbladder stones suggest causal association with gallbladder cancer.

PubMed

Jain, Kajal; Mohapatra, Trilochan; Das, Prasenjit; Misra, Mahesh Chandra; Gupta, Siddhartha Datta; Ghosh, Manju; Kabra, Madhulika; Bansal, Virinder Kumar; Kumar, Subodh; Sreenivas, Vishnubhatla; Garg, Pramod Kumar

2014-12-01

Causal association of gallbladder stones with gallbladder cancer (GBC) is not yet well established. To study the frequency of occurrence of preneoplastic histological lesions and loss of heterozygosity (LOH) of tumor suppressor genes in patients with gallstones. All consecutive patients with gallstones undergoing cholecystectomy from 2007-2011 were included prospectively. Histological examination of the gallbladder specimens was done for preneoplastic lesions. LOH at 8 loci, that is 3p12, 3p14.2, 5q21, 9p21, 9q, 13q, 17p13, and 18q for tumor suppressor genes (DUTT1, FHIT, APC, p16, FCMD, RB1, p53, and DCC genes) that are associated with GBC was tested from microdissected preneoplastic lesions using microsatellite markers. These LOH were also tested in 30 GBC specimens. Of the 350 gallbladder specimens from gallstone patients, hyperplasia was found in 32%, metaplasia in 47.8%, dysplasia in 15.7%, and carcinoma in situ in 0.6%. Hyperplasia, metaplasia, and dysplasia alone were found in 11.7%, 24.6%, and 1.4% of patients, respectively. A combination of hyperplasia and dysplasia, metaplasia and dysplasia, and hyperplasia, metaplasia, and dysplasia was found in 3.4%, 6.3%, and 4.3% of patients, respectively. LOH was present in 2.1% to 47.8% of all the preneoplastic lesions at different loci. Fractional allelic loss was significantly higher in those with dysplasia compared with other preneoplastic lesions (0.31 vs 0.22; P = 0.042). No preneoplastic lesion or LOH was found in normal gallbladders. Patients with gallstones had a high frequency of preneoplastic lesions and accumulation of LOH at various tumor suppressor genes, suggesting a possible causal association of gallstones with GBC.

Loss of heterozygosity patterns provide fingerprints for genetic heterogeneity in multistep cancer progression of tobacco smoke-induced non-small cell lung cancer.

PubMed

Pan, Hongjie; Califano, Joseph; Ponte, Jose F; Russo, Andrea L; Cheng, Kuang-hung; Thiagalingam, Arunthathi; Nemani, Pratima; Sidransky, David; Thiagalingam, Sam

2005-03-01

Dilution end point loss of heterozygosity (LOH) analysis, a novel approach for the analysis of LOH, was used to evaluate allelic losses with the use of 21 highly polymorphic microsatellite markers at nine chromosomal sites most frequently affected in smoking-related non-small cell lung cancers. Allelotyping was done for bronchial epithelial cells and matching blood samples from 23 former and current smokers and six nonsmokers as well as in 33 adenocarcinomas and 25 squamous cell carcinomas (SCC) and corresponding matching blood from smokers. Major conclusions from these studies are as follows: (a) LOH at chromosomal sites 8p, 9p, 11q, and 13q (P >0.05, Fisher's exact test) are targeted at the early stages, whereas LOH at 1p, 5q, 17p, and 18q (P <0.05, Fisher's exact test) occur at the later stages of non-small cell lung cancer progression; (b) LOH at 1p, 3p, 5q, 8p, 9p, 11q, 13q, 17p, and 18q occurs in over 45% of the tobacco smokers with SCC and adenocarcinoma; (c) compared with bronchial epithelial cells from smokers, there is a significantly higher degree of LOH at 1p, 5q, and 18q in adenocarcinoma and at 1p, 3p, and 17p in SCC (P <0.05, Fisher's exact test). We propose that lung cancer progression induced by tobacco smoke occurs in a series of target gene inactivations/activations in defined modules of a global network. The gatekeeper module consists of multiple alternate target genes, which is inclusive of but not limited to genes localized to chromosomal loci 8p, 9p, 11q, and 13q.

Genetic diversities of 21 non-CODIS autosomal STRs of a Chinese Tibetan ethnic minority group in Lhasa.

PubMed

Zhu, Bo-feng; Shen, Chun-mei; Wang, Hong-dan; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Guo, Jian-xin; Huang, Jing-feng; Jing, Hang; Liu, Xin-she

2011-07-01

In the present study, we investigated 21 short tandem repeat (STR) loci (D6S474, D12ATA63, D22S1045, D10S1248, D1S1677, D11S4463, D1S1627, D3S4529, D2S441, D6S1017, D4S2408, D19S433, D17S1301, D1GATA113, D18S853, D20S482, D14S1434, D9S1122, D2S1776, D10S1435, D5S2500), which are not included in the Combined DNA Index System and Amelogenin locus in 104 randomly selected healthy autochthonous individuals from the Tibetan ethnic minority group residing in the Lhasa region, Tibet Autonomous Region of China. Allelic frequencies, common forensic statistical parameters, and the Hardy-Weinberg equilibrium in this population were calculated with a modified PowerState V12.xls. A total of 143 alleles were found in the Tibetan group with corresponding allelic frequencies ranging from 0.005 to 0.582. The observed heterozygosity, the expected heterozygosity, the power of discrimination, the power of exclusion, and the polymorphic information content ranged from 0.615 to 0.817, 0.559 to 0.787, 0.727 to 0.926, 0.310 to 0.632, and 0.488 to 0.760, respectively. Chi-square tests of the observed genotype frequencies and expected genotype frequencies in the samples showed no departure from the Hardy-Weinberg equilibrium at all loci except for D5S2500. Our results demonstrate that these 21 STRs are highly polymorphic and suitable for anthropological research, population genetics, and forensic paternity testing and human individual identification in this region, and can enrich Chinese ethnical genetic informational resources.

BRIEF-REPORT New set of microsatellites for Chinese tallow tree, Triadica sebifera.

PubMed

Zhuang, Y F; Wang, Z F; Wu, L F

2017-04-05

Chinese tallow (Triadica sebifera) is an important crop and ornamental tree. After it was introduced into the USA, it gradually became a noxious invasive tree in south-eastern America since the middle of the 1900s. Because only six microsatellites were reported previously in T. sebifera, to better understand the genetic diversity and population dynamics of such species, we reported here 28 new microsatellite markers. For these 28 microsatellites, the number of alleles per locus ranged from 2-16. The expected heterozygosity and the expected heterozygosity corrected for sample size varied from 0.0796 to 0.9081 and from 0.0805 to 0.9176, respectively. These microsatellites will provide additional choice to investigate the genetic diversity and structure in T. sebifera.

Crystals of Janus colloids at various interaction ranges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Preisler, Z.; Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht; Vissers, T.

We investigate the effect of interaction range on the phase behaviour of Janus particles with a Kern-Frenkel potential. Specifically, we study interaction ranges Δ = 0.1σ, 0.3σ, 0.4σ, 0.5σ with σ the particle diameter, and use variable box shape simulations to predict crystal structures. We found that changing the interaction range beyond 0.2σ drastically increases the variety of possible crystal structures. In addition to close-packed structures, we find body-centered tetragonal and AA-stacked hexagonal crystals, as well as several lamellar crystals. For long interaction ranges and low temperatures, we also observe an extremely large number of metastable structures which compete withmore » the thermodynamically stable ones. These competing structures hinder the detection of the lowest-energy crystal structures, and are also likely to interfere with the spontaneous formation of the ground-state structure. Finally, we determine the gas-liquid coexistence curves for several interaction ranges, and observe that these are metastable with respect to crystallization.« less

Comparative study on the use of specific and heterologous microsatellite primers in the stingless bees Melipona rufiventris and M. mondury (Hymenoptera, Apidae)

PubMed Central

2010-01-01

Due to their high degree of polymorphism, microsatellites are considered useful tools for studying population genetics. Nevertheless, studies of genetic diversity in stingless bees by means of these primers have revealed a low level of polymorphism, possibly the consequence of the heterologous primers used, since in most cases these were not specifically designed for the species under consideration. Herein we compared the number of polymorphic loci and alleles per locus, as well as observed heterozygosity in Melipona rufiventris and M. mondury populations, using specific and heterologous primers. The use of specific primers placed in evidence the greater frequency of polymorphic loci and alleles per locus, besides an expressive increase in observed heterozygosity in M. rufiventris and M. mondury, thereby reinforcing the idea that populational studies should be undertaken by preferably using species-specific microsatellite primers. PMID:21637499

Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides.

PubMed

Jin, Yuqing; Bi, Quanxin; Guan, Wenbin; Mao, Jian-Feng

2015-09-01

Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species.

Isolation and Characterization of Polymorphic Microsatellite Loci from Metapenaeopsis barbata Using PCR-Based Isolation of Microsatellite Arrays (PIMA)

PubMed Central

Chiang, Tzen-Yuh; Tzeng, Tzong-Der; Lin, Hung-Du; Cho, Ching-Ju; Lin, Feng-Jiau

2012-01-01

The red-spot prawn, Metapenaeopsis barbata, is a commercially important, widely distributed demersal species in the Indo-West Pacific Ocean. Overfishing has made its populations decline in the past decade. To study conservation genetics, eight polymorphic microsatellite loci were isolated. Genetic characteristics of the SSR (simple sequence repeat) fingerprints were estimated in 61 individuals from adjacent seas of Taiwan and China. The number of alleles, ranging from 2 to 4, as well as observed and expected heterozygosities in populations, ranging from 0.048 to 0.538, and 0.048 and 0.654, respectively, were detected. No deviation from Hardy–Weinberg expectations was detected at either locus. No significant linkage disequilibrium was detected in locus pairs. The polymorphic microsatellite loci will be useful for investigations of the genetic variation, population structure, and conservation genetics of this species. PMID:22489123

Isolation and characterization of novel microsatellites from the critically endangered hawksbill sea turtle (Eretmochelys imbricata).

PubMed

Miro-Herrans, Aida T; Velez-Zuazo, Ximena; Acevedo, Jenny P; McMillan, W Owen

2008-09-01

We isolated and characterized 12 microsatellite loci from the hawksbill sea turtle (Eretmochelys imbricata). The loci exhibited a variable number of alleles that ranged from three to 14 with an average observed heterozygosity of 0.70 (SD 0.18) across 40 hawksbill turtles from the Caribbean. The polymorphism exhibited individually and in combination makes them suitable for fine-scale genetic studies. In particular, the low probability of identity and high paternity exclusion of these markers makes them highly useful for parentage and relatedness studies. These new markers greatly increase the power of genetic studies directed towards the conservation of this endangered species. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Isolation and characterization of microsatellite markers in Acca sellowiana (Berg) Burret.

PubMed

Santos, K L; Santos, M O; Laborda, P R; Souza, A P; Peroni, N; Nodari, R O

2008-09-01

Acca sellowiana has commercial potential due to the quality and the unique flavor of its fruit. Conservation of natural populations and management of breeding programmes would benefit from the availability of molecular markers that could be used to characterize levels and distribution of genetic variability. Thus, 13 microsatellite markers were developed from an enriched genomic library of A. sellowiana. They were characterized using 40 samples. The expected and observed heterozygosities ranged from 0.513 to 0.913 and from 0.200 to 0.889, respectively. These are the first microsatellite loci characterized from A. sellowiana that will contribute to improve researches on its genetic conservation, characterization and breeding. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Characterization of 10 new nuclear microsatellite markers in Acca sellowiana (Myrtaceae).

PubMed

Klabunde, Gustavo H F; Olkoski, Denise; Vilperte, Vinicius; Zucchi, Maria I; Nodari, Rubens O

2014-06-01

Microsatellite primers were identified and characterized in Acca sellowiana in order to expand the limited number of pre-existing polymorphic markers for use in population genetic studies for conservation, phylogeography, breeding, and domestication. • A total of 10 polymorphic microsatellite primers were designed from clones obtained from a simple sequence repeat (SSR)-enriched genomic library. The primers amplified di- and trinucleotide repeats with four to 27 alleles per locus. In all tested populations, the observed heterozygosity ranged from 0.269 to 1.0. • These new polymorphic SSR markers will allow future genetic studies to be denser, either for genetic structure characterization of natural populations or for studies involving genetic breeding and domestication process in A. sellowiana.

Genetic differentiation and population structure of five ethnic groups of Punjab (North-West India).

PubMed

Singh, Gagandeep; Talwar, Indu; Sharma, Rubina; Matharoo, Kawaljit; Bhanwer, A J S

2016-12-01

The state of Punjab in the North-West part of India has acted as the main passage for all the major human invasions into the Indian subcontinent. It has resulted in the mixing of foreign gene pool into the local populations, which led to an extensive range of genetic diversity and has influenced the genetic structure of populations in Punjab, North-West India. The present study was conducted to examine the genetic structure, relationships, and extent of genetic differentiation in five Indo-European speaking ethnic groups of Punjab. A total of 1021 unrelated samples belonging to Banias, Brahmins, Jat Sikhs, Khatris, and Scheduled castes were analyzed for four human-specific Ins/Del polymorphic loci (ACE, APO, PLAT, and D1) and three restriction fragment length polymorphisms ESR (PvuII), LPL (PvuII), and T2 (MspI) using Polymerase chain reaction (PCR). All the loci were found to be polymorphic among the studied populations. The frequency of the Alu insertion at APO locus was observed to exhibit the highest value (82.6-96.3 %), whereas D1 exhibited the lowest (26.5-45.6 %) among all the ethnic groups. The average heterozygosity among the studied populations ranged from 0.3816 in Banias to 0.4163 in Khatris. The F ST values ranged from 0.0418 to 0.0033 for the PLAT and LPL loci, respectively, with an average value being 0.0166. Phylogenetic analysis revealed that Banias and Khatris are genetically closest to each other. The Jat Sikhs are genetically close to Brahmins and are distant from the Banias. The Jat Sikhs, Banias, Brahmins, and Khatris are genetically very distant from the Scheduled castes. Overall, Uniform allele frequency distribution patterns, high average heterozygosity values, and a small degree of genetic differentiation in this study suggest a genetic proximity among the selected populations. A low level of genetic differentiation was observed in the studied population groups indicating that genetic drift might have been small or negligible in shaping

Climate-Driven Range Extension of Amphistegina (Protista, Foraminiferida): Models of Current and Predicted Future Ranges

PubMed Central

Langer, Martin R.; Weinmann, Anna E.; Lötters, Stefan; Bernhard, Joan M.; Rödder, Dennis

2013-01-01

Species-range expansions are a predicted and realized consequence of global climate change. Climate warming and the poleward widening of the tropical belt have induced range shifts in a variety of marine and terrestrial species. Range expansions may have broad implications on native biota and ecosystem functioning as shifting species may perturb recipient communities. Larger symbiont-bearing foraminifera constitute ubiquitous and prominent components of shallow water ecosystems, and range shifts of these important protists are likely to trigger changes in ecosystem functioning. We have used historical and newly acquired occurrence records to compute current range shifts of Amphistegina spp., a larger symbiont-bearing foraminifera, along the eastern coastline of Africa and compare them to analogous range shifts currently observed in the Mediterranean Sea. The study provides new evidence that amphisteginid foraminifera are rapidly progressing southwestward, closely approaching Port Edward (South Africa) at 31°S. To project future species distributions, we applied a species distribution model (SDM) based on ecological niche constraints of current distribution ranges. Our model indicates that further warming is likely to cause a continued range extension, and predicts dispersal along nearly the entire southeastern coast of Africa. The average rates of amphisteginid range shift were computed between 8 and 2.7 km year−1, and are projected to lead to a total southward range expansion of 267 km, or 2.4° latitude, in the year 2100. Our results corroborate findings from the fossil record that some larger symbiont-bearing foraminifera cope well with rising water temperatures and are beneficiaries of global climate change. PMID:23405081

Climate-driven range extension of Amphistegina (protista, foraminiferida): models of current and predicted future ranges.

PubMed

Langer, Martin R; Weinmann, Anna E; Lötters, Stefan; Bernhard, Joan M; Rödder, Dennis

2013-01-01

Species-range expansions are a predicted and realized consequence of global climate change. Climate warming and the poleward widening of the tropical belt have induced range shifts in a variety of marine and terrestrial species. Range expansions may have broad implications on native biota and ecosystem functioning as shifting species may perturb recipient communities. Larger symbiont-bearing foraminifera constitute ubiquitous and prominent components of shallow water ecosystems, and range shifts of these important protists are likely to trigger changes in ecosystem functioning. We have used historical and newly acquired occurrence records to compute current range shifts of Amphistegina spp., a larger symbiont-bearing foraminifera, along the eastern coastline of Africa and compare them to analogous range shifts currently observed in the Mediterranean Sea. The study provides new evidence that amphisteginid foraminifera are rapidly progressing southwestward, closely approaching Port Edward (South Africa) at 31°S. To project future species distributions, we applied a species distribution model (SDM) based on ecological niche constraints of current distribution ranges. Our model indicates that further warming is likely to cause a continued range extension, and predicts dispersal along nearly the entire southeastern coast of Africa. The average rates of amphisteginid range shift were computed between 8 and 2.7 km year(-1), and are projected to lead to a total southward range expansion of 267 km, or 2.4° latitude, in the year 2100. Our results corroborate findings from the fossil record that some larger symbiont-bearing foraminifera cope well with rising water temperatures and are beneficiaries of global climate change.

Microsatellite analysis of loss of heterozygosity on chromosomes 9q, 11p and 17p in medulloblastomas.

PubMed

Albrecht, S; von Deimling, A; Pietsch, T; Giangaspero, F; Brandner, S; Kleihues, P; Wiestler, O D

1994-02-01

Medulloblastoma (MB) is a primitive neuroectodermal tumour of the cerebellum whose pathogenesis is poorly understood. Previous studies suggest a role for loci on chromosomes 11p and 17p in the pathogenesis of MB. Evidence for another potential MB locus has recently emerged from studies on Gorlin syndrome (GS), an autosomal dominant syndrome with multiple basal cell carcinomas, epithelial jaw cysts, and skeletal anomalies. Since GS can be associated with MB, we examined sporadic (non-GS) cases of MB for evidence of loss of heterozygosity (LOH) on chromosome 9 where a putative GS locus has been localized to band q31. Nineteen paired blood and MB DNA specimens from 16 patients (11 primary tumours, two primary with recurrent tumours, one primary tumour and cell line, two cell lines) were studied by PCR analysis of microsatellites at D9S55 (9p12), D9S15 (9q13-q21.1), D9S127 (9q21.1-21.3), D9S12 (9q22.3), D9S58 (9q22.3-q31), D9S109 (9q31), D9S53 (9q31), GSN (9q33), D9S60 (9q33-q34), D9S65 (9q33-q34), ASS (9q34), D9S67 (9q34.3), TH (11p15.5), D11S490 (11q23.3), D17S261 (17p11.2-12), D17S520 (17p12), TP53 (17p13.1), D17S5 (17p13.3), D17S515 (17q22-qter), and by RFLP analysis at the WT-1 locus (11p13). Only two tumours had LOH on 9q. One was non-informative at D9S15, D9S65, and GSN but showed LOH at D9S127, D9S12, D9S58, D9S109, D9S53, D9S60, ASS, and D9S67. The other was uninterpretable at D9S65 and non-informative at D9S15, D9S58, D9S53, and D9S67 but exhibited LOH at D9S127, D9S12, D9S109, GSN, D9S60, and ASS. Both these cases were informative at D9S55 without LOH.(ABSTRACT TRUNCATED AT 250 WORDS)

Fossil preservation and the stratigraphic ranges of taxa

NASA Technical Reports Server (NTRS)

Foote, M.; Raup, D. M.

1996-01-01

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of

Development and characterization of 17 polymorphic microsatellite loci in the faucet snail, Bithynia tentaculata (Gastroposa: Caenogastropoda; Bithyniidae)

USGS Publications Warehouse

Henningsen, Justin P.; Lance, Stacey L.; Jones, Kenneth L.; Hagen, Chris; Laurila, Joshua; Cole, Rebecca A.; Perez, Kathryn E.

2010-01-01

Bithynia tentaculata (Linnaeus, 1758), a snail native to Europe, was introduced into the US Great Lakes in the 1870's and has spread to rivers throughout the Northeastern US and Upper Mississippi River (UMR). Trematode parasites, for which B. tentaculata is a host, have also been introduced and are causing widespread waterfowl mortality in the UMR. Waterfowl mortality is caused by ingestion of trematode-infected B. tentaculata or insects infected with parasites released from the snails. We isolated and characterized 17 microsatellite loci from the invasive faucet snail, B. tentaculata (Gastropoda: Caenogastropoda: Bithyniidae). Loci were screened in 24 individuals of B. tentaculata. The number of alleles per locus ranged from 2 to 6, observed heterozygosity ranged from 0.050 to 0.783, and the probability of identity values ranged from 0.10 to 0.91. These new loci provide tools for examining the origin and spread of invasive populations in the US and management activities to prevent waterfowl mortality.

Development and Molecular Characterization of Novel Polymorphic Genomic DNA SSR Markers in Lentinula edodes.

PubMed

Moon, Suyun; Lee, Hwa-Yong; Shim, Donghwan; Kim, Myungkil; Ka, Kang-Hyeon; Ryoo, Rhim; Ko, Han-Gyu; Koo, Chang-Duck; Chung, Jong-Wook; Ryu, Hojin

2017-06-01

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

Genetic diversity and the mating system of a rare Mexican Piñon, Pinus pinceana, and a comparison with Pinus maximartinezii (Pinaceae)

Treesearch

F. Thomas Ledig; Miguel A. Capó-Arteaga; Paul D. Hodgskiss; Hassan Sbay; Celestino Flores-López; M. Thompson Conkle; Basilio Bermejo-Velázquez

2001-01-01

Weeping piñon (Pinus pinceana) has a restricted and fragmented range, trees are widely scattered within populations, and reproduction is limited. Nevertheless, genetic diversity was high; based on 27 isozyme loci in 18 enzyme systems, unbiased expected heterozygosity averaged 0.174. Differentiation also was high (FST = 0.152),...

Molecular and morphological characterization of local apple cultivars in Southern Spain.

PubMed

Pérez-Romero, L F; Suárez, M P; Dapena, E; Rallo, P

2015-02-20

The number of local and traditional fruit cultivars in Andalusia (Southern Spain) has decreased dramatically since the 1970s when new commercial cultivars from breeding programs were introduced, replacing old varieties, and thus decreasing genetic diversity. The present study was included in a genetic resources project with the objective of identifying and preserving traditional fruit tree cultivars in Southern Spain. The goal of this study was to begin the characterization of 29 apple accessions (Malus x domestica Borkh) belonging to 13 traditional cultivar denominations. For molecular characterization studies, 12 simple sequence repeat markers previously developed for apple species were used. Morphological characterization was performed using 33 fruit traits. A total of 115 alleles were amplified for the 12 loci, ranging from 7 (CH01h01, CH01h10, and GD 12) to 13 alleles per locus (CH02c11). Forty-one alleles were unique to specific genotypes. The locus with the highest number of detected unique alleles was CH01f03b with 6 alleles. Expected heterozygosity ranged from 0.74 for CH01h10 to 0.88 for CH02c11, with an average of 0.82. Observed heterozygosity varied from 0.45 for CH01h01 to 1.0 for CH02d08, with an average of 0.86. Three homonyms were found for accessions belonging to varieties 'Maguillo', 'Pero Minguela', and 'Castellana'. The most discriminant morphological characters studied revealed no homonyms or synonyms among cultivar denominations, although they are useful for describing varietal characteristics that have not been previously defined.

Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers*

PubMed Central

Zhang, Gu-wen; Xu, Sheng-chun; Mao, Wei-hua; Hu, Qi-zan; Gong, Ya-ming

2013-01-01

The development of expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating plant genetic diversity. In the present study, 22 polymorphic EST-SSRs from grain soybean were identified and used to assess the genetic diversity in 48 vegetable soybean accessions. Among the 22 EST-SSR loci, tri-nucleotides were the most abundant repeats, accounting for 50.00% of the total motifs. GAA was the most common motif among tri-nucleotide repeats, with a frequency of 18.18%. Polymorphic analysis identified a total of 71 alleles, with an average of 3.23 per locus. The polymorphism information content (PIC) values ranged from 0.144 to 0.630, with a mean of 0.386. Observed heterozygosity (H o) values varied from 0.0196 to 1.0000, with an average of 0.6092, while the expected heterozygosity (H e) values ranged from 0.1502 to 0.6840, with a mean value of 0.4616. Principal coordinate analysis and phylogenetic tree analysis indicated that the accessions could be assigned to different groups based to a large extent on their geographic distribution, and most accessions from China were clustered into the same groups. These results suggest that Chinese vegetable soybean accessions have a narrow genetic base. The results of this study indicate that EST-SSRs from grain soybean have high transferability to vegetable soybean, and that these new markers would be helpful in taxonomy, molecular breeding, and comparative mapping studies of vegetable soybean in the future. PMID:23549845

Foraging optimally for home ranges

USGS Publications Warehouse

Mitchell, Michael S.; Powell, Roger A.

2012-01-01

Economic models predict behavior of animals based on the presumption that natural selection has shaped behaviors important to an animal's fitness to maximize benefits over costs. Economic analyses have shown that territories of animals are structured by trade-offs between benefits gained from resources and costs of defending them. Intuitively, home ranges should be similarly structured, but trade-offs are difficult to assess because there are no costs of defense, thus economic models of home-range behavior are rare. We present economic models that predict how home ranges can be efficient with respect to spatially distributed resources, discounted for travel costs, under 2 strategies of optimization, resource maximization and area minimization. We show how constraints such as competitors can influence structure of homes ranges through resource depression, ultimately structuring density of animals within a population and their distribution on a landscape. We present simulations based on these models to show how they can be generally predictive of home-range behavior and the mechanisms that structure the spatial distribution of animals. We also show how contiguous home ranges estimated statistically from location data can be misleading for animals that optimize home ranges on landscapes with patchily distributed resources. We conclude with a summary of how we applied our models to nonterritorial black bears (Ursus americanus) living in the mountains of North Carolina, where we found their home ranges were best predicted by an area-minimization strategy constrained by intraspecific competition within a social hierarchy. Economic models can provide strong inference about home-range behavior and the resources that structure home ranges by offering falsifiable, a priori hypotheses that can be tested with field observations.

Long-range acoustic observations of the Eyjafjallajökull eruption, Iceland, April-May 2010

NASA Astrophysics Data System (ADS)

Matoza, Robin S.; Vergoz, Julien; Le Pichon, Alexis; Ceranna, Lars; Green, David N.; Evers, Läslo G.; Ripepe, Maurizio; Campus, Paola; Liszka, Ludwik; Kvaerna, Tormod; Kjartansson, Einar; Höskuldsson, Ármann

2011-03-01

The April-May 2010 summit eruption of Eyjafjallajökull, Iceland, was recorded by 14 atmospheric infrasound sensor arrays at ranges between 1,700 and 3,700 km, indicating that infrasound from modest-size eruptions can propagate for thousands of kilometers in atmospheric waveguides. Although variations in both atmospheric propagation conditions and background noise levels at the sensors generate fluctuations in signal-to-noise ratios and signal detectability, array processing techniques successfully discriminate between volcanic infrasound and ambient coherent and incoherent noise. The current global infrasound network is significantly more dense and sensitive than any previously operated network and signals from large volcanic explosions are routinely recorded. Because volcanic infrasound is generated during the explosive release of fluid into the atmosphere, it is a strong indicator that an eruption has occurred. Therefore, long-range infrasonic monitoring may aid volcanic explosion detection by complementing other monitoring technologies, especially in remote regions with sparse ground-based instrument networks.

Connecting Surface Emissions, Convective Uplifting, and Long-Range Transport of Carbon Monoxide in the Upper Troposphere: New Observations from the Aura Microwave Limb Sounder

NASA Technical Reports Server (NTRS)

Jiang, Jonathan H.; Livesey, Nathaniel J.; Su, Hui; Neary, Lori; McConnell, John C.; Richards, Nigel A. D.

2007-01-01

Two years of observations of upper tropospheric (UT) carbon monoxide (CO) from the Aura Microwave Limb Sounder are analyzed; in combination with the CO surface emission climatology and data from the NCEP analyses. It is shown that spatial distribution, temporal variation and long-range transport of UT CO are closely related to the surface emissions, deep-convection and horizontal winds. Over the Asian monsoon region, surface emission of CO peaks in boreal spring due to high biomass burning in addition to anthropogenic emission. However, the UT CO peaks in summer when convection is strongest and surface emission of CO is dominated by anthropogenic source. The long-range transport of CO from Southeast Asia across the Pacific to North America, which occurs most frequently during boreal summer, is thus a clear imprint of Asian anthropogenic pollution influencing global air quality.

Use of X-Chromosome Inactivation Pattern to Analyze the Clonality of 14 Female Cases of Kaposi Sarcoma.

PubMed

Yuan, Ding; XiuJuan, Wu; Yan, Zhang; JunQin, Liang; Fang, Xiang; Shirong, Yu; Xiaojing, Kang; Yanyan, Feng; Weidong, Wu; Dong, Luo; Qingli, Lu; DeZhi, Zhang; XiongMing, Pu

2015-06-16

Kaposi sarcoma (KS) has features of both neoplastic growth and hyperplastic proliferation. It is the most common tumor seen in patients with HIV infection. Whether KS is a real tumor or a benign hyperplastic disease is not known. Tissues from KS and cutaneous hemangioma lesion DNA were extracted, and then digested with methylation-sensitive restriction endonuclease HpaII. Human androgen receptor gene (HUMARA) was amplified with PCR method and the product was separated on 10% denaturing polyacrylamide gels and stained with ethylene dibromide (EB) to show the polymorphism of HUMARA. Phosphoglycerate kinase (PGK) was amplified and the product was digested by BStXI, agarose gel and EB stained to show the polymorphism of PGK. Finally, we analyzed the clonality of KS. In the 14 patients with KS, heterozygosity of the HUMARA gene was observed in 12 (85.7%) cases. Loss of heterozygosity of HUMARA gene on X-chromosome (without HpaII digestion there were 2 bands, after HpaII digestion there were just 1 of the bands), representing monoclonal origin, was present in 11 cases of Kaposi sarcoma. Heterozygosity of the PGK gene was observed in 5 (35.7%) cases, which all represent monoclonal origin. There was no significant difference according to country, stage, or HIV and HHV-8 (P>0.05). The current findings suggest that Kaposi sarcoma is a clonal neoplasm, not a reactive proliferation.

Gene diversity and genetic structure in a narrow endemic, torrey pine (Pinus torreyana Parry ex Carr.)

Treesearch

F. Thomas Ledig; M. Thompson Conkle

1983-01-01

Recent reviews have suggested that tree species are the most variable of organisms, as measured by proportion of polymorphic loci or average heterozygosity (Hamrick, 1979; Hamrick et al., 1979). Average heterozygosity is greater than 0.30 for several conifers. By contrast, annual herbaceous species have a mean heterozygosity of 0.13 (Hamrick et al., 1979).

The Long Range Reconnaissance and Observation System (LORROS) with the Kollsman, Inc. Model LH-40, Infrared (Erbium) Laser Rangefinder hazard analysis and safety assessment.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Augustoni, Arnold L.

A laser hazard analysis and safety assessment was performed for the LH-40 IR Laser Rangefinder based on the 2000 version of the American National Standard Institute's Standard Z136.1, for the Safe Use of Lasers and Z136.6, for the Safe Use of Lasers Outdoors. The LH-40 IR Laser is central to the Long Range Reconnaissance and Observation System (LORROS). The LORROS is being evaluated by the Department 4149 Group to determine its capability as a long-range assessment tool. The manufacture lists the laser rangefinder as 'eye safe' (Class 1 laser classified under the CDRH Compliance Guide for Laser Products and 21more » CFR 1040 Laser Product Performance Standard). It was necessary that SNL validate this prior to its use involving the general public. A formal laser hazard analysis is presented for the typical mode of operation.« less

Stable method for estimation of laser ranging

NASA Astrophysics Data System (ADS)

Kurbasova, G. S.; Rykhlova, L. V.

A noise-immunity variant of the least squares method was developed for the preliminary analysis of laser-ranging data. The method takes into account the influence of many physical phenomena accompanying the generation of the laser-ranging signals, their passing through the optical channel, the distribution in the atmosphere, the scattering on the corner reflector, and their registration. The method was demonstrated on the example of Lageos observations made with the Intercosmos laser radar.

Home range defense in the red fox, Vulpes vulpes L

USGS Publications Warehouse

Preston, E.M.

1975-01-01

This paper describes the home range defense behavior observed when nonresident male red foxes were introduced into established home ranges of resident male-female pairs. In 12 observation periods, four intruders were introduced to each of three mated pairs which had been given three weeks to acclimate to a 4.05-hectare, fenced enclosure. The residents centered their activities around a natural den and the frequency of intruder-resident encounters decreased rapidly with increasing distance from the den. The primary home range defense was continual harassment of the intruders by the resident males through agonistic displays and chases. Physical contact was rare. Even though the resident males were dominant in less than a majority of the interactions observed, they were usually successful in displacing the intruders within a few hours. The resident females seldom interacted with the intruders.

Spatial Autocorrelation Can Generate Stronger Correlations between Range Size and Climatic Niches Than the Biological Signal - A Demonstration Using Bird and Mammal Range Maps.

PubMed

Boucher-Lalonde, Véronique; Currie, David J

2016-01-01

Species' geographic ranges could primarily be physiological tolerances drawn in space. Alternatively, geographic ranges could be only broadly constrained by physiological climatic tolerances: there could generally be much more proximate constraints on species' ranges (dispersal limitation, biotic interactions, etc.) such that species often occupy a small and unpredictable subset of tolerable climates. In the literature, species' climatic tolerances are typically estimated from the set of conditions observed within their geographic range. Using this method, studies have concluded that broader climatic niches permit larger ranges. Similarly, other studies have investigated the biological causes of incomplete range filling. But, when climatic constraints are measured directly from species' ranges, are correlations between species' range size and climate necessarily consistent with a causal link? We evaluated the extent to which variation in range size among 3277 bird and 1659 mammal species occurring in the Americas is statistically related to characteristics of species' realized climatic niches. We then compared how these relationships differed from the ones expected in the absence of a causal link. We used a null model that randomizes the predictor variables (climate), while retaining their broad spatial autocorrelation structure, thereby removing any causal relationship between range size and climate. We found that, although range size is strongly positively related to climatic niche breadth, range filling and, to a lesser extent, niche position in nature, the observed relationships are not always stronger than expected from spatial autocorrelation alone. Thus, we conclude that equally strong relationships between range size and climate would result from any processes causing ranges to be highly spatially autocorrelated.

Genetic diversity and seed production in Santa Lucia fir (Abies bracteata),a relict of the Miocene broadleaved evergreen forest

Treesearch

F. Thomas Ledig; Paul D. Hodgskiss; David R. Johnson

2006-01-01

Santa Lucia fir (Abies bracteata), is a unique fir, the sole member of the subgenus Pseudotorreya. It is a relict of the Miocene broadleaved evergreen sclerophyll forest, and is now restricted to a highly fragmented range in the Santa Lucia Mountains of central coastal California. Expected heterozygosity for 30 isozyme loci in 18 enzyme systems...

Genetic diversity, genetic structure, and mating system of brewer spruce (Pinaceae), a relict of the acto-tertiary forest

Treesearch

F. Thomas Ledig; Paul D. Hodgskiss; David R. Johnson

2005-01-01

Brewer spruce (Picea breweriana), a relict of the widespread Arcto-Tertiary forests, is now restricted to a highly fragmented range in the Klamath Region of California and Oregon. Expected heterozygosity for 26 isozyme loci, averaged over 10 populations, was 0.121. More notable than the relatively high level of diversity when compared to other woody...

Tonopah test range - outpost of Sandia National Laboratories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, L.

Tonopah Test Range is a unique historic site. Established in 1957 by Sandia Corporation, Tonopah Test Range in Nevada provided an isolated place for the Atomic Energy Commission to test ballistics and non-nuclear features of atomic weapons. It served this and allied purposes well for nearly forty years, contributing immeasurably to a peaceful conclusion to the long arms race remembered as the Cold War. This report is a brief review of historical highlights at Tonopah Test Range. Sandia`s Los Lunas, Salton Sea, Kauai, and Edgewood testing ranges also receive abridged mention. Although Sandia`s test ranges are the subject, the centralmore » focus is on the people who managed and operated the range. Comments from historical figures are interspersed through the narrative to establish this perspective, and at the end a few observations concerning the range`s future are provided.« less

Development, characterization, and cross-amplification of 16 microsatellite primers for Atriplex tatarica (Amaranthaceae)1

PubMed Central

Kondrysová, Eva; Krak, Karol; Mandák, Bohumil

2017-01-01

Premise of the study: Microsatellite primers were developed to characterize the genetic diversity and structure of the annual herb Atriplex tatarica (Amaranthaceae) and to facilitate ecological and evolutionary studies of A. tatarica and its relatives. Methods and Results: Sixteen novel microsatellite primers were developed for A. tatarica based on high-throughput sequencing of enriched libraries. All markers were polymorphic, with the number of alleles per locus ranging from three to 25 and observed and expected heterozygosity ranging from 0.08 to 0.74 and 0.10 to 0.87, respectively. In addition, some of these loci were successfully amplified and showed polymorphisms in four Atriplex and seven Chenopodium species. Conclusions: The microsatellite markers published here will be useful in assessing genetic diversity, structure, and gene flow within and across populations of A. tatarica, as well as in other species of Atriplex and the related genus Chenopodium. PMID:29188148

Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides1

PubMed Central

Jin, Yuqing; Bi, Quanxin; Guan, Wenbin; Mao, Jian-Feng

2015-01-01

Premise of the study: Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. Methods and Results: We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. Conclusions: These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species. PMID:26421250

Microsatellite markers for the Pilosella alpicola group (Hieraciinae, Asteraceae) and their cross-amplification in other Hieraciinae genera.

PubMed

Vít, Petr; Šingliarová, Barbora; Zozomová-Lihová, Judita; Marhold, Karol; Krak, Karol

2015-08-01

Microsatellite markers were developed for the Pilosella alpicola group (Asteraceae), comprising four closely related species distributed in subalpine areas of Europe. These species are believed to have diverged recently, but display contrasting cytogeographic patterns and variation in breeding systems, representing a promising model system for studying plant speciation, adaptation, and recent polyploidization. We developed 17 microsatellite markers for the P. alpicola group using 454 sequencing. Sixteen markers were polymorphic, with the number of alleles per locus ranging from seven to 16 and observed and expected heterozygosity ranging from 0.45 to 0.84 and 0.72 to 0.92, respectively. Ten and five loci amplified in the related species, P. echioides and P. officinarum, respectively, but only two in Andryala and one in Hieracium s. str. The developed microsatellite markers have high potential to become useful tools to study microevolutionary processes in the P. alpicola group and related Pilosella species.

Development and characterization of microsatellite markers in the African forest elephant (Loxodonta cyclotis).

PubMed

Gugala, Natalie A; Ishida, Yasuko; Georgiadis, Nicholas J; Roca, Alfred L

2016-07-26

African elephants comprise two species, the savanna elephant (Loxodonta africana) and the forest elephant (L. cyclotis), which are distinct morphologically and genetically. Forest elephants are seriously threatened by poaching for meat and ivory, and by habitat destruction. However, microsatellite markers have thus far been developed only in African savanna elephants and Asian elephants, Elephas maximus. The application of microsatellite markers across deeply divergent lineages may produce irregular patterns such as large indels or null alleles. Thus we developed novel microsatellite markers using DNA from two African forest elephants. One hundred microsatellite loci were identified in next generation shotgun sequences from two African forest elephants, of which 53 were considered suitable for testing. Twenty-three microsatellite markers successfully amplified elephant DNA without amplifying human DNA; these were further characterized in 15 individuals from Lope National Park, Gabon. Three of the markers were monomorphic and four of them carried only two alleles. The remaining sixteen polymorphic loci carried from 3 to 8 alleles, with observed heterozygosity ranging from 0.27 to 0.87, expected heterozygosity from 0.40 to 0.86, and the Shannon diversity index from 0.73 to 1.86. Linkage disequilibrium was not detected between loci, and no locus deviated from Hardy-Weinberg equilibrium. The markers developed in this study will be useful for genetic analyses of the African forest elephant and contribute to their conservation and management.

Active Dendrites Enhance Neuronal Dynamic Range

PubMed Central

Gollo, Leonardo L.; Kinouchi, Osame; Copelli, Mauro

2009-01-01

Since the first experimental evidences of active conductances in dendrites, most neurons have been shown to exhibit dendritic excitability through the expression of a variety of voltage-gated ion channels. However, despite experimental and theoretical efforts undertaken in the past decades, the role of this excitability for some kind of dendritic computation has remained elusive. Here we show that, owing to very general properties of excitable media, the average output of a model of an active dendritic tree is a highly non-linear function of its afferent rate, attaining extremely large dynamic ranges (above 50 dB). Moreover, the model yields double-sigmoid response functions as experimentally observed in retinal ganglion cells. We claim that enhancement of dynamic range is the primary functional role of active dendritic conductances. We predict that neurons with larger dendritic trees should have larger dynamic range and that blocking of active conductances should lead to a decrease in dynamic range. PMID:19521531

Observation of short range order driven large refrigerant capacity in chemically disordered single phase compound Dy2Ni0.87Si2.95.

PubMed

Pakhira, Santanu; Mazumdar, Chandan; Choudhury, Dibyasree; Ranganathan, R; Giri, S

2018-05-16

In this work, we report the successful synthesis of a new intermetallic compound Dy2Ni0.87Si2.95 forming in single phase only with a chemically disordered structure. The random distribution of Ni/Si and crystal defects create a variation in the local electronic environment between the magnetic Dy ions. In the presence of both disorder and competing exchange interactions driven magnetic frustration, originating due to c/a ∼ 1, the compound undergoes spin freezing behaviour below 5.6 K. In the non-equilibrium state below the spin freezing behaviour, the compound exhibits aging phenomena and magnetic memory effects. In the magnetically short-range ordered region, much above the freezing temperature, an unusual occurrence of considerable magnetic entropy change, -ΔSmaxM ∼ 21 J kg-1 K-1 with large cooling power RCP ∼ 531 J kg-1 and adiabatic temperature change, ΔTad ∼ 10 K for a field change of 70 kOe, is observed for this short range ordered cluster-glass compound without any magnetic hysteresis loss.

Effects of sample size on KERNEL home range estimates

USGS Publications Warehouse

Seaman, D.E.; Millspaugh, J.J.; Kernohan, Brian J.; Brundige, Gary C.; Raedeke, Kenneth J.; Gitzen, Robert A.

1999-01-01

Kernel methods for estimating home range are being used increasingly in wildlife research, but the effect of sample size on their accuracy is not known. We used computer simulations of 10-200 points/home range and compared accuracy of home range estimates produced by fixed and adaptive kernels with the reference (REF) and least-squares cross-validation (LSCV) methods for determining the amount of smoothing. Simulated home ranges varied from simple to complex shapes created by mixing bivariate normal distributions. We used the size of the 95% home range area and the relative mean squared error of the surface fit to assess the accuracy of the kernel home range estimates. For both measures, the bias and variance approached an asymptote at about 50 observations/home range. The fixed kernel with smoothing selected by LSCV provided the least-biased estimates of the 95% home range area. All kernel methods produced similar surface fit for most simulations, but the fixed kernel with LSCV had the lowest frequency and magnitude of very poor estimates. We reviewed 101 papers published in The Journal of Wildlife Management (JWM) between 1980 and 1997 that estimated animal home ranges. A minority of these papers used nonparametric utilization distribution (UD) estimators, and most did not adequately report sample sizes. We recommend that home range studies using kernel estimates use LSCV to determine the amount of smoothing, obtain a minimum of 30 observations per animal (but preferably a?Y50), and report sample sizes in published results.

Deep seafloor arrivals in long range ocean acoustic propagation.

PubMed

Stephen, Ralph A; Bolmer, S Thompson; Udovydchenkov, Ilya A; Worcester, Peter F; Dzieciuch, Matthew A; Andrew, Rex K; Mercer, James A; Colosi, John A; Howe, Bruce M

2013-10-01

Ocean bottom seismometer observations at 5000 m depth during the long-range ocean acoustic propagation experiment in the North Pacific in 2004 show robust, coherent, late arrivals that are not readily explained by ocean acoustic propagation models. These "deep seafloor" arrivals are the largest amplitude arrivals on the vertical particle velocity channel for ranges from 500 to 3200 km. The travel times for six (of 16 observed) deep seafloor arrivals correspond to the sea surface reflection of an out-of-plane diffraction from a seamount that protrudes to about 4100 m depth and is about 18 km from the receivers. This out-of-plane bottom-diffracted surface-reflected energy is observed on the deep vertical line array about 35 dB below the peak amplitude arrivals and was previously misinterpreted as in-plane bottom-reflected surface-reflected energy. The structure of these arrivals from 500 to 3200 km range is remarkably robust. The bottom-diffracted surface-reflected mechanism provides a means for acoustic signals and noise from distant sources to appear with significant strength on the deep seafloor.

Development and characterization of microsatellite loci for the endangered scrub Lupine, Lupinus aridorum (Fabaceae)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ricono, Angela; Bupp, Glen; Peterson, Cheryl

Microsatellite primers were developed in scrub lupine ( Lupinus aridorum, Fabaceae), an endemic species to Florida that is listed as endangered in the United States, to assess connectivity among populations, identify hybrids, and examine genetic diversity. We isolated and characterized 12 microsatellite loci polymorphic in scrub lupine or in closely related species (i.e., sky-blue lupine [ L. diffusus] and Gulf Coast lupine [ L. westianus]). Loci showed low to moderate polymorphism, ranging from two to 14 alleles per locus and 0.01 to 0.86 observed heterozygosity. In conclusion, these loci are the first developed for Florida species of lupine and willmore » be used to determine differentiation among species and to aid in conservation of the endangered scrub lupine.« less

Transferability of short tandem repeat markers for two wild Canid species inhabiting the Brazilian Cerrado.

PubMed

Rodrigues, F M; Telles, M P C; Resende, L V; Soares, T N; Diniz-Filho, J A F; Jácomo, A T A; Silveira, L

2006-12-13

The maned wolf (Chrysocyon brachyurus) and the crab-eating fox (Cerdocyon thous) are two wild-canid species found in the Brazilian Cerrado. We tested cross-amplification and transferability of 29 short tandem repeat primers originally developed for cattle and domestic dogs and cats on 38 individuals of each of these two species, collected in the Emas National Park, which is the largest national park in the Cerrado region. Six of these primers were successfully transferred (CSSM-038, PEZ-05, PEZ-12, LOCO-13, LOCO-15, and PEZ-20); five of which were found to be polymorphic. Genetic parameter values (number of alleles per locus, observed and expected heterozygosities, and fixation indices) were within the expected range reported for canid populations worldwide.

Development and characterization of microsatellite loci for the endangered scrub Lupine, Lupinus aridorum (Fabaceae)

DOE PAGES

Ricono, Angela; Bupp, Glen; Peterson, Cheryl; ...

2015-04-01

Microsatellite primers were developed in scrub lupine ( Lupinus aridorum, Fabaceae), an endemic species to Florida that is listed as endangered in the United States, to assess connectivity among populations, identify hybrids, and examine genetic diversity. We isolated and characterized 12 microsatellite loci polymorphic in scrub lupine or in closely related species (i.e., sky-blue lupine [ L. diffusus] and Gulf Coast lupine [ L. westianus]). Loci showed low to moderate polymorphism, ranging from two to 14 alleles per locus and 0.01 to 0.86 observed heterozygosity. In conclusion, these loci are the first developed for Florida species of lupine and willmore » be used to determine differentiation among species and to aid in conservation of the endangered scrub lupine.« less

Development and characterization of 32 microsatellite loci in Genipa americana (Rubiaceae)1

PubMed Central

Manoel, Ricardo O.; Freitas, Miguel L. M.; Barreto, Mariana A.; Moraes, Mário L. T.; Souza, Anete P.; Sebbenn, Alexandre M.

2014-01-01

• Premise of the study: Microsatellite primers were developed for the tree species Genipa americana (Rubiaceae) for further population genetic studies. • Methods and Results: We identified 144 clones containing 65 repeat motifs from a genomic library enriched for (CT)8 and (GT)8 motifs. Primer pairs were developed for 32 microsatellite loci and validated in 40 individuals of two natural G. americana populations. Seventeen loci were polymorphic, revealing from three to seven alleles per locus. The observed and expected heterozygosities ranged from 0.24 to 1.00 and from 0.22 to 0.78, respectively. • Conclusions: The 17 primers identified as polymorphic loci are suitable to study the genetic diversity and structure, mating system, and gene flow in G. americana. PMID:25202610

Development and characterization of microsatellite loci in the endangered species Taxus wallichiana (Taxaceae).

PubMed

Gajurel, Jyoti Prasad; Cornejo, Carolina; Werth, Silke; Shrestha, Krishna Kumar; Scheidegger, Christoph

2013-03-01

Microsatellite primers were developed in the endangered tree species Taxus wallichiana from Nepal to investigate regional genetic differentiation, local genetic diversity, and gene flow for the conservation of this species under climate- and land-use change scenarios in mountain regions of Nepal. • We developed 10 highly polymorphic microsatellite markers from 454 DNA sequencing. Characterization of the new microsatellite loci was done in 99 individuals collected from three valleys with different climatic regimes. The number of alleles per locus varied from four to 12. Observed heterozygosity of populations, averaged across loci, ranged from 0.30 to 0.59. • The new markers provided by this study will substantially increase the resolution for detailed studies in phylogeography, population genetics, and parentage analysis.

Isolation and characterization of microsatellite markers in Acca sellowiana (Berg) Burret.

PubMed

Santos, K L; Santos, M O; Laborda, P R; Souza, A P; Peroni, N; Nodari, R O

2008-11-01

Acca sellowiana has commercial potential because of the quality and the unique flavor of its fruit. Conservation of natural populations and management of breeding programmes would benefit from the availability of molecular markers that could be used to characterize levels and distribution of genetic variability. Thus, 13 microsatellite markers were developed from an enriched genomic library of A. sellowiana. They were characterized using 40 samples. The expected and observed heterozygosities ranged from 0.513 to 0.913 and from 0.200 to 0.889, respectively. These are the first microsatellite loci characterized from A. sellowiana that will contribute to improve researches on the genetic conservation, characterization and breeding. Journal compilation © 2008 Blackwell Publishing Ltd. No claim to original US government works.

Variation of short tandem repeats within and between species belonging to the Canidae family.

PubMed

Fredholm, M; Winterø, A K

1995-01-01

Frequency distribution and allele size in 20 canine microsatellite loci were analyzed in 33 flat-coated retrievers, 32 dachshunds, 10 red foxes, and 10 Arctic foxes. Overall, the major difference between the two dog breeds was the relative allele frequencies rather than the size ranges of alleles at the individual locus. The average heterozygosity within the two dog breeds was not significantly different. Since the average heterozygosity at several polymorphic loci is a relative measure of heterogeneity within the population, analysis of heterozygosity within microsatellite loci is suggested as a measure for the diversity of populations. Eighty percent (16 of 20) of the canine microsatellite primer pairs amplified corresponding loci in the two fox species. This reflects a very high sequence conservation within the Canidae family relative to findings in, for instance, the Muridae family. This indicates that it will be possible to utilize the well-characterized fox karyotype instead of the dog karyotype as a step towards physical mapping of the dog genome. Analysis of exclusion power and probabilities of genetic identity between unrelated animals by use of the seven most informative loci demonstrated that it will be possible to assemble a panel of microsatellite loci that is effective for parentage analysis in all breeds.

Satellite and lunar laser ranging in infrared

NASA Astrophysics Data System (ADS)

Courde, Clement; Torre, Jean-Marie; Samain, Etienne; Martinot-Lagarde, Gregoire; Aimar, Mourad; Albanese, Dominique; Maurice, Nicolas; Mariey, Hervé; Viot, Hervé; Exertier, Pierre; Fienga, Agnes; Viswanathan, Vishnu

2017-05-01

We report on the implementation of a new infrared detection at the Grasse lunar laser ranging station and describe how infrared telemetry improves the situation. We present our first results on the lunar reflectors and show that infrared detection permits us to densify the observations and allows measurements during the new and the full moon periods. We also present the benefit obtained on the ranging of Global Navigation Satellite System (GNSS) satellites and on RadioAstron which have a very elliptic orbit.

Spatial Autocorrelation Can Generate Stronger Correlations between Range Size and Climatic Niches Than the Biological Signal — A Demonstration Using Bird and Mammal Range Maps

PubMed Central

Boucher-Lalonde, Véronique; Currie, David J.

2016-01-01

Species’ geographic ranges could primarily be physiological tolerances drawn in space. Alternatively, geographic ranges could be only broadly constrained by physiological climatic tolerances: there could generally be much more proximate constraints on species’ ranges (dispersal limitation, biotic interactions, etc.) such that species often occupy a small and unpredictable subset of tolerable climates. In the literature, species’ climatic tolerances are typically estimated from the set of conditions observed within their geographic range. Using this method, studies have concluded that broader climatic niches permit larger ranges. Similarly, other studies have investigated the biological causes of incomplete range filling. But, when climatic constraints are measured directly from species’ ranges, are correlations between species’ range size and climate necessarily consistent with a causal link? We evaluated the extent to which variation in range size among 3277 bird and 1659 mammal species occurring in the Americas is statistically related to characteristics of species’ realized climatic niches. We then compared how these relationships differed from the ones expected in the absence of a causal link. We used a null model that randomizes the predictor variables (climate), while retaining their broad spatial autocorrelation structure, thereby removing any causal relationship between range size and climate. We found that, although range size is strongly positively related to climatic niche breadth, range filling and, to a lesser extent, niche position in nature, the observed relationships are not always stronger than expected from spatial autocorrelation alone. Thus, we conclude that equally strong relationships between range size and climate would result from any processes causing ranges to be highly spatially autocorrelated. PMID:27855201

Scientific analysis of satellite ranging data

NASA Technical Reports Server (NTRS)

Smith, David E.

1994-01-01

A network of satellite laser ranging (SLR) tracking systems with continuously improving accuracies is challenging the modelling capabilities of analysts worldwide. Various data analysis techniques have yielded many advances in the development of orbit, instrument and Earth models. The direct measurement of the distance to the satellite provided by the laser ranges has given us a simple metric which links the results obtained by diverse approaches. Different groups have used SLR data, often in combination with observations from other space geodetic techniques, to improve models of the static geopotential, the solid Earth, ocean tides, and atmospheric drag models for low Earth satellites. Radiation pressure models and other non-conservative forces for satellite orbits above the atmosphere have been developed to exploit the full accuracy of the latest SLR instruments. SLR is the baseline tracking system for the altimeter missions TOPEX/Poseidon, and ERS-1 and will play an important role in providing the reference frame for locating the geocentric position of the ocean surface, in providing an unchanging range standard for altimeter calibration, and for improving the geoid models to separate gravitational from ocean circulation signals seen in the sea surface. However, even with the many improvements in the models used to support the orbital analysis of laser observations, there remain systematic effects which limit the full exploitation of SLR accuracy today.

Observation Scheduling System

NASA Technical Reports Server (NTRS)

Chien, Steve A.; Tran, Daniel Q.; Rabideau, Gregg R.; Schaffer, Steven R.

2011-01-01

Software has been designed to schedule remote sensing with the Earth Observing One spacecraft. The software attempts to satisfy as many observation requests as possible considering each against spacecraft operation constraints such as data volume, thermal, pointing maneuvers, and others. More complex constraints such as temperature are approximated to enable efficient reasoning while keeping the spacecraft within safe limits. Other constraints are checked using an external software library. For example, an attitude control library is used to determine the feasibility of maneuvering between pairs of observations. This innovation can deal with a wide range of spacecraft constraints and solve large scale scheduling problems like hundreds of observations and thousands of combinations of observation sequences.

Observability during planetary approach navigation

NASA Technical Reports Server (NTRS)

Bishop, Robert H.; Burkhart, P. Daniel; Thurman, Sam W.

1993-01-01

The objective of the research is to develop an analytic technique to predict the relative navigation capability of different Earth-based radio navigation measurements. In particular, the problem is to determine the relative ability of geocentric range and Doppler measurements to detect the effects of the target planet gravitational attraction on the spacecraft during the planetary approach and near-encounter mission phases. A complete solution to the two-dimensional problem has been developed. Relatively simple analytic formulas are obtained for range and Doppler measurements which describe the observability content of the measurement data along the approach trajectories. An observability measure is defined which is based on the observability matrix for nonlinear systems. The results show good agreement between the analytic observability analysis and the computational batch processing method.

Deep VLA Observations of the Cluster 1RXS J0603.3+4214 in the Frequency Range of 1–2 GHz

DOE PAGES

Rajpurohit, K.; Hoeft, M.; van Weeren, R. J.; ...

2018-01-08

Here, we report L-band VLA observations of 1RXS J0603.3+4214, a cluster that hosts a bright radio relic, known as the Toothbrush, and an elongated giant radio halo. These new observations allow us to study the surface brightness distribution down to 1 arcsec resolution with very high sensitivity. Our images provide an unprecedented detailed view of the Toothbrush, revealing enigmatic filamentary structures. To study the spectral index distribution, we complement our analysis with published LOFAR and GMRT observations. The bright "brush" of the Toothbrush shows a prominent narrow ridge to its north with a sharp outer edge. The spectral index at the ridge is in the range –0.70 ≤ α ≤ –0.80. We suggest that the ridge is caused by projection along the line of sight. With a simple toy model for the smallest region of the ridge, we conclude that the magnetic field is below 5 μG and varies significantly across the shock front. Our model indicates that the actual Mach number is higher than that obtained from the injection index and agrees well with the one derived from the overall spectrum, namelymore » $${ \\mathcal M }={3.78}_{-0.2}^{+0.3}$$. The radio halo shows an average spectral index of α = –1.16 ± 0.05 and a slight gradient from north to south. The southernmost part of the halo is steeper and possibly related to a shock front. Excluding the southernmost part, the halo morphology agrees very well with the X-ray morphology. A power-law correlation is found between the radio and X-ray surface brightness.« less

Deep VLA Observations of the Cluster 1RXS J0603.3+4214 in the Frequency Range of 1–2 GHz

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rajpurohit, K.; Hoeft, M.; van Weeren, R. J.

Here, we report L-band VLA observations of 1RXS J0603.3+4214, a cluster that hosts a bright radio relic, known as the Toothbrush, and an elongated giant radio halo. These new observations allow us to study the surface brightness distribution down to 1 arcsec resolution with very high sensitivity. Our images provide an unprecedented detailed view of the Toothbrush, revealing enigmatic filamentary structures. To study the spectral index distribution, we complement our analysis with published LOFAR and GMRT observations. The bright "brush" of the Toothbrush shows a prominent narrow ridge to its north with a sharp outer edge. The spectral index at the ridge is in the range –0.70 ≤ α ≤ –0.80. We suggest that the ridge is caused by projection along the line of sight. With a simple toy model for the smallest region of the ridge, we conclude that the magnetic field is below 5 μG and varies significantly across the shock front. Our model indicates that the actual Mach number is higher than that obtained from the injection index and agrees well with the one derived from the overall spectrum, namelymore » $${ \\mathcal M }={3.78}_{-0.2}^{+0.3}$$. The radio halo shows an average spectral index of α = –1.16 ± 0.05 and a slight gradient from north to south. The southernmost part of the halo is steeper and possibly related to a shock front. Excluding the southernmost part, the halo morphology agrees very well with the X-ray morphology. A power-law correlation is found between the radio and X-ray surface brightness.« less

Deep VLA Observations of the Cluster 1RXS J0603.3+4214 in the Frequency Range of 1–2 GHz

NASA Astrophysics Data System (ADS)

Rajpurohit, K.; Hoeft, M.; van Weeren, R. J.; Rudnick, L.; Röttgering, H. J. A.; Forman, W. R.; Brüggen, M.; Croston, J. H.; Andrade-Santos, F.; Dawson, W. A.; Intema, H. T.; Kraft, R. P.; Jones, C.; Jee, M. James

2018-01-01

We report L-band VLA observations of 1RXS J0603.3+4214, a cluster that hosts a bright radio relic, known as the Toothbrush, and an elongated giant radio halo. These new observations allow us to study the surface brightness distribution down to 1 arcsec resolution with very high sensitivity. Our images provide an unprecedented detailed view of the Toothbrush, revealing enigmatic filamentary structures. To study the spectral index distribution, we complement our analysis with published LOFAR and GMRT observations. The bright “brush” of the Toothbrush shows a prominent narrow ridge to its north with a sharp outer edge. The spectral index at the ridge is in the range ‑0.70 ≤ α ≤ ‑0.80. We suggest that the ridge is caused by projection along the line of sight. With a simple toy model for the smallest region of the ridge, we conclude that the magnetic field is below 5 μG and varies significantly across the shock front. Our model indicates that the actual Mach number is higher than that obtained from the injection index and agrees well with the one derived from the overall spectrum, namely { M }={3.78}-0.2+0.3. The radio halo shows an average spectral index of α = ‑1.16 ± 0.05 and a slight gradient from north to south. The southernmost part of the halo is steeper and possibly related to a shock front. Excluding the southernmost part, the halo morphology agrees very well with the X-ray morphology. A power-law correlation is found between the radio and X-ray surface brightness.

Eddy Vertical Structure Observed by Deepgliders: Evidence for the Enstrophy Inertial Range Cascade in Geostrophic Turbulence

NASA Astrophysics Data System (ADS)

Eriksen, C. C.

2016-12-01

Full water column temperature and salinity profiles and estimates of average current collected with Deepgliders were used to analyze vertical structure of mesoscale features in the western North Atlantic Ocean. Fortnightly repeat surveys over a 58 km by 58 km region centered at the Bermuda Atlantic Time Series (BATS) site southeast of Bermuda were carried out for 3 and 9 months in successive years. In addition, a section from Bermuda along Line W across the Gulf Stream to the New England Continental Slope and a pair of sections from Bermuda to the Bahamas were carried out. Absolute geostrophic current estimates constructed from these measurements and projected upon flat bottom resting ocean dynamic modes for the regions indicate nearly equal kinetic energy in the barotropic mode and first baroclinic mode. An empirical orthogonal mode decomposition of dynamic mode amplitudes demonstrates strong coupling of the barotropic and first baroclinic modes, a result resembling those reported for the Polymode experiment 3 decades ago. Higher baroclinic modes are largely independent of one another. Energy in baroclinic modes varies in inverse proportion to mode number cubed, a result predicted for an enstrophy inertial range cascade of geostrophic turbulence, believed newly detected by these observations. This (mode number)-3 dependence is found at BATS and across the Gulf Stream and Sargasso Sea. On two occasions, submesoscale anticyclones were detected at BATS whose vertical structure closely resembled the second baroclinic mode. Anomalously cold and fresh water within their cores (by as much as 3.5°C and 0.5 in salinity) suggests they were of subpolar (likely Labrador Sea) origin. These provided temporary perturbations to the vertical mode number energy spectrum.

CLImAT-HET: detecting subclonal copy number alterations and loss of heterozygosity in heterogeneous tumor samples from whole-genome sequencing data.

PubMed

Yu, Zhenhua; Li, Ao; Wang, Minghui

2017-03-15

Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. With the advent of next-generation sequencing technology, inference of subclonal populations has become one of the focused interests in cancer-associated studies, and is usually based on the assessment of combinations of somatic single-nucleotide variations (SNV), CNA and LOH. However, cancer samples often have several inherent issues, such as contamination of normal stroma, tumor aneuploidy and intra-tumor heterogeneity. Addressing these critical issues is imperative for accurate profiling of clonal architecture. We present CLImAT-HET, a computational method designed for capturing clonal diversity in the CNA/LOH dimensions by taking into account the intra-tumor heterogeneity issue, in the case where a reference or matched normal sample is absent. The algorithm quantitatively represents the clonal identification problem using a factorial hidden Markov model, and takes an integrated analysis of read counts and allele frequency data. It is able to infer subclonal CNA and LOH events as well as the fraction of cells harboring each event. The results on simulated datasets indicate that CLImAT-HET has high power to identify CNA/LOH segments, it achieves an average accuracy of 0.87. It can also accurately infer proportion of each clonal population with an overall Pearson correlation coefficient of 0.99 and a mean absolute error of 0.02. CLImAT-HET shows significant advantages when compared with other existing methods. Application of CLImAT-HET to 5 primary triple negative breast cancer samples demonstrates its ability to capture clonal diversity in the CAN

Genomic diversity and affinities in population groups of North West India: an analysis of Alu insertion and a single nucleotide polymorphism.

PubMed

Saini, J S; Kumar, A; Matharoo, K; Sokhi, J; Badaruddoza; Bhanwer, A J S

2012-12-15

The North West region of India is extremely important to understand the peopling of India, as it acted as a corridor to the foreign invaders from Eurasia and Central Asia. A series of these invasions along with multiple migrations led to intermixture of variable populations, strongly contributing to genetic variations. The present investigation was designed to explore the genetic diversities and affinities among the five major ethnic groups from North West India; Brahmin, Jat Sikh, Bania, Rajput and Gujjar. A total of 327 individuals of the abovementioned ethnic groups were analyzed for 4 Alu insertion marker loci (ACE, PV92, APO and D1) and a Single Nucleotide Polymorphism (SNP) rs2234693 in the intronic region of the ESR1 gene. Statistical analysis was performed to interpret the genetic structure and diversity of the population groups. Genotypes for ACE, APO, ESR1 and PV92 loci were found to be in Hardy-Weinberg equilibrium in all the ethnic groups, while significant departures were observed at the D1 locus in every investigated population after Bonferroni's correction. The average heterozygosity for all the loci in these ethnic groups was fairly substantial ranging from 0.3927 ± 0.1877 to 0.4333 ± 0.1416. Inbreeding coefficient indicated an overall 10% decrease in heterozygosity in these North West Indian populations. The gene differentiation among the populations was observed to be of the order of 0.013. Genetic distance estimates revealed that Gujjars were close to Banias and Jat Sikhs were close to Rajputs. Overall the study favored the recent division of the populations of North West India into largely endogamous groups. It was observed that the populations of North West India represent a more or less homogenous genetic entity, owing to their common ancestral history as well as geographical proximity. Copyright © 2012 Elsevier B.V. All rights reserved.

Kelvin-Helmholtz waves in extratropical cyclones passing over mountain ranges: KH Waves in Extratropical Cyclones over Mountain Ranges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Medina, Socorro; Houze, Robert A.

2016-02-19

Kelvin–Helmholtz billows with horizontal scales of 3–4 km have been observed in midlatitude cyclones moving over the Italian Alps and the Oregon Cascades when the atmosphere was mostly statically stable with high amounts of shear and Ri < 0.25. In one case, data from a mobile radar located within a windward facing valley documented a layer in which the shear between down-valley flow below 1.2 km and strong upslope cross-barrier flow above was large. Several episodes of Kelvin–Helmholtz waves were observed within the shear layer. The occurrence of the waves appears to be related to the strength of the shear:more » when the shear attained large values, an episode of billows occurred, followed by a sharp decrease in the shear. The occurrence of large values of shear and Kelvin–Helmholtz billows over two different mountain ranges suggests that they may be important features occurring when extratropical cyclones with statically stable flow pass over mountain ranges.« less

Uncovering Cryptic Asexuality in Daphnia magna by RAD Sequencing

PubMed Central

Svendsen, Nils; Reisser, Celine M. O.; Dukić, Marinela; Thuillier, Virginie; Ségard, Adeline; Liautard-Haag, Cathy; Fasel, Dominique; Hürlimann, Evelin; Lenormand, Thomas; Galimov, Yan; Haag, Christoph R.

2015-01-01

The breeding systems of many organisms are cryptic and difficult to investigate with observational data, yet they have profound effects on a species’ ecology, evolution, and genome organization. Genomic approaches offer a novel, indirect way to investigate breeding systems, specifically by studying the transmission of genetic information from parents to offspring. Here we exemplify this method through an assessment of self-fertilization vs. automictic parthenogenesis in Daphnia magna. Self-fertilization reduces heterozygosity by 50% compared to the parents, but under automixis, whereby two haploid products from a single meiosis fuse, the expected heterozygosity reduction depends on whether the two meiotic products are separated during meiosis I or II (i.e., central vs. terminal fusion). Reviewing the existing literature and incorporating recombination interference, we derive an interchromosomal and an intrachromosomal prediction of how to distinguish various forms of automixis from self-fertilization using offspring heterozygosity data. We then test these predictions using RAD-sequencing data on presumed automictic diapause offspring of so-called nonmale producing strains and compare them with “self-fertilized” offspring produced by within-clone mating. The results unequivocally show that these offspring were produced by automixis, mostly, but not exclusively, through terminal fusion. However, the results also show that this conclusion was only possible owing to genome-wide heterozygosity data, with phenotypic data as well as data from microsatellite markers yielding inconclusive or even misleading results. Our study thus demonstrates how to use the power of genomic approaches for elucidating breeding systems, and it provides the first demonstration of automictic parthenogenesis in Daphnia. PMID:26341660

Charge state distributions of oxygen and carbon in the energy range 1 to 300 keV/e observed with AMPTE/CCE in the magnetosphere

NASA Technical Reports Server (NTRS)

Kremser, G.; Stuedemann, W.; Wilken, B.; Gloeckler, G.; Hamilton, D. C.

1985-01-01

Observations of charge state distributions of oxygen and carbon are presented that were obtained with the charge-energy-mass spectrometer onboard the AMPTE/CCE spacecraft. Data were selected for two different local time sectors (apogee at 1300 LT and 0300 LT, respectively), three L-ranges (4-6, 6-8, and greater than 8), and quiet to moderately disturbed days (Kp less than or equal to 4). The charge state distributions reveal the existence of all charge states of oxygen and carbon in the magnetosphere. The relative importance of the different charge states strongly depends on L and much less on local time. The observations confirm that the solar wind and the ionosphere contribute to the oxygen population, whereas carbon only originates from the solar wind. The L-dependence of the charge state distributions can be interpreted in terms of these different ion sources and of charge exchange and diffusion processes that largely influence the distribution of oxygen and carbon in the magnetosphere.

Methane Hydrate Formation in Thick Sand Reservoirs: Long-range Gas Transport or Short-range Methane Diffusion?

NASA Astrophysics Data System (ADS)

You, K.; Flemings, P. B.

2016-12-01

We developed two 2-D numerical models to simulate hydrate formation by long range methane gas transport and short-range methane diffusion. We interpret that methane hydrates in thick sands are most likely formed by long range gas transport where methane gas is transported upward into the hydrate stability zone (HSZ) under buoyancy and locally forms hydrate to its stability limit. In short-range methane diffusion, methane is generated locally by biodegradation of organic matter in mud and diffused into bounding sands where it forms hydrate. We could not simulate enough methane transport by diffusion to account for its observed concentration in thick sands. In our models, we include the capillary effect on dissolved methane solubility and on the hydrate phase boundary, sedimentation and different compaction in sand and mud, fracture generation as well as the fully coupled multiphase flow and multicomponent transport. We apply our models to a 12 meter-thick hydrate-bearing sand layer at Walker Ridge 313, Northern Gulf of Mexico. With the long-range gas transport, hydrate saturation is greater than 90% and salinity is increased from seawater to about 8 wt.% through the entire sand. With short-range diffusion, hydrate saturation is more than 90% at the sand base and is less than 10% in the overlying section; salinity is close to seawater when sand is deposited to 800 meter below seafloor by short-range methane diffusion. With short-range diffusion, the amount of hydrate formed is much less than that interpreted from the well log data. Two transient gas layers separated by a hydrate layer are formed from short-range diffusion caused by capillary effect. This could be interpreted as a double bottom simulating reflector. This study provides further insights into different hydrate formation mechanisms, and could serve as a base to confirm the hydrate formation mechanism in fields.

Multi-GNSS orbit determination using satellite laser ranging

NASA Astrophysics Data System (ADS)

Bury, Grzegorz; Sośnica, Krzysztof; Zajdel, Radosław

2018-04-01

Galileo, BeiDou, QZSS, and NavIC are emerging global navigation satellite systems (GNSSs) and regional navigation satellite systems all of which are equipped with laser retroreflector arrays for range measurements. This paper summarizes the GNSS-intensive tracking campaigns conducted by the International Laser Ranging Service and provides results from multi-GNSS orbit determination using solely SLR observations. We consider the whole constellation of GLONASS, all active Galileo, four BeiDou satellites: 1 MEO, 3 IGSO, and one QZSS. We analyze the influence of the number of SLR observations on the quality of the 3-day multi-GNSS orbit solution. About 60 SLR observations are needed for obtaining MEO orbits of sufficient quality with the root mean square (RMS) of 3 cm for the radial component when compared to microwave-based orbits. From the analysis of a minimum number of tracking stations, when considering the 3-day arcs, 5 SLR stations do not provide a sufficient geometry of observations. The solution obtained using ten stations is characterized with RMS of 4, 9, and 18 cm in the radial, along-track, and cross-track direction, respectively, for MEO satellites. We also investigate the impact of the length of orbital arc on the quality of SLR-derived orbits. Hence, 5- and 7-day arcs constitute the best solution, whereas 3-day arcs are of inferior quality due to an insufficient number of SLR observations and 9-day arcs deteriorate the along-track component. The median RMS from the comparison between 7-day orbital arcs determined using SLR data with microwave-based orbits assumes values in the range of 3-4, 11-16, and 15-27 cm in radial, along-track, and cross-track, respectively, for MEO satellites. BeiDou IGSO and QZSS are characterized by RMS values higher by a factor of 8 and 24, respectively, than MEO orbits.

Equatorial plasma bubbles/range spread F irregularities and the QBO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, P.R.

1993-11-05

This paper reports on a study of plasma bubbles or spread F irregularities, observed at equatorial observation stations, looked at in conjunction with measures of the quasi biennial oscillation (QBO) of the mean lower stratospheric winds. Plasma bubbles and spread F irregularities are thought to be different manifestations of the same basic event, distinguished mainly by the observational method. For the case of range spread F events, ionosonde data has revealed in the past daily and seasonal variations, effects due to the solar cycle, and dependence upon the geomagnetic field and longitudinal location. These relationships have been shown to bemore » statistical in nature, so the authors have looked for other relationships which might be more relational in nature. When correlation with QBO phase variations are investigated, there is an observed increase or decrease in the range spread F, dependent upon whether the QBO is in an easterly or westerly phase, and observed in the American sector or Indian/East African sector.« less

Using a coherent hydrophone array for observing sperm whale range, classification, and shallow-water dive profiles.

PubMed

Tran, Duong D; Huang, Wei; Bohn, Alexander C; Wang, Delin; Gong, Zheng; Makris, Nicholas C; Ratilal, Purnima

2014-06-01

Sperm whales in the New England continental shelf and slope were passively localized, in both range and bearing, and classified using a single low-frequency (<2500 Hz), densely sampled, towed horizontal coherent hydrophone array system. Whale bearings were estimated using time-domain beamforming that provided high coherent array gain in sperm whale click signal-to-noise ratio. Whale ranges from the receiver array center were estimated using the moving array triangulation technique from a sequence of whale bearing measurements. Multiple concurrently vocalizing sperm whales, in the far-field of the horizontal receiver array, were distinguished and classified based on their horizontal spatial locations and the inter-pulse intervals of their vocalized click signals. The dive profile was estimated for a sperm whale in the shallow waters of the Gulf of Maine with 160 m water-column depth located close to the array's near-field where depth estimation was feasible by employing time difference of arrival of the direct and multiply reflected click signals received on the horizontal array. By accounting for transmission loss modeled using an ocean waveguide-acoustic propagation model, the sperm whale detection range was found to exceed 60 km in low to moderate sea state conditions after coherent array processing.

POD experiments using real and simulated time-sharing observations for GEO satellites in C-band transfer ranging system

NASA Astrophysics Data System (ADS)

Fen, Cao; XuHai, Yang; ZhiGang, Li; ChuGang, Feng

2016-08-01

The normal consecutive observing model in Chinese Area Positioning System (CAPS) can only supply observations of one GEO satellite in 1 day from one station. However, this can't satisfy the project need for observing many GEO satellites in 1 day. In order to obtain observations of several GEO satellites in 1 day like GPS/GLONASS/Galileo/BeiDou, the time-sharing observing model for GEO satellites in CAPS needs research. The principle of time-sharing observing model is illuminated with subsequent Precise Orbit Determination (POD) experiments using simulated time-sharing observations in 2005 and the real time-sharing observations in 2015. From time-sharing simulation experiments before 2014, the time-sharing observing 6 GEO satellites every 2 h has nearly the same orbit precision with the consecutive observing model. From POD experiments using the real time-sharing observations, POD precision for ZX12# and Yatai7# are about 3.234 m and 2.570 m, respectively, which indicates the time-sharing observing model is appropriate for CBTR system and can realize observing many GEO satellites in 1 day.

Ranging behavior relates to welfare indicators pre- and post-range access in commercial free-range broilers.

PubMed

Taylor, Peta S; Hemsworth, Paul H; Groves, Peter J; Gebhardt-Henrich, Sabine G; Rault, Jean-Loup

2018-06-01

Little is known about the effect of accessing an outdoor range on chicken welfare. We tracked individual ranging behavior of 538 mixed-sex Ross 308 chickens on a commercial farm across 4 flocks in winter and summer. Before range access, at 17 to 19 d of age, and post-range access, at 30 to 33 and 42 to 46 d of age in winter and summer flocks respectively, welfare indicators were measured on chickens (pre-range: winter N = 292; summer N = 280; post-range: winter N = 131; summer N = 140), including weight, gait score, dermatitis and plumage condition. Post-ranging autopsies were performed (winter: N = 170; summer: N = 60) to assess breast burn, leg health, and ascites. Fewer chickens accessed the range in winter flocks (32.5%) than summer flocks (82.1%). Few relationships between welfare and ranging were identified in winter, likely due to minimal ranging and the earlier age of post-ranging data collection compared to summer flocks. In summer flocks prior to range access, chickens that accessed the range weighed 4.9% less (P = 0.03) than chickens that did not access the range. Pre-ranging weight, gait score, and overall plumage cover predicted the amount of range use by ranging chickens in summer flocks (P < 0.01), but it explained less than 5% of the variation, suggesting other factors are associated with ranging behavior. In summer flocks post-range access, ranging chickens weighed 12.8% less than non-ranging chickens (P < 0.001). More range visits were associated with lower weight (P < 0.01), improved gait scores (P = 0.02), greater breast plumage cover (P = 0.02), lower ascites index (P = 0.01), and less pericardial fluid (P = 0.04). More time spent on the range was associated with lower weight (P < 0.01) and better gait scores (P < 0.01). These results suggest that accessing an outdoor range in summer is partly related to changes in broiler chicken welfare. Further investigations are required to determine causation.

Long-range and short-range dihadron angular correlations in central PbPb collisions at sqrt {{{s_{text{NN}}}}} = 2.76 TeV

NASA Astrophysics Data System (ADS)

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Fabjan, C.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hammer, J.; Hänsel, S.; Hoch, M.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Krammer, M.; Liko, D.; Mikulec, I.; Pernicka, M.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Taurok, A.; Teischinger, F.; Wagner, P.; Waltenberger, W.; Walzel, G.; Widl, E.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Gonzalez, J. Suarez; Bansal, S.; Benucci, L.; De Wolf, E. A.; Janssen, X.; Maes, J.; Maes, T.; Mucibello, L.; Ochesanu, S.; Roland, B.; Rougny, R.; Selvaggi, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Blekman, F.; Blyweert, S.; D'Hondt, J.; Devroede, O.; Suarez, R. Gonzalez; Kalogeropoulos, A.; Maes, M.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Villella, I.; Charaf, O.; Clerbaux, B.; De Lentdecker, G.; Dero, V.; Gay, A. P. R.; Hammad, G. H.; Hreus, T.; Marage, P. E.; Thomas, L.; Velde, C. Vander; Vanlaer, P.; Adler, V.; Cimmino, A.; Costantini, S.; Grunewald, M.; Klein, B.; Lellouch, J.; Marinov, A.; Mccartin, J.; Ryckbosch, D.; Thyssen, F.; Tytgat, M.; Vanelderen, L.; Verwilligen, P.; Walsh, S.; Zaganidis, N.; Basegmez, S.; Bruno, G.; Caudron, J.; Ceard, L.; Cortina Gil, E.; De Favereau De Jeneret, J.; Delaere, C.; Favart, D.; Giammanco, A.; Grégoire, G.; Hollar, J.; Lemaitre, V.; Liao, J.; Militaru, O.; Ovyn, S.; Pagano, D.; Pin, A.; Piotrzkowski, K.; Schul, N.; Beliy, N.; Caebergs, T.; Daubie, E.; Alves, G. A.; De Jesus Damiao, D.; Pol, M. E.; Souza, M. H. G.; Carvalho, W.; Da Costa, E. M.; De Oliveira Martins, C.; Fonseca De Souza, S.; Mundim, L.; Nogima, H.; Oguri, V.; Prado Da Silva, W. L.; Santoro, A.; Silva Do Amaral, S. M.; Sznajder, A.; Bernardes, C. A.; Dias, F. A.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Lagana, C.; Marinho, F.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Darmenov, N.; Dimitrov, L.; Genchev, V.; Iaydjiev, P.; Piperov, S.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Tcholakov, V.; Trayanov, R.; Vankov, I.; Dimitrov, A.; Hadjiiska, R.; Karadzhinova, A.; Kozhuharov, V.; Litov, L.; Mateev, M.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Jiang, C. H.; Liang, D.; Liang, S.; Meng, X.; Tao, J.; Wang, J.; Wang, J.; Wang, X.; Wang, Z.; Xiao, H.; Xu, M.; Zang, J.; Zhang, Z.; Ban, Y.; Guo, S.; Guo, Y.; Li, W.; Mao, Y.; Qian, S. J.; Teng, H.; Zhang, L.; Zhu, B.; Zou, W.; Cabrera, A.; Moreno, B. Gomez; Ocampo Rios, A. A.; Osorio Oliveros, A. F.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Lelas, K.; Plestina, R.; Polic, D.; Puljak, I.; Antunovic, Z.; Dzelalija, M.; Brigljevic, V.; Duric, S.; Kadija, K.; Morovic, S.; Attikis, A.; Galanti, M.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Finger, M.; Finger, M.; Assran, Y.; Khalil, S.; Mahmoud, M. A.; Hektor, A.; Kadastik, M.; Müntel, M.; Raidal, M.; Rebane, L.; Azzolini, V.; Eerola, P.; Fedi, G.; Czellar, S.; Härkönen, J.; Heikkinen, A.; Karimäki, V.; Kinnunen, R.; Kortelainen, M. J.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Ungaro, D.; Wendland, L.; Banzuzi, K.; Korpela, A.; Tuuva, T.; Sillou, D.; Besancon, M.; Choudhury, S.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Ferri, F.; Ganjour, S.; Gentit, F. X.; Givernaud, A.; Gras, P.; de Monchenault, G. Hamel; Jarry, P.; Locci, E.; Malcles, J.; Marionneau, M.; Millischer, L.; Rander, J.; Rosowsky, A.; Shreyber, I.; Titov, M.; Verrecchia, P.; Baffioni, S.; Beaudette, F.; Benhabib, L.; Bianchini, L.; Bluj, M.; Broutin, C.; Busson, P.; Charlot, C.; Dahms, T.; Dobrzynski, L.; Elgammal, S.; Granier de Cassagnac, R.; Haguenauer, M.; Miné, P.; Mironov, C.; Ochando, C.; Paganini, P.; Sabes, D.; Salerno, R.; Sirois, Y.; Thiebaux, C.; Wyslouch, B.; Zabi, A.; Agram, J.-L.; Andrea, J.; Bloch, D.; Bodin, D.; Brom, J.-M.; Cardaci, M.; Chabert, E. C.; Collard, C.; Conte, E.; Drouhin, F.; Ferro, C.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Greder, S.; Juillot, P.; Karim, M.; Le Bihan, A.-C.; Mikami, Y.; Van Hove, P.; Fassi, F.; Mercier, D.; Baty, C.; Beauceron, S.; Beaupere, N.; Bedjidian, M.; Bondu, O.; Boudoul, G.; Boumediene, D.; Brun, H.; Chasserat, J.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fay, J.; Gascon, S.; Ille, B.; Kurca, T.; LeGrand, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Sordini, V.; Tosi, S.; Tschudi, Y.; Verdier, P.; Lomidze, D.; Anagnostou, G.; Edelhoff, M.; Feld, L.; Heracleous, N.; Hindrichs, O.; Jussen, R.; Klein, K.; Merz, J.; Mohr, N.; Ostapchuk, A.; Perieanu, A.; Raupach, F.; Sammet, J.; Schael, S.; Sprenger, D.; Weber, H.; Weber, M.; Wittmer, B.; Ata, M.; Bender, W.; Dietz-Laursonn, E.; Erdmann, M.; Frangenheim, J.; Hebbeker, T.; Hinzmann, A.; Hoepfner, K.; Klimkovich, T.; Klingebiel, D.; Kreuzer, P.; Lanske, D.; Magass, C.; Merschmeyer, M.; Meyer, A.; Papacz, P.; Pieta, H.; Reithler, H.; Schmitz, S. A.; Sonnenschein, L.; Steggemann, J.; Teyssier, D.; Bontenackels, M.; Davids, M.; Duda, M.; Flügge, G.; Geenen, H.; Giffels, M.; Haj Ahmad, W.; Heydhausen, D.; Kress, T.; Kuessel, Y.; Linn, A.; Nowack, A.; Perchalla, L.; Pooth, O.; Rennefeld, J.; Sauerland, P.; Stahl, A.; Thomas, M.; Tornier, D.; Zoeller, M. H.; Martin, M. Aldaya; Behrenhoff, W.; Behrens, U.; Bergholz, M.; Bethani, A.; Borras, K.; Cakir, A.; Campbell, A.; Castro, E.; Dammann, D.; Eckerlin, G.; Eckstein, D.; Flossdorf, A.; Flucke, G.; Geiser, A.; Hauk, J.; Jung, H.; Kasemann, M.; Katkov, I.; Katsas, P.; Kleinwort, C.; Kluge, H.; Knutsson, A.; Krämer, M.; Krücker, D.; Kuznetsova, E.; Lange, W.; Lohmann, W.; Mankel, R.; Marienfeld, M.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mnich, J.; Mussgiller, A.; Olzem, J.; Pitzl, D.; Raspereza, A.; Raval, A.; Rosin, M.; Schmidt, R.; Schoerner-Sadenius, T.; Sen, N.; Spiridonov, A.; Stein, M.; Tomaszewska, J.; Walsh, R.; Wissing, C.; Autermann, C.; Blobel, V.; Bobrovskyi, S.; Draeger, J.; Enderle, H.; Gebbert, U.; Kaschube, K.; Kaussen, G.; Klanner, R.; Lange, J.; Mura, B.; Naumann-Emme, S.; Nowak, F.; Pietsch, N.; Sander, C.; Schettler, H.; Schleper, P.; Schröder, M.; Schum, T.; Schwandt, J.; Stadie, H.; Steinbrück, G.; Thomsen, J.; Barth, C.; Bauer, J.; Berger, J.; Buege, V.; Chwalek, T.; De Boer, W.; Dierlamm, A.; Dirkes, G.; Feindt, M.; Gruschke, J.; Hackstein, C.; Hartmann, F.; Heinrich, M.; Held, H.; Hoffmann, K. H.; Honc, S.; Komaragiri, J. R.; Kuhr, T.; Martschei, D.; Mueller, S.; Müller, Th.; Niegel, M.; Oberst, O.; Oehler, A.; Ott, J.; Peiffer, T.; Quast, G.; Rabbertz, K.; Ratnikov, F.; Ratnikova, N.; Renz, M.; Saout, C.; Scheurer, A.; Schieferdecker, P.; Schilling, F.-P.; Schott, G.; Simonis, H. J.; Stober, F. M.; Troendle, D.; Wagner-Kuhr, J.; Weiler, T.; Zeise, M.; Zhukov, V.; Ziebarth, E. B.; Daskalakis, G.; Geralis, T.; Kesisoglou, S.; Kyriakis, A.; Loukas, D.; Manolakos, I.; Markou, A.; Markou, C.; Mavrommatis, C.; Ntomari, E.; Petrakou, E.; Gouskos, L.; Mertzimekis, T. J.; Panagiotou, A.; Stiliaris, E.; Evangelou, I.; Foudas, C.; Kokkas, P.; Manthos, N.; Papadopoulos, I.; Patras, V.; Triantis, F. A.; Aranyi, A.; Bencze, G.; Boldizsar, L.; Hajdu, C.; Hidas, P.; Horvath, D.; Kapusi, A.; Krajczar, K.; Sikler, F.; Veres, G. I.; Vesztergombi, G.; Beni, N.; Molnar, J.; Palinkas, J.; Szillasi, Z.; Veszpremi, V.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Beri, S. B.; Bhatnagar, V.; Dhingra, N.; Gupta, R.; Jindal, M.; Kaur, M.; Kohli, J. M.; Mehta, M. Z.; Nishu, N.; Saini, L. K.; Sharma, A.; Singh, A. P.; Singh, J. B.; Singh, S. P.; Ahuja, S.; Bhattacharya, S.; Choudhary, B. C.; Gomber, B.; Gupta, P.; Jain, S.; Jain, S.; Khurana, R.; Kumar, A.; Naimuddin, M.; Ranjan, K.; Shivpuri, R. K.; Choudhury, R. K.; Dutta, D.; Kailas, S.; Kumar, V.; Mehta, P.; Mohanty, A. K.; Pant, L. M.; Shukla, P.; Aziz, T.; Guchait, M.; Gurtu, A.; Maity, M.; Majumder, D.; Majumder, G.; Mazumdar, K.; Mohanty, G. B.; Saha, A.; Sudhakar, K.; Wickramage, N.; Banerjee, S.; Dugad, S.; Mondal, N. K.; Arfaei, H.; Bakhshiansohi, H.; Etesami, S. M.; Fahim, A.; Hashemi, M.; Jafari, A.; Khakzad, M.; Mohammadi, A.; Najafabadi, M. Mohammadi; Mehdiabadi, S. Paktinat; Safarzadeh, B.; Zeinali, M.; Abbrescia, M.; Barbone, L.; Calabria, C.; Colaleo, A.; Creanza, D.; De Filippis, N.; De Palma, M.; Fiore, L.; Iaselli, G.; Lusito, L.; Maggi, G.; Maggi, M.; Manna, N.; Marangelli, B.; My, S.; Nuzzo, S.; Pacifico, N.; Pierro, G. A.; Pompili, A.; Pugliese, G.; Romano, F.; Roselli, G.; Selvaggi, G.; Silvestris, L.; Trentadue, R.; Tupputi, S.; Zito, G.; Abbiendi, G.; Benvenuti, A. C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Brigliadori, L.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Giunta, M.; Grandi, C.; Marcellini, S.; Masetti, G.; Meneghelli, M.; Montanari, A.; Navarria, F. L.; Odorici, F.; Perrotta, A.; Primavera, F.; Rossi, A. M.; Rovelli, T.; Siroli, G.; Travaglini, R.; Albergo, S.; Cappello, G.; Chiorboli, M.; Costa, S.; Tricomi, A.; Tuve, C.; Barbagli, G.; Ciulli, V.; Civinini, C.; D'Alessandro, R.; Focardi, E.; Frosali, S.; Gallo, E.; Gonzi, S.; Lenzi, P.; Meschini, M.; Paoletti, S.; Sguazzoni, G.; Tropiano, A.; Benussi, L.; Bianco, S.; Colafranceschi, S.; Fabbri, F.; Piccolo, D.; Fabbricatore, P.; Musenich, R.; Benaglia, A.; De Guio, F.; Di Matteo, L.; Gennai, S.; Ghezzi, A.; Malvezzi, S.; Martelli, A.; Massironi, A.; Menasce, D.; Moroni, L.; Paganoni, M.; Pedrini, D.; Ragazzi, S.; Redaelli, N.; Sala, S.; de Fatis, T. Tabarelli; Buontempo, S.; Montoya, C. A. Carrillo; Cavallo, N.; De Cosa, A.; Fabozzi, F.; Iorio, A. O. M.; Lista, L.; Merola, M.; Paolucci, P.; Azzia, P.; Bacchetta, N.; Bellan, P.; Bellato, M.; Biasotto, M.; Bisello, D.; Branca, A.; Checchia, P.; De Mattia, M.; Dorigo, T.; Gasparini, F.; Gonella, F.; Gozzelino, A.; Gulmini, M.; Lacaprara, S.; Lazzizzera, I.; Margoni, M.; Maron, G.; Meneguzzo, A. T.; Nespolo, M.; Passaseo, M.; Perrozzi, L.; Pozzobon, N.; Ronchese, P.; Simonetto, F.; Torassa, E.; Tosi, M.; Triossi, A.; Vanini, S.; Baesso, P.; Berzano, U.; Ratti, S. P.; Riccardi, C.; Torre, P.; Vitulo, P.; Viviani, C.; Biasini, M.; Bilei, G. M.; Caponeri, B.; Fanò, L.; Lariccia, P.; Lucaroni, A.; Mantovani, G.; Menichelli, M.; Nappi, A.; Romeo, F.; Santocchia, A.; Taroni, S.; Valdata, M.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Broccolo, G.; Castaldi, R.; D'Agnolo, R. T.; Dell'Orso, R.; Fiori, F.; Foò, L.; Giassi, A.; Kraan, A.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Palla, F.; Segneri, G.; Serban, A. T.; Spagnolo, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Barone, L.; Cavallari, F.; Del Re, D.; Di Marco, E.; Diemoz, M.; Franci, D.; Grassi, M.; Longo, E.; Nourbakhsh, S.; Organtini, G.; Pandolfi, F.; Paramatti, R.; Rahatlou, S.; Rovelli, C.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Biino, C.; Botta, C.; Cartiglia, N.; Castello, R.; Costa, M.; Demaria, N.; Graziano, A.; Mariotti, C.; Marone, M.; Maselli, S.; Migliore, E.; Mila, G.; Monaco, V.; Musich, M.; Obertino, M. M.; Pastrone, N.; Pelliccioni, M.; Romero, A.; Ruspa, M.; Sacchi, R.; Sola, V.; Solano, A.; Staiano, A.; Vilela Pereira, A.; Belforte, S.; Cossutti, F.; Della Ricca, G.; Gobbo, B.; Montanino, D.; Penzo, A.; Heo, S. G.; Nam, S. K.; Chang, S.; Chung, J.; Kim, D. H.; Kim, G. N.; Kim, J. E.; Kong, D. J.; Park, H.; Ro, S. R.; Son, D.; Son, D. C.; Son, T.; Kim, Zero; Kim, J. Y.; Song, S.; Choi, S.; Hong, B.; Jeong, M. S.; Jo, M.; Kim, H.; Kim, J. H.; Kim, T. J.; Lee, K. S.; Moon, D. H.; Park, S. K.; Rhee, H. B.; Seo, E.; Shin, S.; Sim, K. S.; Choi, M.; Kang, S.; Kim, H.; Park, C.; Park, I. C.; Park, S.; Ryu, G.; Choi, Y.; Choi, Y. K.; Goh, J.; Kim, M. S.; Kwon, E.; Lee, J.; Lee, S.; Seo, H.; Yu, I.; Bilinskas, M. J.; Grigelionis, I.; Janulis, M.; Martisiute, D.; Petrov, P.; Sabonis, T.; Castilla-Valdez, H.; De La Cruz-Burelo, E.; Heredia-de La Cruz, I.; Lopez-Fernandez, R.; Magaña Villalba, R.; Sánchez-Hernández, A.; Villasenor-Cendejas, L. M.; Carrillo Moreno, S.; Vazquez Valencia, F.; Salazar Ibarguen, H. A.; Casimiro Linares, E.; Morelos Pineda, A.; Reyes-Santos, M. A.; Krofcheck, D.; Tam, J.; Butler, P. H.; Doesburg, R.; Silverwood, H.; Ahmad, M.; Ahmed, I.; Asghar, M. I.; Hoorani, H. R.; Khan, W. A.; Khurshid, T.; Qazi, S.; Brona, G.; Cwiok, M.; Dominik, W.; Doroba, K.; Kalinowski, A.; Konecki, M.; Krolikowski, J.; Frueboes, T.; Gokieli, R.; Górski, M.; Kazana, M.; Nawrocki, K.; Romanowska-Rybinska, K.; Szleper, M.; Wrochna, G.; Zalewski, P.; Almeida, N.; Bargassa, P.; David, A.; Faccioli, P.; Ferreira Parracho, P. G.; Gallinaro, M.; Musella, P.; Nayak, A.; Ribeiro, P. Q.; Seixas, J.; Varela, J.; Afanasiev, S.; Belotelov, I.; Bunin, P.; Golutvin, I.; Kamenev, A.; Karjavin, V.; Kozlov, G.; Lanev, A.; Moisenz, P.; Palichik, V.; Perelygin, V.; Shmatov, S.; Smirnov, V.; Volodko, A.; Zarubin, A.; Golovtsov, V.; Ivanov, Y.; Kim, V.; Levchenko, P.; Murzin, V.; Oreshkin, V.; Smirnov, I.; Sulimov, V.; Uvarov, L.; Vavilov, S.; Vorobyev, A.; Vorobyev, A.; Andreev, Yu.; Dermenev, A.; Gninenko, S.; Golubev, N.; Kirsanov, M.; Krasnikov, N.; Matveev, V.; Pashenkov, A.; Toropin, A.; Troitsky, S.; Epshteyn, V.; Gavrilov, V.; Kaftanov, V.; Kossov, M.; Krokhotin, A.; Lychkovskaya, N.; Popov, V.; Safronov, G.; Semenov, S.; Stolin, V.; Vlasov, E.; Zhokin, A.; Boos, E.; Ershov, A.; Gribushin, A.; Kodolova, O.; Korotkikh, V.; Lokhtin, I.; Markina, A.; Obraztsov, S.; Perfilov, M.; Petrushanko, S.; Sarycheva, L.; Savrin, V.; Snigirev, A.; Vardanyan, I.; Andreev, V.; Azarkin, M.; Dremin, I.; Kirakosyan, M.; Leonidov, A.; Rusakov, S. V.; Vinogradov, A.; Azhgirey, I.; Bitioukov, S.; Grishin, V.; Kachanov, V.; Konstantinov, D.; Korablev, A.; Krychkine, V.; Petrov, V.; Ryutin, R.; Slabospitsky, S.; Sobol, A.; Tourtchanovitch, L.; Troshin, S.; Tyurin, N.; Uzunian, A.; Volkov, A.; Adzic, P.; Djordjevic, M.; Krpic, D.; Milosevic, J.; Aguilar-Benitez, M.; Alcaraz Maestre, J.; Arce, P.; Battilana, C.; Calvo, E.; Cepeda, M.; Cerrada, M.; Chamizo Llatas, M.; Colino, N.; De La Cruz, B.; Delgado Peris, A.; Diez Pardos, C.; Domínguez Vázquez, D.; Fernandez Bedoya, C.; Fernández Ramos, J. P.; Ferrando, A.; Flix, J.; Fouz, M. C.; Garcia-Abia, P.; Gonzalez Lopez, O.; Goy Lopez, S.; Hernandez, J. M.; Josa, M. I.; Merino, G.; Puerta Pelayo, J.; Redondo, I.; Romero, L.; Santaolalla, J.; Soares, M. S.; Willmott, C.; Albajar, C.; Codispoti, G.; de Trocóniz, J. F.; Cuevas, J.; Fernandez Menendez, J.; Folgueras, S.; Caballero, I. Gonzalez; Lloret Iglesias, L.; Vizan Garcia, J. M.; Brochero Cifuentes, J. A.; Cabrillo, I. J.; Calderon, A.; Chuang, S. H.; Campderros, J. Duarte; Felcini, M.; Fernandez, M.; Gomez, G.; Gonzalez Sanchez, J.; Jorda, C.; Lobelle Pardo, P.; Lopez Virto, A.; Marco, J.; Marco, R.; Martinez Rivero, C.; Matorras, F.; Munoz Sanchez, F. J.; Piedra Gomez, J.; Rodrigo, T.; Rodríguez-Marrero, A. Y.; Ruiz-Jimeno, A.; Scodellaro, L.; Sanudo, M. Sobron; Vila, I.; Vilar Cortabitarte, R.; Abbaneo, D.; Auffray, E.; Auzinger, G.; Baillon, P.; Ball, A. H.; Barney, D.; Bell, A. J.; Benedetti, D.; Bernet, C.; Bialas, W.; Bloch, P.; Bocci, A.; Bolognesi, S.; Bona, M.; Breuker, H.; Bunkowski, K.; Camporesi, T.; Cerminara, G.; Coarasa Perez, J. A.; Curé, B.; D'Enterria, D.; De Roeck, A.; Di Guida, S.; Dupont-Sagorin, N.; Elliott-Peisert, A.; Frisch, B.; Funk, W.; Gaddi, A.; Georgiou, G.; Gerwig, H.; Gigi, D.; Gill, K.; Giordano, D.; Glege, F.; Gomez-Reino Garrido, R.; Gouzevitch, M.; Govoni, P.; Gowdy, S.; Guiducci, L.; Hansen, M.; Hartl, C.; Harvey, J.; Hegeman, J.; Hegner, B.; Hoffmann, H. F.; Honma, A.; Innocente, V.; Janot, P.; Kaadze, K.; Karavakis, E.; Lecoq, P.; Lourenço, C.; Mäki, T.; Malberti, M.; Malgeri, L.; Mannelli, M.; Masetti, L.; Maurisset, A.; Meijers, F.; Mersi, S.; Meschi, E.; Moser, R.; Mozer, M. U.; Mulders, M.; Nesvold, E.; Nguyen, M.; Orimoto, T.; Orsini, L.; Perez, E.; Petrilli, A.; Pfeiffer, A.; Pierini, M.; Pimiä, M.; Piparo, D.; Polese, G.; Racz, A.; Rodrigues Antunes, J.; Rolandi, G.; Rommerskirchen, T.; Rovere, M.; Sakulin, H.; Schäfer, C.; Schwick, C.; Segoni, I.; Sharma, A.; Siegrist, P.; Simon, M.; Sphicas, P.; Spiropulu, M.; Stoye, M.; Tadel, M.; Tropea, P.; Tsirou, A.; Vichoudis, P.; Voutilainen, M.; Zeuner, W. D.; Bertl, W.; Deiters, K.; Erdmann, W.; Gabathuler, K.; Horisberger, R.; Ingram, Q.; Kaestli, H. C.; König, S.; Kotlinski, D.; Langenegger, U.; Meier, F.; Renker, D.; Rohe, T.; Sibille, J.; Starodumov, A.; Bortignon, P.; Caminada, L.; Chanon, N.; Chen, Z.; Cittolin, S.; Dissertori, G.; Dittmar, M.; Eugster, J.; Freudenreich, K.; Grab, C.; Hintz, W.; Lecomte, P.; Lustermann, W.; Marchica, C.; Martinez Ruiz del Arbol, P.; Meridiani, P.; Milenovic, P.; Moortgat, F.; Nägeli, C.; Nef, P.; Nessi-Tedaldi, F.; Pape, L.; Pauss, F.; Punz, T.; Rizzi, A.; Ronga, F. J.; Rossini, M.; Sala, L.; Sanchez, A. K.; Sawley, M.-C.; Stieger, B.; Tauscher, L.; Thea, A.; Theofilatos, K.; Treille, D.; Urscheler, C.; Wallny, R.; Weber, M.; Wehrli, L.; Weng, J.; Aguiló, E.; Amsler, C.; Chiochia, V.; De Visscher, S.; Favaro, C.; Ivova Rikova, M.; Millan Mejias, B.; Otiougova, P.; Regenfus, C.; Robmann, P.; Schmidt, A.; Snoek, H.; Chang, Y. H.; Chen, K. H.; Dutta, S.; Kuo, C. M.; Li, S. W.; Lin, W.; Liu, Z. K.; Lu, Y. J.; Mekterovic, D.; Volpe, R.; Wu, J. H.; Yu, S. S.; Bartalini, P.; Chang, P.; Chang, Y. H.; Chang, Y. W.; Chao, Y.; Chen, K. F.; Hou, W.-S.; Hsiung, Y.; Kao, K. Y.; Lei, Y. J.; Lu, R.-S.; Shiu, J. G.; Tzeng, Y. M.; Wang, M.; Adiguzel, A.; Bakirci, M. N.; Cerci, S.; Dozen, C.; Dumanoglu, I.; Ekenel, A.; Eskut, E.; Girgis, S.; Gokbulut, G.; Hos, I.; Kangal, E. E.; Kayis Topaksu, A.; Onengut, G.; Ozdemir, K.; Ozturk, S.; Polatoz, A.; Sogut, K.; Sunar Cerci, D.; Tali, B.; Topakli, H.; Uzun, D.; Vergili, L. N.; Vergili, M.; Yilmaz, S.; Akin, I. V.; Aliev, T.; Bilmis, S.; Deniz, M.; Gamsizkan, H.; Guler, A. M.; Ocalan, K.; Ozpineci, A.; Serin, M.; Sever, R.; Surat, U. E.; Yildirim, E.; Zeyrek, M.; Deliomeroglu, M.; Demir, D.; Gülmez, E.; Isildak, B.; Kaya, M.; Kaya, O.; Ozkorucuklu, S.; Sonmez, N.; Levchuk, L.; Bostock, F.; Brooke, J. J.; Cheng, T. L.; Clement, E.; Cussans, D.; Frazier, R.; Goldstein, J.; Grimes, M.; Hansen, M.; Hartley, D.; Heath, G. P.; Heath, H. F.; Kreczko, L.; Metson, S.; Newbold, D. M.; Nirunpong, K.; Poll, A.; Senkin, S.; Smith, V. J.; Ward, S.; Basso, L.; Belyaev, A.; Brew, C.; Brown, R. M.; Camanzi, B.; Cockerill, D. J. A.; Coughlan, J. A.; Harder, K.; Harper, S.; Jackson, J.; Kennedy, B. W.; Olaiya, E.; Petyt, D.; Radburn-Smith, B. C.; Shepherd-Themistocleous, C. H.; Tomalin, I. R.; Womersley, W. J.; Worm, S. D.; Bainbridge, R.; Ball, G.; Ballin, J.; Beuselinck, R.; Buchmuller, O.; Colling, D.; Cripps, N.; Cutajar, M.; Davies, G.; Della Negra, M.; Ferguson, W.; Fulcher, J.; Futyan, D.; Gilbert, A.; Guneratne Bryer, A.; Hall, G.; Hatherell, Z.; Hays, J.; Iles, G.; Jarvis, M.; Karapostoli, G.; Lyons, L.; MacEvoy, B. C.; Magnan, A.-M.; Marrouche, J.; Mathias, B.; Nandi, R.; Nash, J.; Nikitenko, A.; Papageorgiou, A.; Pesaresi, M.; Petridis, K.; Pioppi, M.; Raymond, D. M.; Rogerson, S.; Rompotis, N.; Rose, A.; Ryan, M. J.; Seez, C.; Sharp, P.; Sparrow, A.; Tapper, A.; Tourneur, S.; Vazquez Acosta, M.; Virdee, T.; Wakefield, S.; Wardle, N.; Wardrope, D.; Whyntie, T.; Barrett, M.; Chadwick, M.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Leslie, D.; Martin, W.; Reid, I. D.; Teodorescu, L.; Hatakeyama, K.; Liu, H.; Bose, T.; Carrera Jarrin, E.; Fantasia, C.; Heister, A.; St. John, J.; Lawson, P.; Lazic, D.; Rohlf, J.; Sperka, D.; Sulak, L.; Avetisyan, A.; Bhattacharya, S.; Chou, J. P.; Cutts, D.; Ferapontov, A.; Heintz, U.; Jabeen, S.; Kukartsev, G.; Landsberg, G.; Luk, M.; Narain, M.; Nguyen, D.; Segala, M.; Sinthuprasith, T.; Speer, T.; Tsang, K. V.; Breedon, R.; Calderon De La Barca Sanchez, M.; Chauhan, S.; Chertok, M.; Conway, J.; Cox, P. T.; Dolen, J.; Erbacher, R.; Friis, E.; Ko, W.; Kopecky, A.; Lander, R.; Liu, H.; Maruyama, S.; Miceli, T.; Nikolic, M.; Pellett, D.; Robles, J.; Salur, S.; Schwarz, T.; Searle, M.; Smith, J.; Squires, M.; Tripathi, M.; Vasquez Sierra, R.; Veelken, C.; Andreev, V.; Arisaka, K.; Cline, D.; Cousins, R.; Deisher, A.; Duris, J.; Erhan, S.; Farrell, C.; Hauser, J.; Ignatenko, M.; Jarvis, C.; Plager, C.; Rakness, G.; Schlein, P.; Tucker, J.; Valuev, V.; Babb, J.; Chandra, A.; Clare, R.; Ellison, J.; Gary, J. W.; Giordano, F.; Hanson, G.; Jeng, G. Y.; Kao, S. C.; Liu, F.; Liu, H.; Long, O. R.; Luthra, A.; Nguyen, H.; Shen, B. C.; Stringer, R.; Sturdy, J.; Sumowidagdo, S.; Wilken, R.; Wimpenny, S.; Andrews, W.; Branson, J. G.; Cerati, G. B.; Evans, D.; Golf, F.; Holzner, A.; Kelley, R.; Lebourgeois, M.; Letts, J.; Mangano, B.; Padhi, S.; Palmer, C.; Petrucciani, G.; Pi, H.; Pieri, M.; Ranieri, R.; Sani, M.; Sharma, V.; Simon, S.; Sudano, E.; Tu, Y.; Vartak, A.; Wasserbaech, S.; Würthwein, F.; Yagil, A.; Yoo, J.; Barge, D.; Bellan, R.; Campagnari, C.; D'Alfonso, M.; Danielson, T.; Flowers, K.; Geffert, P.; Incandela, J.; Justus, C.; Kalavase, P.; Koay, S. A.; Kovalskyi, D.; Krutelyov, V.; Lowette, S.; Mccoll, N.; Pavlunin, V.; Rebassoo, F.; Ribnik, J.; Richman, J.; Rossin, R.; Stuart, D.; T, W.; Vlimant, J. R.; Apresyan, A.; Bornheim, A.; Bunn, J.; Chen, Y.; Gataullin, M.; Ma, Y.; Mott, A.; Newman, H. B.; Rogan, C.; Shin, K.; Timciuc, V.; Traczyk, P.; Veverka, J.; Wilkinson, R.; Yang, Y.; Zhu, R. Y.; Akgun, B.; Carroll, R.; Ferguson, T.; Iiyama, Y.; Jang, D. W.; Jun, S. Y.; Liu, Y. F.; Paulini, M.; Russ, J.; Vogel, H.; Vorobiev, I.; Cumalat, J. P.; Dinardo, M. E.; Drell, B. R.; Edelmaier, C. J.; Ford, W. T.; Gaz, A.; Heyburn, B.; Luiggi Lopez, E.; Nauenberg, U.; Smith, J. G.; Stenson, K.; Ulmer, K. A.; Wagner, S. R.; Zang, S. L.; Agostino, L.; Alexander, J.; Cassel, D.; Chatterjee, A.; Das, S.; Eggert, N.; Gibbons, L. K.; Heltsley, B.; Hopkins, W.; Khukhunaishvili, A.; Kreis, B.; Kaufman, G. Nicolas; Patterson, J. R.; Puigh, D.; Ryd, A.; Salvati, E.; Shi, X.; Sun, W.; Teo, W. D.; Thom, J.; Thompson, J.; Vaughan, J.; Weng, Y.; Winstrom, L.; Wittich, P.; Biselli, A.; Cirino, G.; Winn, D.; Abdullin, S.; Albrow, M.; Anderson, J.; Apollinari, G.; Atac, M.; Bakken, J. A.; Banerjee, S.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bloch, I.; Borcherding, F.; Burkett, K.; Butler, J. N.; Chetluru, V.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Cooper, W.; Eartly, D. P.; Elvira, V. D.; Esen, S.; Fisk, I.; Freeman, J.; Gao, Y.; Gottschalk, E.; Green, D.; Gunthoti, K.; Gutsche, O.; Hanlon, J.; Harris, R. M.; Hirschauer, J.; Hooberman, B.; Jensen, H.; Johnson, M.; Joshi, U.; Khatiwada, R.; Klima, B.; Kousouris, K.; Kunori, S.; Kwan, S.; Leonidopoulos, C.; Limon, P.; Lincoln, D.; Lipton, R.; Lykken, J.; Maeshima, K.; Marraffino, J. M.; Mason, D.; McBride, P.; Miao, T.; Mishra, K.; Mrenna, S.; Musienko, Y.; Newman-Holmes, C.; O'Dell, V.; Pordes, R.; Prokofyev, O.; Saoulidou, N.; Sexton-Kennedy, E.; Sharma, S.; Spalding, W. J.; Spiegel, L.; Tan, P.; Taylor, L.; Tkaczyk, S.; Uplegger, L.; Vaandering, E. W.; Vidal, R.; Whitmore, J.; Wu, W.; Yang, F.; Yumiceva, F.; Yun, J. C.; Acosta, D.; Avery, P.; Bourilkov, D.; Chen, M.; De Gruttola, M.; Di Giovanni, G. P.; Dobur, D.; Drozdetskiy, A.; Field, R. D.; Fisher, M.; Fu, Y.; Furic, I. K.; Gartner, J.; Kim, B.; Konigsberg, J.; Korytov, A.; Kropivnitskaya, A.; Kypreos, T.; Matchev, K.; Mitselmakher, G.; Muniz, L.; Prescott, C.; Remington, R.; Schmitt, M.; Scurlock, B.; Sellers, P.; Skhirtladze, N.; Snowball, M.; Wang, D.; Yelton, J.; Zakaria, M.; Ceron, C.; Gaultney, V.; Kramer, L.; Lebolo, L. M.; Linn, S.; Markowitz, P.; Martinez, G.; Mesa, D.; Rodriguez, J. L.; Adams, T.; Askew, A.; Bochenek, J.; Chen, J.; Diamond, B.; Gleyzer, S. V.; Haas, J.; Hagopian, S.; Hagopian, V.; Jenkins, M.; Johnson, K. F.; Prosper, H.; Quertenmont, L.; Sekmen, S.; Veeraraghavan, V.; Baarmand, M. M.; Dorney, B.; Guragain, S.; Hohlmann, M.; Kalakhety, H.; Ralich, R.; Vodopiyanov, I.; Adams, M. R.; Anghel, I. M.; Apanasevich, L.; Bai, Y.; Bazterra, V. E.; Betts, R. R.; Callner, J.; Cavanaugh, R.; Dragoiu, C.; Gauthier, L.; Gerber, C. E.; Hamdan, S.; Hofman, D. J.; Khalatyan, S.; Kunde, G. J.; Lacroix, F.; Malek, M.; O'Brien, C.; Silvestre, C.; Smoron, A.; Strom, D.; Varelas, N.; Akgun, U.; Albayrak, E. A.; Bilki, B.; Clarida, W.; Duru, F.; Lae, C. K.; McCliment, E.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Newsom, C. R.; Norbeck, E.; Olson, J.; Onel, Y.; Ozok, F.; Sen, S.; Wetzel, J.; Yetkin, T.; Yi, K.; Barnett, B. A.; Blumenfeld, B.; Bonato, A.; Eskew, C.; Fehling, D.; Giurgiu, G.; Gritsan, A. V.; Guo, Z. J.; Hu, G.; Maksimovic, P.; Rappoccio, S.; Swartz, M.; Tran, N. V.; Whitbeck, A.; Baringer, P.; Bean, A.; Benelli, G.; Grachov, O.; Kenny, R. P.; Murray, M.; Noonan, D.; Sanders, S.; Wood, J. S.; Zhukova, V.; Barfuss, A. f.; Bolton, T.; Chakaberia, I.; Ivanov, A.; Khalil, S.; Makouski, M.; Maravin, Y.; Shrestha, S.; Svintradze, I.; Wan, Z.; Gronberg, J.; Lange, D.; Wright, D.; Baden, A.; Boutemeur, M.; Eno, S. C.; Ferencek, D.; Gomez, J. A.; Hadley, N. J.; Kellogg, R. G.; Kirn, M.; Lu, Y.; Mignerey, A. C.; Rossato, K.; Rumerio, P.; Santanastasio, F.; Skuja, A.; Temple, J.; Tonjes, M. B.; Tonwar, S. C.; Twedt, E.; Alver, B.; Bauer, G.; Bendavid, J.; Busza, W.; Butz, E.; Cali, I. A.; Chan, M.; Dutta, V.; Everaerts, P.; Ceballos, G. Gomez; Goncharov, M.; Hahn, K. A.; Harris, P.; Kim, Y.; Klute, M.; Lee, Y.-J.; Li, W.; Loizides, C.; Luckey, P. D.; Ma, T.; Nahn, S.; Paus, C.; Ralph, D.; Roland, C.; Roland, G.; Rudolph, M.; Stephans, G. S. F.; Stöckli, F.; Sumorok, K.; Sung, K.; Wenger, E. A.; Xie, S.; Yang, M.; Yilmaz, Y.; Yoon, A. S.; Zanetti, M.; Cooper, S. I.; Cushman, P.; Dahmes, B.; DeBenedetti, A.; Dudero, P. R.; Franzoni, G.; Haupt, J.; Klapoetke, K.; Kubota, Y.; Mans, J.; Rekovic, V.; Rusack, R.; Sasseville, M.; Singovsky, A.; Cremaldi, L. M.; Godang, R.; Kroeger, R.; Perera, L.; Rahmat, R.; Sanders, D. A.; Summers, D.; Bloom, K.; Bose, S.; Butt, J.; Claes, D. R.; Dominguez, A.; Eads, M.; Keller, J.; Kelly, T.; Kravchenko, I.; Lazo-Flores, J.; Malbouisson, H.; Malik, S.; Snow, G. R.; Baur, U.; Godshalk, A.; Iashvili, I.; Jain, S.; Kharchilava, A.; Kumar, A.; Shipkowski, S. P.; Smith, K.; Alverson, G.; Barberis, E.; Baumgartel, D.; Boeriu, O.; Chasco, M.; Reucroft, S.; Swain, J.; Trocino, D.; Wood, D.; Zhang, J.; Anastassov, A.; Kubik, A.; Odell, N.; Ofierzynski, R. A.; Pollack, B.; Pozdnyakov, A.; Schmitt, M.; Stoynev, S.; Velasco, M.; Won, S.; Antonelli, L.; Berry, D.; Hildreth, M.; Jessop, C.; Karmgard, D. J.; Kolb, J.; Kolberg, T.; Lannon, K.; Luo, W.; Lynch, S.; Marinelli, N.; Morse, D. M.; Pearson, T.; Ruchti, R.; Slaunwhite, J.; Valls, N.; Wayne, M.; Ziegler, J.; Bylsma, B.; Durkin, L. S.; Gu, J.; Hill, C.; Killewald, P.; Kotov, K.; Ling, T. Y.; Rodenburg, M.; Williams, G.; Adam, N.; Berry, E.; Elmer, P.; Gerbaudo, D.; Halyo, V.; Hebda, P.; Hunt, A.; Jones, J.; Laird, E.; Lopes Pegna, D.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Piroué, P.; Quan, X.; Saka, H.; Stickland, D.; Tully, C.; Werner, J. S.; Zuranski, A.; Acosta, J. G.; Huang, X. T.; Lopez, A.; Mendez, H.; Oliveros, S.; Ramirez Vargas, J. E.; Zatserklyaniy, A.; Alagoz, E.; Barnes, V. E.; Bolla, G.; Borrello, L.; Bortoletto, D.; Everett, A.; Garfinkel, A. F.; Gutay, L.; Hu, Z.; Jones, M.; Koybasi, O.; Kress, M.; Laasanen, A. T.; Leonardo, N.; Liu, C.; Maroussov, V.; Merkel, P.; Miller, D. H.; Neumeister, N.; Shipsey, I.; Silvers, D.; Svyatkovskiy, A.; Yoo, H. D.; Zablocki, J.; Zheng, Y.; Jindal, P.; Parashar, N.; Boulahouache, C.; Cuplov, V.; Ecklund, K. M.; Geurts, F. J. M.; Padley, B. P.; Redjimi, R.; Roberts, J.; Zabel, J.; Betchart, B.; Bodek, A.; Chung, Y. S.; Covarelli, R.; de Barbaro, P.; Demina, R.; Eshaq, Y.; Flacher, H.; Garcia-Bellido, A.; Goldenzweig, P.; Gotra, Y.; Han, J.; Harel, A.; Miner, D. C.; Orbaker, D.; Petrillo, G.; Vishnevskiy, D.; Zielinski, M.; Bhatti, A.; Ciesielski, R.; Demortier, L.; Goulianos, K.; Lungu, G.; Malik, S.; Mesropian, C.; Yan, M.; Atramentov, O.; Barker, A.; Duggan, D.; Gershtein, Y.; Gray, R.; Halkiadakis, E.; Hidas, D.; Hits, D.; Lath, A.; Panwalkar, S.; Patel, R.; Richards, A.; Rose, K.; Schnetzer, S.; Somalwar, S.; Stone, R.; Thomas, S.; Cerizza, G.; Hollingsworth, M.; Spanier, S.; Yang, Z. C.; York, A.; Eusebi, R.; Gilmore, J.; Gurrola, A.; Kamon, T.; Khotilovich, V.; Montalvo, R.; Osipenkov, I.; Pakhotin, Y.; Pivarski, J.; Safonov, A.; Sengupta, S.; Tatarinov, A.; Toback, D.; Weinberger, M.; Akchurin, N.; Bardak, C.; Damgov, J.; Jeong, C.; Kovitanggoon, K.; Lee, S. W.; Mane, P.; Roh, Y.; Sill, A.; Volobouev, I.; Wigmans, R.; Yazgan, E.; Appelt, E.; Brownson, E.; Engh, D.; Florez, C.; Gabella, W.; Issah, M.; Johns, W.; Kurt, P.; Maguire, C.; Melo, A.; Sheldon, P.; Snook, B.; Tuo, S.; Velkovska, J.; Arenton, M. W.; Balazs, M.; Boutle, S.; Cox, B.; Francis, B.; Hirosky, R.; Ledovskoy, A.; Lin, C.; Neu, C.; Yohay, R.; Gollapinni, S.; Harr, R.; Karchin, P. E.; Lamichhane, P.; Mattson, M.; Milstène, C.; Sakharov, A.; Anderson, M.; Bachtis, M.; Bellinger, J. N.; Carlsmith, D.; Dasu, S.; Efron, J.; Flood, K.; Gray, L.; Grogg, K. S.; Grothe, M.; Hall-Wilton, R.; Herndon, M.; Hervé, A.; Klabbers, P.; Klukas, J.; Lanaro, A.; Lazaridis, C.; Leonard, J.; Loveless, R.; Mohapatra, A.; Palmonari, F.; Reeder, D.; Ross, I.; Savin, A.; Smith, W. H.; Swanson, J.; Weinberg, M.

2011-07-01

First measurements of dihadron correlationsfor charged particles are presented for central PbPb collisions at a nucleon-nucleon center-of-mass energy of 2.76TeV over a broad range in relative pseudorapidity (∆η) and the full range of relative azimuthal angle (∆ϕ). The data were collected with the CMS detector, at the LHC. A broadening of the away-side (∆ϕ ≈ π) azimuthal correlation is observed at all ∆η, as compared to the measurements in pp collisions. Furthermore, long-range dihadron correlations in ∆η are observed for particles with similar ϕ values. This phenomenon, also known as the "ridge", persists up to at least |∆η| = 4. For particles with transverse momenta ( p T) of2-4 GeV/ c, the ridge is found to be most prominent when these particles are correlated with particles of p T = 2-6 GeV/ c, and to be much reduced when paired with particles of p T = 10-12 GeV/ c.

Prediction and observation of tin and silver plasmas with index of refraction greater than one in the soft x-ray range.

PubMed

Filevich, Jorge; Grava, Jonathan; Purvis, Mike; Marconi, Mario C; Rocca, Jorge J; Nilsen, Joseph; Dunn, James; Johnson, Walter R

2006-07-01

We present the calculated prediction and the experimental confirmation that doubly ionized Ag and Sn plasmas can have an index of refraction greater than one for soft x-ray wavelengths. Interferometry experiments conducted using a capillary discharge soft x-ray laser operating at a wavelength of confirm that in few times ionized laser-created plasmas of these elements the anomalous dispersion from bound electrons can dominate the free electron contribution, making the index of refraction greater than one. The results confirm that bound electrons can strongly influence the index of refraction of numerous plasmas over a broad range of soft x-ray wavelengths confirming recent observations. The understanding of index of refraction at short wavelengths will become even more essential during the next decade as x-ray free electron lasers will become available to probe a wider variety of plasmas at higher densities and shorter wavelengths.

Parameter Estimation for GRACE-FO Geometric Ranging Errors

NASA Astrophysics Data System (ADS)

Wegener, H.; Mueller, V.; Darbeheshti, N.; Naeimi, M.; Heinzel, G.

2017-12-01

Onboard GRACE-FO, the novel Laser Ranging Instrument (LRI) serves as a technology demonstrator, but it is a fully functional instrument to provide an additional high-precision measurement of the primary mission observable: the biased range between the two spacecraft. Its (expectedly) two largest error sources are laser frequency noise and tilt-to-length (TTL) coupling. While not much can be done about laser frequency noise, the mechanics of the TTL error are widely understood. They depend, however, on unknown parameters. In order to improve the quality of the ranging data, it is hence essential to accurately estimate these parameters and remove the resulting TTL error from the data.Means to do so will be discussed. In particular, the possibility of using calibration maneuvers, the utility of the attitude information provided by the LRI via Differential Wavefront Sensing (DWS), and the benefit from combining ranging data from LRI with ranging data from the established microwave ranging, will be mentioned.

A direct evaluation of the Geosat altimeter wet atmospheric range delay using very long baseline interferometry observations

NASA Technical Reports Server (NTRS)

Koblinsky, C. J.; Ryan, J.; Braatz, L.; Klosko, S. M.

1993-01-01

The overall accuracy of the U.S. Navy Geosat altimeter wet atmospheric range delay caused by refraction through the atmosphere is directly assessed by comparing the estimates made from the DMSP Special Sensor Microwave/Imager and the U.S. Navy Fleet Numerical Ocean Center forecast model for Geosat with measurements of total zenith columnar water vapor content from four VLBI sites. The assessment is made by comparing time series of range delay from various methods at each location. To determine the importance of diurnal variation in water vapor content in noncoincident estimates, the VLBI measurements were made at 15-min intervals over a few days. The VLBI measurements showed strong diurnal variations in columnar water vapor at several sites, causing errors of the order 3 cm rms in any noncoincident measurement of the wet troposphere range delay. These errors have an effect on studies of annual and interannual changes in sea level with Geosat data.

[Monitoring of brightness temperature fluctuation of water in SHF range].

PubMed

Ivanov, Yu D; Kozlov, A F; Galiullin, R A; Tatu, V Yu; Vesnin, S G; Ziborov, V S; Ivanova, N D; Pleshakova, T O

2017-01-01

The purpose of the research consisted in detection of fluctuation of brightness temperature (TSHF) of water in the area of the temperature Т = 42°С (that is critical for human) during its evaporation by SHF radiometry. Methods: Monitoring of the changes in brightness temperature of water in superhigh frequency (SHF) range (3.8-4.2 GHz) near the phase transition temperature of water Т = 42°С during its evaporation in the cone dielectric cell. The brightness temperature measurements were carried out using radiometer. Results: Fluctuation with maximum of brightness temperature was detected in 3.8-4.2 GHz frequency range near at the temperature of water Т = 42°С. It was characteristic for these TSHF fluctuations that brightness temperature rise time in this range of frequencies in ~4°С temperature range with 0.05-15°С/min gradient and a sharp decrease during 10 s connected with measuring vapor conditions. Then nonintensive fluctuation series was observed. At that, the environment temperature remained constant. Conclusion: The significant increasing in brightness temperature of water during its evaporation in SHF range near the temperature of Т ~42°С were detected. It was shown that for water, ТSHF pull with the amplitude DТSHF ~4°C are observed. At the same time, thermodynamic temperature virtually does not change. The observed effects can be used in the development of the systems for diadnostics of pathologies in human and analytical system.

Isolation and characterization of polymorphic microsatellite loci in Spondias radlkoferi (Anacardiaceae)1

PubMed Central

Aguilar-Barajas, Esther; Sork, Victoria L.; González-Zamora, Arturo; Rocha-Ramírez, Víctor; Arroyo-Rodríguez, Víctor; Oyama, Ken

2014-01-01

• Premise of the study: Microsatellite markers were developed for Spondias radlkoferi to assess the impact of primate seed dispersal on the genetic diversity and structure of this important tree species of Anacardiaceae. • Methods and Results: Fourteen polymorphic loci were isolated from S. radlkoferi through 454 GS-FLX Titanium pyrosequencing of genomic DNA. The number of alleles ranged from three to 12. The observed and expected heterozygosities ranged from 0.382 to 1.00 and from 0.353 to 0.733, respectively. The amplification was also successful in S. mombin and two genera of Anacardiaceae: Rhus aromatica and Toxicodendron radicans. • Conclusions: These microsatellite loci will be useful to assess the genetic diversity and population structure of S. radlkoferi and related species, and will allow us to investigate the effects of seed dispersal by spider monkeys (Ateles geoffroyi) on the genetic structure and diversity of S. radlkoferi populations in a fragmented rainforest. PMID:25383270

Development and evaluation of microsatellite markers for Acer miyabei (Sapindaceae), a threatened maple species in East Asia.

PubMed

Saeki, Ikuyo; Hirao, Akira S; Kenta, Tanaka

2015-06-01

Twelve microsatellite markers were developed and characterized in a threatened maple species, Acer miyabei (Sapindaceae), for use in population genetic analyses. Using Ion Personal Genome Machine (PGM) sequencing, we developed microsatellite markers with perfect di- and trinucleotide repeats. These markers were tested on a total of 44 individuals from two natural populations of A. miyabei subsp. miyabei f. miyabei in Hokkaido Island, Japan. The number of alleles per locus ranged from two to eight. The observed and expected heterozygosities per locus ranged from 0.05 to 0.75 and from 0.05 to 0.79, respectively. Some of the markers were successfully transferred to the closely related species A. campestre, A. platanoides, and A. pictum. The developed markers will be useful in characterizing the genetic structure and diversity of A. miyabei and will help to understand its spatial genetic variation, levels of inbreeding, and patterns of gene flow, thereby providing a basis for conservation.

A panel of ten microsatellite loci for the Chagas disease vector Rhodnius prolixus (Hemiptera: Reduviidae).

PubMed

Fitzpatrick, S; Watts, P C; Feliciangeli, M D; Miles, M A; Kemp, S J

2009-03-01

Rhodnius prolixus is the main vector of Chagas disease in Venezuela, where it is found colonising rural housing consisting of unplastered adobe walls with palm and/or metal roofs. Vector control failure in Venezuela may be due to the invasion of houses by silvatic populations of R. prolixus found in palms. As part of a study to determine if domestic and silvatic populations of R. prolixus are isolated, thus clarifying the role of silvatic populations in maintaining house infestations, we constructed three partial genomic microsatellite libraries. A panel of ten dinucleotide polymorphic microsatellite markers was selected for genotyping. Allele numbers per locus ranged from three to twelve, with observed and expected heterozygosity ranging from 0.26 to 0.55 and 0.32 to 0.66. The microsatellite markers presented here will contribute to the control of Chagas disease in Venezuela and Colombia through the provision of population information that may allow the design of improved control strategies.

Isolation and Characterization of Eleven Polymorphic Microsatellite Loci for the Valuable Medicinal Plant Dendrobium huoshanense and Cross-Species Amplification

PubMed Central

Wang, Hui; Chen, Nai-Fu; Zheng, Ji-Yang; Wang, Wen-Cai; Pei, Yun-Yun; Zhu, Guo-Ping

2012-01-01

Dendrobium huoshanense (Orchidaceae) is a perennial herb and a widely used medicinal plant in Traditional Chinese medicine (TCM) endemic to Huoshan County town in Anhui province in Southeast China. A microsatellite-enriched genomic DNA library of D. huoshanense was developed and screened to identify marker loci. Eleven polymorphic loci were isolated and analyzed by screening 25 individuals collected from a natural population. The number of alleles per locus ranged from 2 to 5. The observed and expected heterozygosities ranged from 0.227 to 0.818 and from 0.317 to 0.757, respectively. Two loci showed significant deviations from Hardy-Weinberg equilibrium and four of the pairwise comparisons of loci revealed linkage disequilibrium (p < 0.05). These microsatellite loci were cross-amplified for five congeneric species and seven loci can be amplified in all species. These simple sequence repeats (SSR) markers are useful in genetic studies of D. huoshanense and other related species and in conservation decision-making. PMID:23222682

Development and characterization of 33 novel polymorphic microsatellite markers for the brown tree snake Boiga irregularis.

PubMed

Unger, Shem D; Abernethy, Erin F; Lance, Stacey L; Beasley, Rochelle R; Kimball, Bruce A; McAuliffe, Thomas W; Jones, Kenneth L; Rhodes, Olin E

2015-11-07

Boiga irregularis is a widespread invasive species on Guam and has led to extirpation of most of the island's native avifauna. There are presently no microsatellite markers for this invasive species, hence we developed highly polymorphic microsatellite markers to allow for robust population genetic studies on Guam. We isolated and characterized 33 microsatellite loci for the brown tree snake, B. irregularis. The loci were screened across 32 individuals from Guam. The number of alleles per locus ranged from three to ten, with an average of 4.62. The expected (He) and observed heterozygosity (Ho) ranged from 0.294 to 0.856 and from 0.031 to 0.813, with an average of 0.648 and 0.524, respectively. Significant deviations from Hardy-Weinberg equilibrium were detected at seven loci after Bonferoni correction. Probability of identity values ranged from 0.043 to 0.539. These genetic markers are useful for understanding a suite of post-invasion population genetic parameters, sources of invasions, and effectiveness of management strategies for this invasive species.

Long-range repulsion of colloids driven by ion exchange and diffusiophoresis

PubMed Central

Florea, Daniel; Musa, Sami; Huyghe, Jacques M. R.; Wyss, Hans M.

2014-01-01

Interactions between surfaces and particles in aqueous suspension are usually limited to distances smaller than 1 μm. However, in a range of studies from different disciplines, repulsion of particles has been observed over distances of up to hundreds of micrometers, in the absence of any additional external fields. Although a range of hypotheses have been suggested to account for such behavior, the physical mechanisms responsible for the phenomenon still remain unclear. To identify and isolate these mechanisms, we perform detailed experiments on a well-defined experimental system, using a setup that minimizes the effects of gravity and convection. Our experiments clearly indicate that the observed long-range repulsion is driven by a combination of ion exchange, ion diffusion, and diffusiophoresis. We develop a simple model that accounts for our data; this description is expected to be directly applicable to a wide range of systems exhibiting similar long-range forces. PMID:24748113

D1S80 (pMCT118) allele frequencies in a Malay population sample from Malaysia.

PubMed

Koh, C L; Lim, M E; Ng, H S; Sam, C K

1997-01-01

The D1S80 allele frequencies in 124 unrelated Malays from the Malaysian population were determined and 51 genotypes and 19 alleles were encountered. The D1S80 frequency distribution met Hardy-Weinberg expectations. The observed heterozygosity was 0.80 and the power of discrimination was 0.96.

Ranging Behaviour of Commercial Free-Range Laying Hens.

PubMed

Chielo, Leonard Ikenna; Pike, Tom; Cooper, Jonathan

2016-04-26

In this study, the range use and behaviour of laying hens in commercial free-range flocks was explored. Six flocks were each visited on four separate days and data collected from their outdoor area (divided into zones based on distance from shed and available resources). These were: apron (0-10 m from shed normally without cover or other enrichments); enriched belt (10-50 m from shed where resources such as manmade cover, saplings and dust baths were provided); and outer range (beyond 50 m from shed with no cover and mainly grass pasture). Data collection consisted of counting the number of hens in each zone and recording behaviour, feather condition and nearest neighbour distance (NND) of 20 birds per zone on each visit day. In addition, we used techniques derived from ecological surveys to establish four transects perpendicular to the shed, running through the apron, enriched belt and outer range. Number of hens in each 10 m × 10 m quadrat was recorded four times per day as was the temperature and relative humidity of the outer range. On average, 12.5% of hens were found outside. Of these, 5.4% were found in the apron; 4.3% in the enriched zone; and 2.8% were in the outer range. This pattern was supported by data from quadrats, where the density of hens sharply dropped with increasing distance from shed. Consequently, NND was greatest in the outer range, least in the apron and intermediate in the enriched belt. Hens sampled in outer range and enriched belts had better feather condition than those from the apron. Standing, ground pecking, walking and foraging were the most commonly recorded activities with standing and pecking most likely to occur in the apron, and walking and foraging more common in the outer range. Use of the outer range declined with lower temperatures and increasing relative humidity, though use of apron and enriched belt was not affected by variation in these measures. These data support previous findings that outer range areas tend to be

Short-Range Correlated Magnetic Core-Shell CrO₂/Cr₂O₃ Nanorods: Experimental Observations and Theoretical Considerations.

PubMed

Gandhi, Ashish C; Li, Tai-Yue; Chan, Ting Shan; Wu, Sheng Yun

2018-05-09

With the evolution of synthesis and the critical characterization of core-shell nanostructures, short-range magnetic correlation is of prime interest in employing their properties to develop novel devices and widespread applications. In this regard, a novel approach of the magnetic core-shell saturated magnetization (CSSM) cylinder model solely based on the contribution of saturated magnetization in one-dimensional CrO₂/Cr₂O₃ core-shell nanorods (NRs) has been developed and applied for the determination of core-diameter and shell-thickness. The nanosized effect leads to a short-range magnetic correlation of ferromagnetic core-CrO₂ extracted from CSSM, which can be explained using finite size scaling method. The outcome of this study is important in terms of utilizing magnetic properties for the critical characterization of core-shell nanomagnetic materials.

Genetic structure of the threatened Dipterocarpus costatus populations in lowland tropical rainforests of southern Vietnam.

PubMed

Duc, N M; Duy, V D; Xuan, B T T; Thang, B V; Ha, N T H; Tam, N M

2016-10-24

Dipterocarpus costatus is an endangered species restricted to the lowland forests of southern Vietnam. Habitat loss and over-exploitation of D. costatus wood are the major threats to this species. We investigated the level of genetic variability within and among populations of D. costatus in order to provide guidelines for the conservation, management, and restoration of this species to the Forest Protection Department, Vietnam. Nine microsatellite markers were used to analyze 114 samples from four populations representing the natural range of D. costatus in southeast Vietnam. We indicated the low allelic diversity (N A = 2.3) and low genetic diversities with an average observed and expected heterozygosity of 0.130 and 0.151, respectively, in the lowland forests of southeast Vietnam. The low genetic diversity might be a consequence of inbreeding within the small and isolated populations of D. costatus owing to its habitat loss and over-exploitation. All populations deviated from Hardy-Weinberg equilibrium showing reduced heterozygosity. Alleles were lost from the populations by genetic drift. Genetic differentiation among populations was high (average pairwise F ST = 0.405), indicating low gene flow (<1) and isolated populations due to its destructed habitat and large geographical distances (P < 0.05) among populations. Heterozygosity excess tests (except of Bu Gia Map only under infinite allele model) were negative. The high genetic variation (62.7%) was found within populations. The STRUCTURE and neighbor joining tree results suggest strong differentiation among D. costatus populations, with the three genetic clusters, Phu Quoc, Tan Phu and Bu Gia Map, and Lo Go-Xa Mat due to habitat fragmentation and isolation. The threatened status of D. costatus was related to a lack of genetic diversity, with all its populations isolated in small forest patches. We recommend the establishment of an ex situ conservation site for D. costatus with a new big population comprising

Space-Based Range Safety and Future Space Range Applications

NASA Technical Reports Server (NTRS)

Whiteman, Donald E.; Valencia, Lisa M.; Simpson, James C.

2005-01-01

The National Aeronautics and Space Administration (NASA) Space-Based Telemetry and Range Safety (STARS) study is a multiphase project to demonstrate the performance, flexibility and cost savings that can be realized by using space-based assets for the Range Safety [global positioning system (GPS) metric tracking data, flight termination command and range safety data relay] and Range User (telemetry) functions during vehicle launches and landings. Phase 1 included flight testing S-band Range Safety and Range User hardware in 2003 onboard a high-dynamic aircraft platform at Dryden Flight Research Center (Edwards, California, USA) using the NASA Tracking and Data Relay Satellite System (TDRSS) as the communications link. The current effort, Phase 2, includes hardware and packaging upgrades to the S-band Range Safety system and development of a high data rate Ku-band Range User system. The enhanced Phase 2 Range Safety Unit (RSU) provided real-time video for three days during the historic Global Flyer (Scaled Composites, Mojave, California, USA) flight in March, 2005. Additional Phase 2 testing will include a sounding rocket test of the Range Safety system and aircraft flight testing of both systems. Future testing will include a flight test on a launch vehicle platform. This paper discusses both Range Safety and Range User developments and testing with emphasis on the Range Safety system. The operational concept of a future space-based range is also discussed.

Space-Based Range Safety and Future Space Range Applications

NASA Technical Reports Server (NTRS)

Whiteman, Donald E.; Valencia, Lisa M.; Simpson, James C.

2005-01-01

The National Aeronautics and Space Administration Space-Based Telemetry and Range Safety study is a multiphase project to demonstrate the performance, flexibility and cost savings that can be realized by using space-based assets for the Range Safety (global positioning system metric tracking data, flight termination command and range safety data relay) and Range User (telemetry) functions during vehicle launches and landings. Phase 1 included flight testing S-band Range Safety and Range User hardware in 2003 onboard a high-dynamic aircraft platform at Dryden Flight Research Center (Edwards, California) using the NASA Tracking and Data Relay Satellite System as the communications link. The current effort, Phase 2, includes hardware and packaging upgrades to the S-band Range Safety system and development of a high data rate Ku-band Range User system. The enhanced Phase 2 Range Safety Unit provided real-time video for three days during the historic GlobalFlyer (Scaled Composites, Mojave, California) flight in March, 2005. Additional Phase 2 testing will include a sounding rocket test of the Range Safety system and aircraft flight testing of both systems. Future testing will include a flight test on a launch vehicle platform. This report discusses both Range Safety and Range User developments and testing with emphasis on the Range Safety system. The operational concept of a future space-based range is also discussed.

Female mating preferences and offspring survival: testing hypotheses on the genetic basis of mate choice in a wild lekking bird.

PubMed

Sardell, Rebecca J; Kempenaers, Bart; Duval, Emily H

2014-02-01

Indirect benefits of mate choice result from increased offspring genetic quality and may be important drivers of female behaviour. 'Good-genes-for-viability' models predict that females prefer mates of high additive genetic value, such that offspring survival should correlate with male attractiveness. Mate choice may also vary with genetic diversity (e.g. heterozygosity) or compatibility (e.g. relatedness), where the female's genotype influences choice. The relative importance of these nonexclusive hypotheses remains unclear. Leks offer an excellent opportunity to test their predictions, because lekking males provide no material benefits and choice is relatively unconstrained by social limitations. Using 12 years of data on lekking lance-tailed manakins, Chiroxiphia lanceolata, we tested whether offspring survival correlated with patterns of mate choice. Offspring recruitment weakly increased with father attractiveness (measured as reproductive success, RS), suggesting attractive males provide, if anything, only minor benefits via offspring viability. Both male RS and offspring survival until fledging increased with male heterozygosity. However, despite parent-offspring correlation in heterozygosity, offspring survival was unrelated to its own or maternal heterozygosity or to parental relatedness, suggesting survival was not enhanced by heterozygosity per se. Instead, offspring survival benefits may reflect inheritance of specific alleles or nongenetic effects. Although inbreeding depression in male RS should select for inbreeding avoidance, mates were not less related than expected under random mating. Although mate heterozygosity and relatedness were correlated, selection on mate choice for heterozygosity appeared stronger than that for relatedness and may be the primary mechanism maintaining genetic variation in this system despite directional sexual selection. © 2014 John Wiley & Sons Ltd.

Correlation of electron path lengths observed in the highly wound outer region of magnetic clouds with the slab fraction of magnetic turbulence in the dissipation range

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Lun C.; Shao, Xi; Reames, Donald V.

2014-05-10

Three magnetic cloud events, in which solar impulsive electron events occurred in their outer region, are employed to investigate the difference of path lengths L {sub 0eIII} traveled by non-relativistic electrons from their release site near the Sun to the observer at 1 AU, where L {sub 0eIII} = v {sub l} × (t {sub l} – t {sub III}), v {sub l} and t {sub l} being the velocity and arrival time of electrons in the lowest energy channel (∼27 keV) of the Wind/3DP/SST sensor, respectively, and t {sub III} being the onset time of type III radio bursts.more » The deduced L {sub 0eIII} value ranges from 1.3 to 3.3 AU. Since a negligible interplanetary scattering level can be seen in both L {sub 0eIII} > 3 AU and ∼1.2 AU events, the difference in L {sub 0eIII} could be linked to the turbulence geometry (slab or two-dimensional) in the solar wind. By using the Wind/MFI magnetic field data with a time resolution of 92 ms, we examine the turbulence geometry in the dissipation range. In our examination, ∼6 minutes of sampled subintervals are used in order to improve time resolution. We have found that, in the transverse turbulence, the observed slab fraction is increased with an increasing L {sub 0eIII} value, reaching ∼100% in the L {sub 0eIII} > 3 AU event. Our observation implies that when only the slab spectral component exists, magnetic flux tubes (magnetic surfaces) are closed and regular for a very long distance along the transport route of particles.« less

A comparison of water vapor quantities from model short-range forecasts and ARM observations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hnilo, J J

2006-03-17

Model evolution and improvement is complicated by the lack of high quality observational data. To address a major limitation of these measurements the Atmospheric Radiation Measurement (ARM) program was formed. For the second quarter ARM metric we will make use of new water vapor data that has become available, and called the 'Merged-sounding' value added product (referred to as OBS, within the text) at three sites: the North Slope of Alaska (NSA), Darwin Australia (DAR) and the Southern Great Plains (SGP) and compare these observations to model forecast data. Two time periods will be analyzed March 2000 for the SGPmore » and October 2004 for both DAR and NSA. The merged-sounding data have been interpolated to 37 pressure levels (e.g., from 1000hPa to 100hPa at 25hPa increments) and time averaged to 3 hourly data for direct comparison to our model output.« less

Improving Global Analysis and Short-Range Forecast Using Rainfall and Moisture Observations Derived from TRMM and SSM/I Passive Microwave Instruments

NASA Technical Reports Server (NTRS)

Hou, Arthur Y.; Zhang, Sara Q.; daSilva, Arlindo M.; Olson, William S.; Kummerow, Christian D.; Simpson, Joanne

2000-01-01

The Global Precipitation Mission, a satellite project under consideration as a follow-on to the Tropical Rainfall Measuring Mission (TRMM) by the National Aeronautics and Space Agency (NASA) in the United States, the National Space Development Agency (NASDA) in Japan, and other international partners, comprises an improved TRMM-like satellite and a constellation of 8 satellites carrying passive microwave radiometers to provide global rainfall measurements at 3-hour intervals. The success of this concept relies on the merits of rainfall estimates derived from passive microwave radiometers. This article offers a proof-of-concept demonstration of the benefits of using, rainfall and total precipitable water (TPW) information derived from such instruments in global data assimilation with observations from the TRMM Microwave Imager (TMI) and 2 Special Sensor Microwave/Imager (SSM/I) instruments. Global analyses that optimally combine observations from diverse sources with physical models of atmospheric and land processes can provide a comprehensive description of the climate systems. Currently, such data analyses contain significant errors in primary hydrological fields such as precipitation and evaporation, especially in the tropics. We show that assimilating the 6-h averaged TMI and SSM/I surface rainrate and TPW retrievals improves not only the hydrological cycle but also key climate parameters such as clouds, radiation, and the upper tropospheric moisture in the analysis produced by the Goddard Earth Observing System (GEOS) Data Assimilation System, as verified against radiation measurements by the Clouds and the Earth's Radiant Energy System (CERES) instrument and brightness temperature observations by the TIROS Operational Vertical Sounder (TOVS) instruments. Typically, rainfall assimilation improves clouds and radiation in areas of active convection, as well as the latent heating and large-scale motions in the tropics, while TPW assimilation leads to reduced

Super-ranging. A new ranging strategy in European badgers.

PubMed

Gaughran, Aoibheann; Kelly, David J; MacWhite, Teresa; Mullen, Enda; Maher, Peter; Good, Margaret; Marples, Nicola M

2018-01-01

We monitored the ranging of a wild European badger (Meles meles) population over 7 years using GPS tracking collars. Badger range sizes varied seasonally and reached their maximum in June, July and August. We analysed the summer ranging behaviour, using 83 home range estimates from 48 individuals over 6974 collar-nights. We found that while most adult badgers (males and females) remained within their own traditional social group boundaries, several male badgers (on average 22%) regularly ranged beyond these traditional boundaries. These adult males frequently ranged throughout two (or more) social group's traditional territories and had extremely large home ranges. We therefore refer to them as super-rangers. While ranging across traditional boundaries has been recorded over short periods of time for extraterritorial mating and foraging forays, or for pre-dispersal exploration, the animals in this study maintained their super-ranges from 2 to 36 months. This study represents the first time such long-term extra-territorial ranging has been described for European badgers. Holding a super-range may confer an advantage in access to breeding females, but could also affect local interaction networks. In Ireland & the UK, badgers act as a wildlife reservoir for bovine tuberculosis (TB). Super-ranging may facilitate the spread of disease by increasing both direct interactions between conspecifics, particularly across social groups, and indirect interactions with cattle in their shared environment. Understanding super-ranging behaviour may both improve our understanding of tuberculosis epidemiology and inform future control strategies.

Super-ranging. A new ranging strategy in European badgers

PubMed Central

Kelly, David J.; Good, Margaret; Marples, Nicola M.

2018-01-01

We monitored the ranging of a wild European badger (Meles meles) population over 7 years using GPS tracking collars. Badger range sizes varied seasonally and reached their maximum in June, July and August. We analysed the summer ranging behaviour, using 83 home range estimates from 48 individuals over 6974 collar-nights. We found that while most adult badgers (males and females) remained within their own traditional social group boundaries, several male badgers (on average 22%) regularly ranged beyond these traditional boundaries. These adult males frequently ranged throughout two (or more) social group’s traditional territories and had extremely large home ranges. We therefore refer to them as super-rangers. While ranging across traditional boundaries has been recorded over short periods of time for extraterritorial mating and foraging forays, or for pre-dispersal exploration, the animals in this study maintained their super-ranges from 2 to 36 months. This study represents the first time such long-term extra-territorial ranging has been described for European badgers. Holding a super-range may confer an advantage in access to breeding females, but could also affect local interaction networks. In Ireland & the UK, badgers act as a wildlife reservoir for bovine tuberculosis (TB). Super-ranging may facilitate the spread of disease by increasing both direct interactions between conspecifics, particularly across social groups, and indirect interactions with cattle in their shared environment. Understanding super-ranging behaviour may both improve our understanding of tuberculosis epidemiology and inform future control strategies. PMID:29444100

Characterization of microsatellite markers for the Restinga Antwren, Formicivora littoralis (Thamnophilidae), an endangered bird endemic to Brazil.

PubMed

Chaves, F G; Vecchi, M B; Webster, M S; Alves, M A S

2015-07-17

Molecular markers are important tools in determining parentage, gene flow, and the genetic structure of species. In the case of rare, endemic, and/or threatened species, these markers can be used to understand key ecological questions and support conservation actions. We developed seven microsatellite markers for the only bird endemic to the Restinga ecosystem. Microsatellite loci were isolated from a library that was based on 10 individuals (six males and four females). Primers were tested in 107 individuals of the same population. The number of alleles per locus ranged from 4 to 19, and the observed and expected heterozygosity varied from 0.15 to 0.84 and from 0.60 to 0.89, respectively. We expect that the polymorphic microsatellite loci we describe will be useful for other studies, particularly in the Tropics.

Development and characterization of EST-SSR markers for Ottelia acuminata var. jingxiensis (Hydrocharitaceae).

PubMed

Li, Zhi-Zhong; Lu, Meng-Xue; Saina, Josphat K; Gichira, Andrew W; Wang, Qing-Feng; Chen, Jin-Ming

2017-11-01

Simple sequence repeat (SSR) markers were derived from transcriptomic data for Ottelia acuminata (Hydrocharitaceae), a species comprising five endemic and highly endangered varieties in China. Sixteen novel SSR markers were developed for O. acuminata var. jingxiensis . One to eight alleles per locus were found, with a mean of 2.896. The observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.793, respectively. Interestingly, in cross-varietal amplification, 13 out of the 16 loci were successfully amplified in O. acuminata var. acuminata , and 12 amplified in each of the other three varieties of O. acuminata . These newly developed SSR markers will facilitate further study of genetic variation and provide important genetic data needed for appropriate conservation of natural populations of all varieties of O. acuminata .

Characterization of 10 new nuclear microsatellite markers in Acca sellowiana (Myrtaceae)1

PubMed Central

Klabunde, Gustavo H. F.; Olkoski, Denise; Vilperte, Vinicius; Zucchi, Maria I.; Nodari, Rubens O.

2014-01-01

• Premise of the study: Microsatellite primers were identified and characterized in Acca sellowiana in order to expand the limited number of pre-existing polymorphic markers for use in population genetic studies for conservation, phylogeography, breeding, and domestication. • Methods and Results: A total of 10 polymorphic microsatellite primers were designed from clones obtained from a simple sequence repeat (SSR)–enriched genomic library. The primers amplified di- and trinucleotide repeats with four to 27 alleles per locus. In all tested populations, the observed heterozygosity ranged from 0.269 to 1.0. • Conclusions: These new polymorphic SSR markers will allow future genetic studies to be denser, either for genetic structure characterization of natural populations or for studies involving genetic breeding and domestication process in A. sellowiana. PMID:25202632

Symptomatic erythrocytosis associated with a compound heterozygosity for Hb Lepore-Boston-Washington (δ87-β116) and Hb Johnstown [β109(G11)Val→Leu, GTG>TTG].

PubMed

Inoue, Susumu; Oliveira, Jennifer L; Hoyer, James D; Sharman, Mahesh

2012-01-01

Hb Johnstown [β109(G11)Val→Leu, GTG>TTG] has previously been described as a high oxygen affinity variant in a heterozygous state and in combination with β(0)-thalassemia (β(0)-thal). Because the variant does not separate from Hb A by routine methods it may be easily missed unless clinical suspicion is high. Hb Lepore-Boston-Washington (Hb LBW; δ87-β116) is a δβ hybrid variant that clinically manifests similarly to a β(+)-thal. Hb LBW is not detected by routine polymerase chain reaction (PCR) sequencing but is easily detected by electrophoretic methods. We describe a 19-year-old African American male with a compound heterozygosity for Hb Johnstown and Hb LBW. The patient presented with progressively worsening chest pains, headaches and erythrocytosis. He was repeatedly phlebotomized with symptomatic improvement and subsequently was confirmed to have the high oxygen affinity hemoglobin (Hb) variant. The lowest Hb and hematocrit (packed cell volume, PCV) achieved by phlebotomy was 16.1 g/dL and 0.51 L/L, respectively. Currently, he is no longer being phlebotomized, and is feeling relatively well except for minor chest pain. It is unclear to what degree the phlebotomies contributed to his subjective improvement. The combination of Hbs Johnstown and LBW has not been heretofore described, and in this case, was associated with marked symptomatic erythrocytosis. This unique combination results in a more pronounced phenotype, similar to or slightly more severe than, compound Hb Johnstown/β(0)-thal. This compound hemoglobinopathy will likely not be correctly classified using a single method of Hb detection and underscores the need for multiple characterization methods when indicated by the clinical picture.

A Novel Monoallelically Expressed Candidate Tumor Suppressor Gene for Breast Carcinogenesis on Chromosome 11p15.5

DTIC Science & Technology

2002-07-01

Loss of heterozygosity is also observed in a number of other tumor types, notably rhabdomyosarcoma [3,4], adrenocortical carcinoma [5], hepatocellular ... carcinoma [6], and Wilm’s tumor [7]. A second line of evidence suggesting that 1 lp15.5 may play a key role in tumorigenesis is the association of a

Interplay of long-range and short-range Coulomb interactions in an Anderson-Mott insulator

NASA Astrophysics Data System (ADS)

Baćani, Mirko; Novak, Mario; Orbanić, Filip; Prša, Krunoslav; Kokanović, Ivan; Babić, Dinko

2017-07-01

In this paper, we tackle the complexity of coexisting disorder and Coulomb electron-electron interactions (CEEIs) in solids by addressing a strongly disordered system with intricate CEEIs and a screening that changes both with charge carrier doping level Q and temperature T . We report on an experimental comparative study of the T dependencies of the electrical conductivity σ and magnetic susceptibility χ of polyaniline pellets doped with dodecylbenzenesulfonic acid over a wide range. This material is special within the class of doped polyaniline by exhibiting in the electronic transport a crossover between a low-T variable range hopping (VRH) and a high-T nearest-neighbor hopping (NNH) well below room temperature. Moreover, there is evidence of a soft Coulomb gap ΔC in the disorder band, which implies the existence of a long-range CEEI. Simultaneously, there is an onsite CEEI manifested as a Hubbard gap U and originating in the electronic structure of doped polyaniline, which consists of localized electron states with dynamically varying occupancy. Therefore, our samples represent an Anderson-Mott insulator in which long-range and short-range CEEIs coexist. The main result of the study is the presence of a crossover between low- and high-T regimes not only in σ (T ) but also in χ (T ) , the crossover temperature T* being essentially the same for both observables over the entire doping range. The relatively large electron localization length along the polymer chains results in U being small, between 12 and 20 meV for the high and low Q , respectively. Therefore, the thermal energy at T* is sufficiently large to lead to an effective closing of the Hubbard gap and the consequent appearance of NNH in the electronic transport within the disorder band. ΔC is considerably larger than U , decreasing from 190 to 30 meV as Q increases, and plays the role of an activation energy in the NNH.

Effect of simple solutes on the long range dipolar correlations in liquid water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baul, Upayan, E-mail: upayanb@imsc.res.in; Anishetty, Ramesh, E-mail: ramesha@imsc.res.in; Vemparala, Satyavani, E-mail: vani@imsc.res.in

2016-03-14

Intermolecular correlations in liquid water at ambient conditions have generally been characterized through short range density fluctuations described through the atomic pair distribution functions. Recent numerical and experimental results have suggested that such a description of order or structure in liquid water is incomplete and there exist considerably longer ranged orientational correlations in water that can be studied through dipolar correlations. In this study, using large scale classical, atomistic molecular dynamics simulations using TIP4P-Ew and TIP3P models of water, we show that salts such as sodium chloride (NaCl), potassium chloride (KCl), caesium chloride (CsCl), and magnesium chloride (MgCl{sub 2}) havemore » a long range effect on the dipolar correlations, which cannot be explained by the notion of structure making and breaking by dissolved ions. Observed effects are explained through orientational stratification of water molecules around ions and their long range coupling to the global hydrogen bond network by virtue of the sum rule for water. The observations for single hydrophilic solutes are contrasted with the same for a single methane (CH{sub 4}) molecule. We observe that even a single small hydrophobe can result in enhancement of long range orientational correlations in liquid water, contrary to the case of dissolved ions, which have been observed to have a reducing effect. The observations from this study are discussed in the context of hydrophobic effect.« less

Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa

PubMed Central

Ramachandran, Sohini; Deshpande, Omkar; Roseman, Charles C.; Rosenberg, Noah A.; Feldman, Marcus W.; Cavalli-Sforza, L. Luca

2005-01-01

Equilibrium models of isolation by distance predict an increase in genetic differentiation with geographic distance. Here we find a linear relationship between genetic and geographic distance in a worldwide sample of human populations, with major deviations from the fitted line explicable by admixture or extreme isolation. A close relationship is shown to exist between the correlation of geographic distance and genetic differentiation (as measured by FST) and the geographic pattern of heterozygosity across populations. Considering a worldwide set of geographic locations as possible sources of the human expansion, we find that heterozygosities in the globally distributed populations of the data set are best explained by an expansion originating in Africa and that no geographic origin outside of Africa accounts as well for the observed patterns of genetic diversity. Although the relationship between FST and geographic distance has been interpreted in the past as the result of an equilibrium model of drift and dispersal, simulation shows that the geographic pattern of heterozygosities in this data set is consistent with a model of a serial founder effect starting at a single origin. Given this serial-founder scenario, the relationship between genetic and geographic distance allows us to derive bounds for the effects of drift and natural selection on human genetic variation. PMID:16243969

Tree range expansion in eastern North America fails to keep pace with climate warming at northern range limits.

PubMed

Sittaro, Fabian; Paquette, Alain; Messier, Christian; Nock, Charles A

2017-08-01

Rising global temperatures are suggested to be drivers of shifts in tree species ranges. The resulting changes in community composition may negatively impact forest ecosystem function. However, long-term shifts in tree species ranges remain poorly documented. We test for shifts in the northern range limits of 16 temperate tree species in Quebec, Canada, using forest inventory data spanning three decades, 15° of longitude and 7° of latitude. Range shifts were correlated with climate warming and dispersal traits to understand potential mechanisms underlying changes. Shifts were calculated as the change in the 95th percentile of latitudinal occurrence between two inventory periods (1970-1978, 2000-2012) and for two life stages: saplings and adults. We also examined sapling and adult range offsets within each inventory, and changes in the offset through time. Tree species ranges shifted predominantly northward, although species responses varied. As expected shifts were greater for tree saplings, 0.34 km yr -1 , than for adults, 0.13 km yr -1 . Range limits were generally further north for adults compared to saplings, but the difference diminished through time, consistent with patterns observed for range shifts within each life stage. This suggests caution should be exercised when interpreting geographic range offsets between life stages as evidence of range shifts in the absence of temporal data. Species latitudinal velocities were on average <50% of the velocity required to equal the spatial velocity of climate change and were mostly unrelated to dispersal traits. Finally, our results add to the body of evidence suggesting tree species are mostly limited in their capacity to track climate warming, supporting concerns that warming will negatively impact the functioning of forest ecosystems. © 2017 John Wiley & Sons Ltd.

A set of autosomal multiple InDel markers for forensic application and population genetic analysis in the Chinese Xinjiang Hui group.

PubMed

Xie, Tong; Guo, Yuxin; Chen, Ling; Fang, Yating; Tai, Yunchun; Zhou, Yongsong; Qiu, Pingming; Zhu, Bofeng

2018-07-01

In recent years, insertion/deletion (InDel) markers have become a promising and useful supporting tool in forensic identification cases and biogeographic research field. In this study, 30 InDel loci were explored to reveal the genetic diversities and genetic relationships between Chinese Xinjiang Hui group and the 25 previously reported populations using various biostatistics methods such as forensic statistical parameter analysis, phylogenetic reconstruction, multi-dimensional scaling, principal component analysis, and STRUCTURE analysis. No deviations from Hardy-Weinberg equilibrium tests were found at all 30 loci in the Chinese Xinjiang Hui group. The observed heterozygosity and expected heterozygosity ranged from 0.1971 (HLD118) to 0.5092 (HLD92), 0.2222 (HLD118) to 0.5000 (HLD6), respectively. The cumulative probability of exclusion and combined power of discrimination were 0.988849 and 0.99999999999378, respectively, which indicated that these 30 loci could be qualified for personal identification and used as complementary genetic markers for paternity tests in forensic cases. The results of present research based on the different methods of population genetic analysis revealed that the Chinese Xinjiang Hui group had close relationships with most Chinese groups, especially Han populations. In spite of this, for a better understanding of genetic background of the Chinese Xinjiang Hui group, more molecular genetic markers such as ancestry informative markers, single nucleotide polymorphisms (SNPs), and copy number variations will be conducted in future studies. Copyright © 2018 Elsevier B.V. All rights reserved.

Molecular genetic variation and structure of Southeast Asian crocodile (Tomistoma schlegelii): Comparative potentials of SSRs versus ISSRs.

PubMed

Shafiei-Astani, Behnam; Ong, Alan Han Kiat; Valdiani, Alireza; Tan, Soon Guan; Yien, Christina Yong Seok; Ahmady, Fatemeh; Alitheen, Noorjahan Banu; Ng, Wei Lun; Kuar, Taranjeet

2015-10-15

Tomistoma schlegelii, also referred to as the "false gharial", is one of the most exclusive and least known of the world's fresh water crocodilians, limited to Southeast Asia. Indeed, lack of economic value for its skin has led to neglect the biodiversity of the species. The current study aimed to investigate the mentioned case using 40 simple sequence repeat (SSR) primer pairs and 45 inter-simple sequence repeat (ISSR) primers. DNA analysis of 17 T. schlegelii samples using the SSR and ISSR markers resulted in producing a total of 49 and 108 polymorphic bands, respectively. Furthermore, the SSR- and ISSR-based cluster analyses both generated two main clusters. However, the SSR based results were found to be more in line with the geographical distributions of the crocodile samples collected across the country as compared with the ISSR-based results. The observed heterozygosity (HO) and expected heterozygosity (HE) of the polymorphic SSRs ranged between 0.588-1 and 0.470-0.891, respectively. The present results suggest that the Malaysian T. schlegelii populations had originated from a core population of crocodiles. In cooperation with the SSR markers, the ISSRs showed high potential for studying the genetic variation of T. schlegelii, and these markers are suitable to be employed in conservation genetic programs of this endangered species. Both SSR- and ISSR-based STRUCTURE analyses suggested that all the individuals of T. schlegelii are genetically similar with each other. Copyright © 2015 Elsevier B.V. All rights reserved.

Genetic Analysis of Termite Colonies in Wisconsin.

PubMed

Arango, R A; Marschalek, D A; Green, F; Raffa, K F; Berres, M E

2015-06-01

The objective of this study was to document current areas of subterranean termite activity in Wisconsin and to evaluate genetic characteristics of these northern, peripheral colonies. Here, amplified fragment-length polymorphism was used to characterize levels of inbreeding, expected heterozygosity, and percent polymorphism within colonies as well as genetic structure among populations sampled. Genetic analysis revealed two species of termites occur in Wisconsin, Reticulitermes flavipes (Kollar) and Reticulitermes tibialis Banks, both found in the southern half of the state. Colonies of both species in Wisconsin are thought to represent the northern boundary of their current distributions. Measurements of within colony genetic variation showed the proportion of polymorphic loci to be between 52.9-63.9% and expected heterozygosity to range from 0.122-0.189. Consistent with geographical isolation, strong intercolony genetic differences were observed, with over 50% of FST values above 0.25 and the remaining showing moderate levels of genetic differentiation. Combined with low levels of inbreeding in most collection locations (FIS 0.042-0.123), we hypothesize termites were introduced numerous times in the state, likely by anthropogenic means. We discuss the potential effects of these genetic characteristics on successful colony establishment of termites along the northern boundary compared with termites in the core region of their distribution. Published by Oxford University Press on behalf of Entomological Society of America 2015. This work is written by US Government employees and is in the public domain in the US.

Polymorphic SSR Markers for Plasmopara obducens (Peronosporaceae), the Newly Emergent Downy Mildew Pathogen of Impatiens (Balsaminaceae)

DOE PAGES

Salgado-Salazar, Catalina; Rivera, Yazmín; Veltri, Daniel; ...

2015-11-10

Premise of the study: Simple sequence repeat (SSR) markers were developed for Plasmopara obducens, the causal agent of the newly emergent downy mildew disease of Impatiens walleriana. Methods and Results: A 202-Mb draft genome assembly was generated from P. obducens using Illumina technology and mined to identify 13,483 SSR motifs. Primers were synthesized for 62 marker candidates, of which 37 generated reliable PCR products. Testing of the 37 markers using 96 P. obducens samples showed 96% of the markers were polymorphic, with 2-6 alleles observed. Observed and expected heterozygosity ranged from 0.000-0.892 and 0.023-0.746, respectively. Just 17 markers were sufficientmore » to identify all multilocus genotypes. Conclusions: These are the first SSR markers available for this pathogen, and one of the first molecular resources. These markers will be useful in assessing variation in pathogen populations and determining the factors contributing to the emergence of destructive impatiens downy mildew disease.« less

Genomic conservation of cattle microsatellite loci in wild gaur (Bos gaurus) and current genetic status of this species in Vietnam.

PubMed

Nguyen, Trung Thanh; Genini, Sem; Bui, Linh Chi; Voegeli, Peter; Stranzinger, Gerald; Renard, Jean-Paul; Maillard, Jean-Charles; Nguyen, Bui Xuan

2007-11-06

The wild gaur (Bos gaurus) is an endangered wild cattle species. In Vietnam, the total number of wild gaurs is estimated at a maximum of 500 individuals. Inbreeding and genetic drift are current relevant threats to this small population size. Therefore, information about the genetic status of the Vietnamese wild gaur population is essential to develop strategies for conservation and effective long-term management for this species. In the present study, we performed cross-species amplification of 130 bovine microsatellite markers, in order to evaluate the applicability and conservation of cattle microsatellite loci in the wild gaur genome. The genetic diversity of Vietnamese wild gaur was also investigated, based on data collected from the 117 successfully amplified loci. One hundred-thirty cattle microsatellite markers were tested on a panel of 11 animals. Efficient amplifications were observed for 117 markers (90%) with a total of 264 alleles, and of these, 68 (58.1%) gave polymorphic band patterns. The number of alleles per locus among the polymorphic markers ranged from two to six. Thirteen loci (BM1314, BM2304, BM6017, BMC2228, BMS332, BMS911, CSSM023, ETH123, HAUT14, HEL11, HEL5, ILSTS005 and INRA189) distributed on nine different cattle chromosomes failed to amplify wild gaur genomic DNA. Three cattle Y-chromosome specific microsatellite markers (INRA124, INRA126 and BM861) were also highly specific in wild gaur, only displaying an amplification product in the males. Genotype data collected from the 117 successfully amplified microsatellites were used to assess the genetic diversity of this species in Vietnam. Polymorphic Information Content (PIC) values varied between 0.083 and 0.767 with a mean of 0.252 while observed heterozygosities (Ho) ranged from 0.091 to 0.909 (mean of 0.269). Nei's unbiased mean heterozygosity and the mean allele number across loci were 0.298 and 2.2, respectively. Extensive conservation of cattle microsatellite loci in the wild gaur

NCAR Earth Observing Laboratory - An End-to-End Observational Science Enterprise

NASA Astrophysics Data System (ADS)

Rockwell, A.; Baeuerle, B.; Grubišić, V.; Hock, T. F.; Lee, W. C.; Ranson, J.; Stith, J. L.; Stossmeister, G.

2017-12-01

Researchers who want to understand and describe the Earth System require high-quality observations of the atmosphere, ocean, and biosphere. Making these observations not only requires capable research platforms and state-of-the-art instrumentation but also benefits from comprehensive in-field project management and data services. NCAR's Earth Observing Laboratory (EOL) is an end-to-end observational science enterprise that provides leadership in observational research to scientists from universities, U.S. government agencies, and NCAR. Deployment: EOL manages the majority of the NSF Lower Atmosphere Observing Facilities, which includes research aircraft, radars, lidars, profilers, and surface and sounding systems. This suite is designed to address a wide range of Earth system science - from microscale to climate process studies and from the planet's surface into the Upper Troposphere/Lower Stratosphere. EOL offers scientific, technical, operational, and logistics support to small and large field campaigns across the globe. Development: By working closely with the scientific community, EOL's engineering and scientific staff actively develop the next generation of observing facilities, staying abreast of emerging trends, technologies, and applications in order to improve our measurement capabilities. Through our Design and Fabrication Services, we also offer high-level engineering and technical expertise, mechanical design, and fabrication to the atmospheric research community. Data Services: EOL's platforms and instruments collect unique datasets that must be validated, archived, and made available to the research community. EOL's Data Management and Services deliver high-quality datasets and metadata in ways that are transparent, secure, and easily accessible. We are committed to the highest standard of data stewardship from collection to validation to archival. Discovery: EOL promotes curiosity about Earth science, and fosters advanced understanding of the

Metrology and ionospheric observation standards

NASA Astrophysics Data System (ADS)

Panshin, Evgeniy; Minligareev, Vladimir; Pronin, Anton

Accuracy and ionospheric observation validity are urgent trends nowadays. WMO, URSI and national metrological and standardisation services bring forward requirements and descriptions of the ionospheric observation means. Researches in the sphere of metrological and standardisation observation moved to the next level in the Russian Federation. Fedorov Institute of Applied Geophysics (IAG) is in charge of ionospheric observation in the Russian Federation and the National Technical Committee, TC-101 , which was set up on the base of IAG- of the standardisation in the sphere. TC-101 can be the platform for initiation of the core international committee in the network of ISO The new type of the ionosounde “Parus-A” is engineered, which is up to the national requirements. “Parus-A” calibration and test were conducted by National metrological Institute (NMI) -D.I. Mendeleyev Institute for Metrology (VNIIM), signed CIMP MRA in 1991. VNIIM is a basic NMI in the sphere of Space weather (including ionospheric observations), the founder of which was celebrated chemist and metrologist Dmitriy I. Mendeleyev. Tests and calibration were carried out for the 1st time throughout 50-year-history of ionosonde exploitation in Russia. The following metrological characteristics were tested: -measurement range of radiofrequency time delay 0.5-10 ms; -time measurement inaccuracy of radio- frequency pulse ±12mcs; -frequency range of radio impulse 1-20 MHz ; -measurement inaccuracy of radio impulse carrier frequency± 5KHz. For example, the sound impulse simulator that was built-in in the ionosounde was used for measurement range of radiofrequency time delay testing. The number of standards on different levels is developed. - “Ionospheric observation guidance”; - “The Earth ionosphere. Terms and definitions”.

High-range resolution spectral analysis of precipitation through range imaging of the Chung-Li VHF radar

NASA Astrophysics Data System (ADS)

Tsai, Shih-Chiao; Chen, Jenn-Shyong; Chu, Yen-Hsyang; Su, Ching-Lun; Chen, Jui-Hsiang

2018-01-01

Multi-frequency range imaging (RIM) has been operated in the Chung-Li very high-frequency (VHF) radar, located on the campus of National Central University, Taiwan, since 2008. RIM processes the echo signals with a group of closely spaced transmitting frequencies through appropriate inversion methods to obtain high-resolution distribution of echo power in the range direction. This is beneficial to the investigation of the small-scale structure embedded in dynamic atmosphere. Five transmitting frequencies were employed in the radar experiment for observation of the precipitating atmosphere during the period between 21 and 23 August 2013. Using the Capon and Fourier methods, the radar echoes were synthesized to retrieve the temporal signals at a smaller range step than the original range resolution defined by the pulse width, and such retrieved temporal signals were then processed in the Doppler frequency domain to identify the atmosphere and precipitation echoes. An analysis called conditional averaging was further executed for echo power, Doppler velocity, and spectral width to verify the potential capabilities of the retrieval processing in resolving small-scale precipitation and atmosphere structures. Point-by-point correction of range delay combined with compensation of range-weighting function effect has been performed during the retrieval of temporal signals to improve the continuity of power spectra at gate boundaries, making the small-scale structures in the power spectra more natural and reasonable. We examined stratiform and convective precipitation and demonstrated their different structured characteristics by means of the Capon-processed results. The new element in this study is the implementation of RIM on spectral analysis, especially for precipitation echoes.

Early enrichment in free-range laying hens: effects on ranging behaviour, welfare and response to stressors.

PubMed

Campbell, D L M; Hinch, G N; Downing, J A; Lee, C

2018-03-01

Free-range laying hen systems are increasing within Australia. The pullets for these systems are typically reared indoors before being provided first range access around 21 to 26 weeks of age. Thus, the rearing and laying environments are disparate and hens may not adapt well to free-range housing. In this study, we reared 290 Hy-Line® Brown day-old chicks divided into two rooms each with feed, water and litter. In the enriched room, multiple structural, manipulable, visual and auditory stimuli were also provided from 4 to 21 days, the non-enriched room had no additional objects or stimuli. Pullets were transferred to the laying facility at 12 weeks of age and divided into six pens (three enriched-reared, three non-enriched-reared) with identical indoor resources and outdoor range area. All birds were first provided range access at 21 weeks of age. Video observations of natural disturbance behaviours on the range at 22 to 23 and 33 to 34 weeks of age showed no differences in frequency of disturbance occurrences between treatment groups (P=0.09) but a decrease in disturbance occurrences over time (P<0.0001). Radio-frequency identification tracking of individually tagged birds from 21 to 37 weeks of age showed enriched birds on average, spent less time on the range each day (P<0.04) but with a higher number of range visits than non-enriched birds from 21 to 24 weeks of age (P=0.01). Enriched birds accessed the range on more days (P=0.03) but over time, most birds in both treatment groups accessed the range daily. Basic external health scoring showed minimal differences between treatment groups with most birds in visibly good condition. At 38 weeks of age all birds were locked inside for 2 days and from 40 to 42 weeks of age the outdoor range was reduced to 20% of its original size to simulate stressful events. The eggs from non-enriched birds had higher corticosterone concentrations following lock-in and 2 weeks following range reduction compared with the

Probing Long-Range Configurations of Molecular Hydrogen

NASA Astrophysics Data System (ADS)

McCormack, Elizabeth

2011-05-01

Very long-range molecular configurations are of interest in a variety of contexts, for example, in the astro-chemistry of cold molecular clouds and in planetary atmospheres, including our own. Such states can be more than 10 times the size of the ground state and often possess energies above multiple ionization potentials and dissociation limits resulting in diverse and complex decay dynamics. Many of these configurations possess a double-well character arising from the interaction of molecular Rydberg states, repulsive doubly-excited states, and ionic states. The ion pair in hydrogen, an unusual molecular configuration consisting of one proton shrouded in a cloud of two electrons separated very far from the other proton, is notoriously difficult to create and study. We report results from on our investigation of such states using resonantly enhanced multi-photon ionization via the E,F v = 6, J = 0, 1, and 2 states to probe the H(n = 1) + H(n = 3) dissociation threshold energy region. Both molecular and atomic ion production were detected as a function of wavelength by using a time-of-flight mass spectrometer. Below threshold a series of highly excited vibrational levels of several long range states are observed. Above threshold broad resonances are observed with energies that agree well with the predictions of a mass-scaled Rydberg formula for bound states of the H+ H- ion pair. Measured linewidths, quantum defects, and rotational dependences are reported for ion pair principal quantum numbers in the range of n = 130 to 206. Our new results can be compared to recent experimental work using a different excitation scheme, which was the first spectroscopic observation of heavy Rydberg states in hydrogen, and new ab initio theoretical work. Supported by the National Science Foundation.

Search for three-nucleon short-range correlations in light nuclei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye, Z.; Solvignon, P.; Nguyen, D.

Here, we present new data probing short-range correlations (SRCs) in nuclei through the measurement of electron scattering off high-momentum nucleons in nuclei. The inclusive 4He/ 3He cross section ratio is observed to be both x and Q 2 independent for 1.5 < x < 2, confirming the dominance of two- nucleon (2N) short-range correlations (SRCs). For x > 2, our data do not support a previous claim of three-nucleon (3N) correlation dominance. While contributions beyond those from stationary 2N- SRCs are observed, our data show that isolating 3N-SRCs is more complicated than for 2N-SRCs.

Search for three-nucleon short-range correlations in light nuclei

DOE PAGES

Ye, Z.; Solvignon, P.; Nguyen, D.; ...

2018-06-18

Here, we present new data probing short-range correlations (SRCs) in nuclei through the measurement of electron scattering off high-momentum nucleons in nuclei. The inclusive 4He/ 3He cross section ratio is observed to be both x and Q 2 independent for 1.5 < x < 2, confirming the dominance of two- nucleon (2N) short-range correlations (SRCs). For x > 2, our data do not support a previous claim of three-nucleon (3N) correlation dominance. While contributions beyond those from stationary 2N- SRCs are observed, our data show that isolating 3N-SRCs is more complicated than for 2N-SRCs.

Ten-year chemical signatures associated with long-range transport observed in the free troposphere over the central North Atlantic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, B.; Owen, R. C.; Perlinger, J. A.

Ten-year observations of trace gases at Pico Mountain Observatory (PMO), a free troposphere site in the central North Atlantic, were classified by transport patterns using the Lagrangian particle dispersion model, FLEXPART. The classification enabled identifying trace gas mixing ratios associated with background air and long- range transport of continental emissions, which were defined as chemical signatures. Comparison between the chemical signatures revealed the impacts of natural and anthropogenic sources, as well as chemical and physical processes during long transport, on air composition in the remote North Atlantic. Transport of North American anthropogenic emissions (NA-Anthro) and summertime wildfire plumes (Fire) significantlymore » enhanced CO and O 3 at PMO. Summertime CO enhancements caused by NA-Anthro were found to have been decreasing by a rate of 0.67 ± 0.60 ppbv/year in the ten-year period, due possibly to reduction of emissions in North America. Downward mixing from the upper troposphere and stratosphere due to the persistent Azores-Bermuda anticyclone causes enhanced O 3 and nitrogen oxides. The d [O 3]/d [CO] value was used to investigate O 3 sources and chemistry in different transport patterns. The transport pattern affected by Fire had the lowest d [O 3]/d [CO], which was likely due to intense CO production and depressed O 3 production in wildfire plumes. Slightly enhanced O 3 and d [O 3]/d [CO] were found in the background air, suggesting that weak downward mixing from the upper troposphere is common at PMO. Enhancements of both butane isomers were found during upslope flow periods, indicating contributions from local sources. The consistent ratio of butane isomers associated with the background air and NA-anthro implies no clear difference in the oxidation rates of the butane isomers during long transport. Based on observed relationships between non-methane hydrocarbons, the averaged photochemical age of the air masses at PMO was

Ten-year chemical signatures associated with long-range transport observed in the free troposphere over the central North Atlantic

DOE PAGES

Zhang, B.; Owen, R. C.; Perlinger, J. A.; ...

2017-03-06

Ten-year observations of trace gases at Pico Mountain Observatory (PMO), a free troposphere site in the central North Atlantic, were classified by transport patterns using the Lagrangian particle dispersion model, FLEXPART. The classification enabled identifying trace gas mixing ratios associated with background air and long- range transport of continental emissions, which were defined as chemical signatures. Comparison between the chemical signatures revealed the impacts of natural and anthropogenic sources, as well as chemical and physical processes during long transport, on air composition in the remote North Atlantic. Transport of North American anthropogenic emissions (NA-Anthro) and summertime wildfire plumes (Fire) significantlymore » enhanced CO and O 3 at PMO. Summertime CO enhancements caused by NA-Anthro were found to have been decreasing by a rate of 0.67 ± 0.60 ppbv/year in the ten-year period, due possibly to reduction of emissions in North America. Downward mixing from the upper troposphere and stratosphere due to the persistent Azores-Bermuda anticyclone causes enhanced O 3 and nitrogen oxides. The d [O 3]/d [CO] value was used to investigate O 3 sources and chemistry in different transport patterns. The transport pattern affected by Fire had the lowest d [O 3]/d [CO], which was likely due to intense CO production and depressed O 3 production in wildfire plumes. Slightly enhanced O 3 and d [O 3]/d [CO] were found in the background air, suggesting that weak downward mixing from the upper troposphere is common at PMO. Enhancements of both butane isomers were found during upslope flow periods, indicating contributions from local sources. The consistent ratio of butane isomers associated with the background air and NA-anthro implies no clear difference in the oxidation rates of the butane isomers during long transport. Based on observed relationships between non-methane hydrocarbons, the averaged photochemical age of the air masses at PMO was

Global Test Range: Toward Airborne Sensor Webs

NASA Technical Reports Server (NTRS)

Mace, Thomas H.; Freudinger, Larry; DelFrate John H.

2008-01-01

This viewgraph presentation reviews the planned global sensor network that will monitor the Earth's climate, and resources using airborne sensor systems. The vision is an intelligent, affordable Earth Observation System. Global Test Range is a lab developing trustworthy services for airborne instruments - a specialized Internet Service Provider. There is discussion of several current and planned missions.

Observing Teaching. SEDA Paper 79.

ERIC Educational Resources Information Center

Brown, Sally, Ed.; And Others

This publication offers practical support to those in British higher education implementing the Observation of Teaching governmental directives. It provides discussion of key issues as well as a range of materials on how to carry out teaching observation including 23 checklists. The materials are grouped in four main areas: general issues, self…

Gene surfing in expanding populations.

PubMed

Hallatschek, Oskar; Nelson, David R

2008-02-01

Large scale genomic surveys are partly motivated by the idea that the neutral genetic variation of a population may be used to reconstruct its migration history. However, our ability to trace back the colonization pathways of a species from their genetic footprints is limited by our understanding of the genetic consequences of a range expansion. Here, we study, by means of simulations and analytical methods, the neutral dynamics of gene frequencies in an asexual population undergoing a continual range expansion in one dimension. During such a colonization period, lineages can fix at the wave front by means of a "surfing" mechanism [Edmonds, C.A., Lillie, A.S., Cavalli-Sforza, L.L., 2004. Mutations arising in the wave front of an expanding population. Proc. Natl. Acad. Sci. 101, 975-979]. We quantify this phenomenon in terms of (i) the spatial distribution of lineages that reach fixation and, closely related, (ii) the continual loss of genetic diversity (heterozygosity) at the wave front, characterizing the approach to fixation. Our stochastic simulations show that an effective population size can be assigned to the wave that controls the (observable) gradient in heterozygosity left behind the colonization process. This effective population size is markedly higher in the presence of cooperation between individuals ("pushed waves") than when individuals proliferate independently ("pulled waves"), and increases only sub-linearly with deme size. To explain these and other findings, we develop a versatile analytical approach, based on the physics of reaction-diffusion systems, that yields simple predictions for any deterministic population dynamics. Our analytical theory compares well with the simulation results for pushed waves, but is less accurate in the case of pulled waves when stochastic fluctuations in the tip of the wave are important.

Geographic distribution of genetic diversity in populations of Rio Grande Chub Gila pandora

USGS Publications Warehouse

Galindo, Rene; Wilson, Wade; Caldwell, Colleen A.

2016-01-01

In the southwestern United States (US), the Rio Grande chub (Gila pandora) is state-listed as a fish species of greatest conservation need and federally listed as sensitive due to habitat alterations and competition with non-native fishes. Characterizing genetic diversity, genetic population structure, and effective number of breeders will assist with conservation efforts by providing a baseline of genetic metrics. Genetic relatedness within and among G. pandora populations throughout New Mexico was characterized using 11 microsatellite loci among 15 populations in three drainage basins (Rio Grande, Pecos, Canadian). Observed heterozygosity (HO) ranged from 0.71–0.87 and was similar to expected heterozygosity (0.75–0.87). Rio Ojo Caliente (Rio Grande) had the highest allelic richness (AR = 15.09), while Upper Rio Bonito (Pecos) had the lowest allelic richness (AR = 6.75). Genetic differentiation existed among all populations with the lowest genetic variation occurring within the Pecos drainage. STRUCTURE analysis revealed seven genetic clusters. Populations of G. pandora within the upper Rio Grande drainage (Rio Ojo Caliente, Rio Vallecitos, Rio Pueblo de Taos) had high levels of admixture with Q-values ranging from 0.30–0.50. In contrast, populations within the Pecos drainage (Pecos River and Upper Rio Bonito) had low levels of admixture (Q = 0.94 and 0.87, respectively). Estimates of effective number of breeders (N b ) varied from 6.1 (Pecos: Upper Rio Bonito) to 109.7 (Rio Grande: Rio Peñasco) indicating that populations in the Pecos drainage are at risk of extirpation. In the event that management actions are deemed necessary to preserve or increase genetic diversity of G. pandora, consideration must be given as to which populations are selected for translocation.

A generalised model of secondary circulation for a wide range of geophysical flows from direct observations of natural turbidity currents

NASA Astrophysics Data System (ADS)

Azpiroz, M.; Cartigny, M.; Sumner, E. J.; Talling, P.; Parsons, D. R.; Clare, M. A.; Cooper, C.

2017-12-01

Turbidity currents transport sediment through submarine channel systems for hundreds of kilometres to form vast deposits of sediment in the deep sea called submarine fans. The largest submarine fans are fed by meandering channels suggesting that bends may enhance sediment transport distances. The interaction between meander bends and turbidity currents has been a topic of intense debate. Due to the absence of observations of deep-sea turbidity currents flowing through meander bends, our understanding has been based on experimental and numerical models. Measurements of geophysical flows demonstrate a common helical flow structure around meanders. Previous work has demonstrated that helical circulation in rivers is dominated by a single helix that rotates towards the inner bend at near-bed depths. In contrast, initial numerical and experimental models for turbidity currents found both river-like and river-reversed circulations. Saline flows in well-mixed estuaries show a river-like basal helical circulation, while stratified estuaries and saline flows are river-reversed. The existence of lateral stratification in stratified flows is thought to be the key factor in the change of direction of rotation. Stratification causes lateral pressure gradients that can govern the rotation of the flow helix. Turbidity currents are stratified due to their upwards-decreasing sediment load. It has therefore been proposed that stratified turbidity currents behave like stratified saline flow, but this hypothesis remains so far untested. Here we present the first observations of the helical flow in turbidity currents, which occurred within the deep-sea Congo Canyon. The measurements show a consistent river-reversed pattern downstream of the bend apex. Those results lead us to develop a new generalised model for a wide range of flows around meanders. Our conclusions have implications for understanding the flow erosional and depositional patterns, the evolution of channel systems and the

Determination of plant growth rate and growth temperature range from measurement of physiological parameters

Treesearch

R. S. Criddle; B. N. Smith; L. D. Hansen; J. N. Church

2001-01-01

Many factors influence species range and diversity, but temperature and temperature variability are always major global determinants, irrespective of local constraints. On a global scale, the ranges of many taxa have been observed to increase and their diversity decrease with increasing latitude. On a local scale, gradients in species distribution are observable with...

Isolation and characterization of 14 tetranucleotide microsatellite loci for the cannonball jellyfish (Stomolophus sp.) by next generation sequencing.

PubMed

Getino-Mamet, Leandro Nicolás; Valdivia-Carrillo, Tania; Gómez Daglio, Liza; García-De León, Francisco Javier

2017-04-01

The Cannonball jellyfish (Stomolophus sp.) is a species of jellyfish with high relevance in artisanal fishing. Studies of their populations do not extend beyond the morphological descriptions knowing that presents a great morphological variability. However, there are no genetic studies to determine the number of independent populations, so microsatellite markers become a suitable option. Since there are no species-specific microsatellite loci, in this paper, 14 new microsatellite loci are characterized. Microsatellite loci were isolated de novo through next generation sequencing, by two runs on Illumina MiSeq. A total of 506,771,269 base pair were obtained, from which 142,616 were microsatellite loci, and 1546 of them could design primers. We tested 14 primer pairs on 32 individuals from Bahía de La Paz, Gulf of California. We observed low genetic variation among loci (mean number of alleles per locus = 4.33, mean observed heterozygosity 0.381, mean expected heterozygosity 0.501). These loci are the first ones described for the species and will be helpful to carry out genetic diversity and population genetics studies.

Results of Joint Observations of Jupiter's Atmosphere by Juno and a Network of Earth-Based Observing Stations

NASA Astrophysics Data System (ADS)

Orton, G. S.; Momary, T.; Tabataba-Vakili, F.; Bolton, S.; Levin, S.; Adriani, A.; Gladstone, G. R.; Hansen, C. J.; Janssen, M.

2017-09-01

Well over sixty investigator/instrument investigations are actively engaged in the support of the Juno mission. These observations range from X-ray to the radio wavelengths and involve both space- and ground-based astronomical facilities. These observations enhance and expand Juno measurements by (1) providing a context that expands the area covered by often narrow spatial coverage of Juno's instruments, (2) providing a temporal context that shows how phenomena evolve over Juno's 53-day orbit period, (3) providing observations in spectral ranges not covered by Juno's instruments, and (4) monitoring the behavior of external influences to Jupiter's magnetosphere. Intercommunication between the Juno scientists and the support program is maintained by reference to a Google table that describes the observation and its current status, as well as by occasional group emails. A non-interactive version of this invitation-only site is mirrored in a public site. Several sets of these supporting observations are described at this meeting.

Ranging Behaviour of Commercial Free-Range Broiler Chickens 2: Individual Variation

PubMed Central

Groves, Peter J.; Rault, Jean-Loup

2017-01-01

Simple Summary Although the consumption of free-range chicken meat has increased, little is known about the ranging behaviour of meat chickens on commercial farms. Studies suggest range use is low and not all chickens access the range when given the opportunity. Whether ranging behaviour differs between individuals within a flock remains largely unknown and may have consequences for animal welfare and management. We monitored individual chicken ranging behaviour from four mixed sex flocks on a commercial farm across two seasons. Not all chickens accessed the range. We identified groups of chickens that differed in ranging behaviour (classified by frequency of range visits): chickens that accessed the range only once, low frequency ranging chickens and high frequency ranging chickens, the latter accounting for one-third to one half of all range visits. Sex was not predictive of whether a chicken would access the range or the number of range visits, but males spent more time on the range in winter. We found evidence that free-range chicken ranging varies between individuals within the same flock on a commercial farm. Whether such variation in ranging behaviour relates to variation in chicken welfare remains to be investigated. Abstract Little is known about broiler chicken ranging behaviour. Previous studies have monitored ranging behaviour at flock level but whether individual ranging behaviour varies within a flock is unknown. Using Radio Frequency Identification technology, we tracked 1200 individual ROSS 308 broiler chickens across four mixed sex flocks in two seasons on one commercial farm. Ranging behaviour was tracked from first day of range access (21 days of age) until 35 days of age in winter flocks and 44 days of age in summer flocks. We identified groups of chickens that differed in frequency of range visits: chickens that never accessed the range (13 to 67% of tagged chickens), low ranging chickens (15 to 44% of tagged chickens) that accounted for <15

Satellite laser ranging to low Earth orbiters: orbit and network validation

NASA Astrophysics Data System (ADS)

Arnold, Daniel; Montenbruck, Oliver; Hackel, Stefan; Sośnica, Krzysztof

2018-04-01

Satellite laser ranging (SLR) to low Earth orbiters (LEOs) provides optical distance measurements with mm-to-cm-level precision. SLR residuals, i.e., differences between measured and modeled ranges, serve as a common figure of merit for the quality assessment of orbits derived by radiometric tracking techniques. We discuss relevant processing standards for the modeling of SLR observations and highlight the importance of line-of-sight-dependent range corrections for the various types of laser retroreflector arrays. A 1-3 cm consistency of SLR observations and GPS-based precise orbits is demonstrated for a wide range of past and present LEO missions supported by the International Laser Ranging Service (ILRS). A parameter estimation approach is presented to investigate systematic orbit errors and it is shown that SLR validation of LEO satellites is not only able to detect radial but also along-track and cross-track offsets. SLR residual statistics clearly depend on the employed precise orbit determination technique (kinematic vs. reduced-dynamic, float vs. fixed ambiguities) but also reveal pronounced differences in the ILRS station performance. Using the residual-based parameter estimation approach, corrections to ILRS station coordinates, range biases, and timing offsets are derived. As a result, root-mean-square residuals of 5-10 mm have been achieved over a 1-year data arc in 2016 using observations from a subset of high-performance stations and ambiguity-fixed orbits of four LEO missions. As a final contribution, we demonstrate that SLR can not only validate single-satellite orbit solutions but also precise baseline solutions of formation flying missions such as GRACE, TanDEM-X, and Swarm.

Population genetic analysis of Theileria parva isolated in cattle and buffaloes in Tanzania using minisatellite and microsatellite markers.

PubMed

Rukambile, Elpidius; Machuka, Eunice; Njahira, Moses; Kyalo, Martina; Skilton, Robert; Mwega, Elisa; Chota, Andrew; Mathias, Mkama; Sallu, Raphael; Salih, Diaeldin

2016-07-15

A population genetic study of Theileria parva was conducted on 103 cattle and 30 buffalo isolates from Kibaha, Lushoto, Njombe Districts and selected National parks in Tanzania. Bovine blood samples were collected from these study areas and categorized into 5 populations; Buffalo, Cattle which graze close to buffalo, Kibaha, Lushoto and Njombe. Samples were tested by nested PCR for T. parva DNA and positives were compared for genetic diversity to the T. parva Muguga vaccine reference strain, using 3micro and 11 minisatellite markers selected from all 4 chromosomes of the parasite genome. The diversity across populations was determined by the mean number of different alleles, mean number of effective alleles, mean number of private allele and expected heterozygosity. The mean number of allele unique to populations for Cattle close to buffalo, Muguga, Njombe, Kibaha, Lushoto and Buffalo populations were 0.18, 0.24, 0.63, 0.71, 1.63 and 3.37, respectively. The mean number of different alleles ranged from 6.97 (Buffalo) to 0.07 (Muguga). Mean number of effective alleles ranged from 4.49 (Buffalo) to 0.29 (Muguga). The mean expected heterozygosity were 0.07 0.29, 0.45, 0.48, 0.59 and 0.64 for Muguga, cattle close to buffalo, Kibaha, Njombe, Lushoto and Buffalo populations, respectively. The Buffalo and Lushoto isolates possessed a close degree of diversity in terms of mean number of different alleles, effective alleles, private alleles and expected heterozygosity. The study revealed more diversity in buffalo isolates and further studies are recommended to establish if there is sharing of parasites between cattle and buffaloes which may affect the effectiveness of the control methods currently in use. Copyright © 2016 Elsevier B.V. All rights reserved.

Universal relations for range corrections to Efimov features

DOE PAGES

Ji, Chen; Braaten, Eric; Phillips, Daniel R.; ...

2015-09-09

In a three-body system of identical bosons interacting through a large S-wave scattering length a, there are several sets of features related to the Efimov effect that are characterized by discrete scale invariance. Effective field theory was recently used to derive universal relations between these Efimov features that include the first-order correction due to a nonzero effective range r s. We reveal a simple pattern in these range corrections that had not been previously identified. The pattern is explained by the renormalization group for the effective field theory, which implies that the Efimov three-body parameter runs logarithmically with the momentummore » scale at a rate proportional to r s/a. The running Efimov parameter also explains the empirical observation that range corrections can be largely taken into account by shifting the Efimov parameter by an adjustable parameter divided by a. Furthermore, the accuracy of universal relations that include first-order range corrections is verified by comparing them with various theoretical calculations using models with nonzero range.« less

Long-range memory and multifractality in gold markets

NASA Astrophysics Data System (ADS)

Mali, Provash; Mukhopadhyay, Amitabha

2015-03-01

Long-range correlation and fluctuation in the gold market time series of the world's two leading gold consuming countries, namely China and India, are studied. For both the market series during the period 1985-2013 we observe a long-range persistence of memory in the sequences of maxima (minima) of returns in successive time windows of fixed length, but the series, as a whole, are found to be uncorrelated. Multifractal analysis for these series as well as for the sequences of maxima (minima) is carried out in terms of the multifractal detrended fluctuation analysis (MF-DFA) method. We observe a weak multifractal structure for the original series that mainly originates from the fat-tailed probability distribution function of the values, and the multifractal nature of the original time series is enriched into their sequences of maximal (minimal) returns. A quantitative measure of multifractality is provided by using a set of ‘complexity parameters’.

Cultural transmission of snake-mobbing in free-ranging Hanuman langurs.

PubMed

Srivastava, A

1991-01-01

A focal troop of free-ranging Hanuman langurs (Presbytis entellus) living in an open scrub forest around Jodhpur was observed mobbing poisonous snakes on two different occasions during field observations of about 4,109 h. These observations of snake-mobbing demonstrate that langurs exhibit a special behaviour against 'potentially dangerous animals' which is similar to the mobbing displays of birds, and of other primates. It is suggested that the adaptive significance of snake-mobbing among langurs lies in the 'cultural transmission' of this information. These observations further support the 'kin-selection' model.

Observation of excess flux for negative cosmic ray penetrating particles in bubble chamber "SKAT" for momentum range (30GeV/c

NASA Astrophysics Data System (ADS)

Bazhutov, Yu. N.; Baranov, D. S.

2001-08-01

There are presented the first results of the new heavy stable cosmic ray particles search in the bubble chamber "SKAT" (450 x 160 x 90 cm3 ), which was exposed in the neutrino beam of Serpukhov Accelerator during 1976 - 1992 years and was viewed along the horizontal direction so as the magnet field direction (MDM > 150 GeV/c). From looking over 1,270 stills (1 roll for April 23, 1979) it was selected 757 tracks of cosmic ray particles with zenith angle θ < 45°, track length - L > 50 cm and momentum P>2.0GeV/c. From this events there were constructed momentum spectrums for both negative and positive vertical cosmic ray penetrating particles in the (2.0 - 126) GeV/c range and calculated their charge ratio. For positive particles the momentum spectrum has normal shape in all studied range the same as for negative particles but only for momentum range (2.0 - 32) GeV/c and charge ratio for this range is normal and the same as for cosmic muons. But for momentum P>32GeV/c it was observed negative particles excess flux (~10-5 cm-2 s-1 sr-1 ) with changed charge ratio - R = 0.62 +/0.18 (˜>3.5σ) for momentum range (32GeV/cobserved from another "SKAT" 3 rolls (1717 stills in December 11-12, 1991). Here it was measured from selected near vertical 736 events for momentum range (36GeV/c3σ) and for momentum range (3.6GeV/c107 cm2 ṡsṡsr); 2) the installation place

Long-range ordering effect in electrodeposition of zinc and zinc oxide.

PubMed

Liu, Tao; Wang, Sheng; Shi, Zi-Liang; Ma, Guo-Bin; Wang, Mu; Peng, Ru-Wen; Hao, Xi-Ping; Ming, Nai-Ben

2007-05-01

In this paper, we report the long-range ordering effect observed in the electro-crystallization of Zn and ZnO from an ultrathin aqueous electrolyte layer of ZnSO4 . The deposition branches are regularly angled, covered with random-looking, scalelike crystalline platelets of ZnO. Although the orientation of each crystalline platelet of ZnO appears random, transmission electron microscopy shows that they essentially possess the same crystallographic orientation as the single-crystalline zinc electrodeposit underneath. Based on the experimental observations, we suggest that this unique long-range ordering effect results from an epitaxial nucleation effect in electrocrystallization.

Crustal movement and plate motion as observed by GPS baseline ranging - trial to make teaching materials for middle- and high-school earth science education by teachers

NASA Astrophysics Data System (ADS)

Matsumoto, T.

2009-12-01

Japanese government established the system for renewing educational personnel certificates in 2007 and mandated the adoption of it in April 2009 (cf. “2007 White Paper on Education, Culture, Sports, Science and Technology”, available at http://www.mext.go.jp/english/). The new system shows that the valid period for each regular certificate after the renewal system adoption (April 1, 2009) is until the end of the fiscal year after ten years from satisfying the qualifications required for the certificate. Only persons who have attended over 30 hours and passed the examination in the certificate renewal courses before the expiration of the valid period can renew their certificate which is valid for next ten years. The purpose of this system is for teachers to acquire the latest knowledge and skills. Certificate renewal courses authorized by Ministry of Education, Culture, Sports, Science and Technology of Japan are offered by universities. Attendees will choose based on their specialty and awareness of issues from the various courses with education curriculums and. To renew their certificates, they should include (1) items regarding the latest trends and issues in education (12 hours) and (2) items regarding their speciality and other educational enhancement (three 6-hours course: total 18 hours). In 2008, before the adoption, provisional certificate renewal courses were offered for trial by more than 100 universities. The author offered a 6-hour course titled by “Development of teaching materials for school pupils to make understand the dynamic motion of the earth - utilising the results of the GPS ranging”. This course was targeted mainly for science teachers of middle- and high-schools. The goal of this course was for the attendees to understand the role of GPS ranging for the direct observation of the crustal movement and plate motion, and to produce the teaching materials possibly used in the classrooms. The offering of this course is aiming finally at

Vortex variable range hopping in a conventional superconducting film

NASA Astrophysics Data System (ADS)

Percher, Ilana M.; Volotsenko, Irina; Frydman, Aviad; Shklovskii, Boris I.; Goldman, Allen M.

2017-12-01

The behavior of a disordered amorphous thin film of superconducting indium oxide has been studied as a function of temperature and magnetic field applied perpendicular to its plane. A superconductor-insulator transition has been observed, though the isotherms do not cross at a single point. The curves of resistance versus temperature on the putative superconducting side of this transition, where the resistance decreases with decreasing temperature, obey two-dimensional Mott variable-range hopping of vortices over wide ranges of temperature and resistance. To estimate the parameters of hopping, the film is modeled as a granular system and the hopping of vortices is treated in a manner analogous to hopping of charges. The reason the long-range interaction between vortices over the range of magnetic fields investigated does not lead to a stronger variation of resistance with temperature than that of two-dimensional Mott variable-range hopping remains unresolved.

Two-way laser ranging and time transfer experiments between LOLA and an Earth-based satellite laser ranging station

NASA Astrophysics Data System (ADS)

Mao, D.; Sun, X.; Neumann, G. A.; Barker, M. K.; Mazarico, E. M.; Hoffman, E.; Zagwodzki, T. W.; Torrence, M. H.; Mcgarry, J.; Smith, D. E.; Zuber, M. T.

2017-12-01

Satellite Laser Ranging (SLR) has established time-of-flight measurements with mm precision to targets orbiting the Earth and the Moon using single-ended round-trip laser ranging to passive optical retro-reflectors. These high-precision measurements enable advances in fundamental physics, solar system dynamics. However, the received signal strength suffers from a 1/R4 decay, which makes it impractical for measuring distances beyond the Moon's orbit. On the other hand, for a two-way laser transponder pair, where laser pulses are both transmitted to and received from each end of the laser links, the signal strength at both terminals only decreases by 1/R2, thus allowing a greater range of distances to be covered. The asynchronous transponder concept has been previously demonstrated by a test in 2005 between the Mercury Laser Altimeter (MLA) aboard the MESSENGER (MErcury Surface, Space ENvironment, Geochemistry, and Ranging) spacecraft and NASA's Goddard Geophysical and Astronomical Observatory (GGAO) at a distance of ˜0.16 AU. In October 2013, regular two-way transponder-type range measurements were obtained over 15 days between the Lunar Laser Communication Demonstration (LLCD) aboard the Lunar Atmosphere and Dust Environment Explorer (LADEE) spacecraft and NASA's ground station at White Sands, NM. The Lunar Orbiter Laser Altimeter (LOLA) aboard the Lunar Reconnaissance Orbiter (LRO) provides us a unique capability to test time-transfer beyond near Earth orbit. Here we present results from two-way transponder-type experiments between LOLA and GGAO conducted in March 2014 and 2017. As in the time-transfer by laser link (T2L2) experiments between a ground station and an earth-orbiting satellite, LOLA and GGAO ranged to each other simultaneously in these two-way tests at lunar distance. We measured the time-of-flight while cross-referencing the spacecraft clock to the ground station time. On May 4th, 2017, about 20 minutes of two-way measurements were collected. The

Phobos laser ranging: Numerical Geodesy experiments for Martian system science

NASA Astrophysics Data System (ADS)

Dirkx, D.; Vermeersen, L. L. A.; Noomen, R.; Visser, P. N. A. M.

2014-09-01

Laser ranging is emerging as a technology for use over (inter)planetary distances, having the advantage of high (mm-cm) precision and accuracy and low mass and power consumption. We have performed numerical simulations to assess the science return in terms of geodetic observables of a hypothetical Phobos lander performing active two-way laser ranging with Earth-based stations. We focus our analysis on the estimation of Phobos and Mars gravitational, tidal and rotational parameters. We explicitly include systematic error sources in addition to uncorrelated random observation errors. This is achieved through the use of consider covariance parameters, specifically the ground station position and observation biases. Uncertainties for the consider parameters are set at 5 mm and at 1 mm for the Gaussian uncorrelated observation noise (for an observation integration time of 60 s). We perform the analysis for a mission duration up to 5 years. It is shown that a Phobos Laser Ranging (PLR) can contribute to a better understanding of the Martian system, opening the possibility for improved determination of a variety of physical parameters of Mars and Phobos. The simulations show that the mission concept is especially suited for estimating Mars tidal deformation parameters, estimating degree 2 Love numbers with absolute uncertainties at the 10-2 to 10-4 level after 1 and 4 years, respectively and providing separate estimates for the Martian quality factors at Sun and Phobos-forced frequencies. The estimation of Phobos libration amplitudes and gravity field coefficients provides an estimate of Phobos' relative equatorial and polar moments of inertia with an absolute uncertainty of 10-4 and 10-7, respectively, after 1 year. The observation of Phobos tidal deformation will be able to differentiate between a rubble pile and monolithic interior within 2 years. For all parameters, systematic errors have a much stronger influence (per unit uncertainty) than the uncorrelated Gaussian

Visual information for judging temporal range

NASA Technical Reports Server (NTRS)

Kaiser, Mary K.; Mowafy, Lyn

1993-01-01

Work in our laboratory suggests that pilots can extract temporal range information (i.e., the time to pass a given waypoint) directly from out-the-window motion information. This extraction does not require the use of velocity or distance, but rather operates solely on a 2-D motion cue. In this paper, we present the mathematical derivation of this information, psychophysical evidence of human observers' sensitivity, and possible advantages and limitations of basing vehicle control on this parameter.

Swift observations of GS 1826-238

NASA Astrophysics Data System (ADS)

Ji, L.; Santangelo, A.; Zhang, S.; Ducci, L.; Suleimanov, V.

2018-02-01

GS 1826-238 is a well-studied low-mass X-ray binary neutron star. This source was in a persistent hard state since its discovery in 1988 and until 2014 June. After that, the source exhibited several softer periods of enhanced intensity in the energy range 2-20 keV. We studied the long-term light curves of MAXI (Monitor of All Sky X-ray Image) and Swift/BAT, and found clearly two branches in the MAXI-BAT and hardness-intensity diagrams, which correspond to the persistent state and softer periods, respectively. We analysed 21 Swift/XRT observations, of which four were located in the persistent state while the others were in softer periods or in a state between them. The XRT spectra could be generally fitted by using an absorbed Comptonization model with no other components required. We found a peculiar relationship between the luminosity and the hardness in the energy range of 0.6-10 keV: when the luminosity is larger (smaller) than 4 per cent-6 per cent Ledd, the hardness is anti-correlated (correlated) with luminosity. We also estimated the variability for each observation by using the fractional rms in the 0.1-10 Hz range. We found that the observations in the persistent state had a large fractional rms of ˜25 per cent, similar to other low-mass X-ray binaries. However, the variability is mainly found in the range of 5 per cent-20 per cent during softer periods. We suggest that GS 1826-238 did not evolve into the soft state of atoll sources, and all the observed XRT observations during the softer periods resemble a peculiar intermediate state of atoll sources.

Ranging Behaviour of Commercial Free-Range Broiler Chickens 2: Individual Variation.

PubMed

Taylor, Peta S; Hemsworth, Paul H; Groves, Peter J; Gebhardt-Henrich, Sabine G; Rault, Jean-Loup

2017-07-20

Little is known about broiler chicken ranging behaviour. Previous studies have monitored ranging behaviour at flock level but whether individual ranging behaviour varies within a flock is unknown. Using Radio Frequency Identification technology, we tracked 1200 individual ROSS 308 broiler chickens across four mixed sex flocks in two seasons on one commercial farm. Ranging behaviour was tracked from first day of range access (21 days of age) until 35 days of age in winter flocks and 44 days of age in summer flocks. We identified groups of chickens that differed in frequency of range visits: chickens that never accessed the range (13 to 67% of tagged chickens), low ranging chickens (15 to 44% of tagged chickens) that accounted for <15% of all range visits and included chickens that used the range only once (6 to 12% of tagged chickens), and high ranging chickens (3 to 9% of tagged chickens) that accounted for 33 to 50% of all range visits. Males spent longer on the range than females in winter ( p < 0.05). Identifying the causes of inter-individual variation in ranging behaviour may help optimise ranging opportunities in free-range systems and is important to elucidate the potential welfare implications of ranging.

Long range science scheduling for the Hubble Space Telescope

NASA Technical Reports Server (NTRS)

Miller, Glenn; Johnston, Mark

1991-01-01

Observations with NASA's Hubble Space Telescope (HST) are scheduled with the assistance of a long-range scheduling system (SPIKE) that was developed using artificial intelligence techniques. In earlier papers, the system architecture and the constraint representation and propagation mechanisms were described. The development of high-level automated scheduling tools, including tools based on constraint satisfaction techniques and neural networks is described. The performance of these tools in scheduling HST observations is discussed.

Short Range Acoustic Propagation Under Arctic Ice Cover During Icex 16

DTIC Science & Technology

2016-09-01

There is no immediately apparent pattern to the discontinuity between modeled and observed transmission loss . In some cases, the modeled values are...Reeder THIS PAGE INTENTIONALLY LEFT BLANK i REPORT DOCUMENTATION PAGE Form Approved OMB No . 0704–0188 Public reporting burden for this...transmission loss in the observed frequency, range, and depth combinations. The received signals were processed and analyzed to determine observed

Observations and modelling of enhanced AOD at Spitsbergen - long-range transport of biomass burning emissions from Alaska fires in July 2015

NASA Astrophysics Data System (ADS)

Struzewska, Joanna; Kaminski, Jacek W.; Markowicz, Krzysztof; Lisok, Justyna

2017-04-01

In the scope of the IAREA project (http://www.igf.fuw.edu.pl/iAREA) several measurement campaigns were undertaken at Svalbard in order to assess the variability of absorbing aerosols in this region during spring and summertime 2014-2016. During the summer campaign of 2015 a significant increase of aerosol concentrations and AOD were observed at NyAlesund station from 9 to 15 of July. This episode was connected with the long range transport of smoke plum emitted from biomass burning at Alaska. A tropospheric chemistry model GEM-AQ (Global Environmental Multiscale Air Quality) was used to analyse the pathways and vertical distribution of the biomass burning aerosol observed over Svalbard. The core of the model is based on a weather prediction model with environmental processes (chemistry and aerosols) implanted on-line and are interactive (i.e. providing feedback of chemistry on radiation and dynamics). Aerosol module includes 5 size-resolved types of aerosols: sulphates, black carbon, organic carbon, sea salt and mineral dust. Aerosol mass is distributed into 12 logarithmically spaced bins. Anthropogenic emissions developed by NILU in the ECLIPSE project were used for this study. Biomass burning emissions were applied using daily GFAS fields obtained from the Copernicus Services. We will present the GEM-AQ model results and comparison with available measurement. The GEM-AQ model correctly reproduced the inflow of polluted air masses and sharp increase of AOD values. PM10 analysis showed elevated concentration values up to 700 hPa level, with the maximum reaching 35 ppb at 900 hPa. Model analysis showed over Svalbard shows transport of a thick layer with enhanced extinction above the planetary boundary layer.

Detection of cryptic pathogenic copy number variations and constitutional loss of heterozygosity using high resolution SNP microarray analysis in 117 patients referred for cytogenetic analysis and impact on clinical practice.

PubMed

Bruno, D L; Ganesamoorthy, D; Schoumans, J; Bankier, A; Coman, D; Delatycki, M; Gardner, R J M; Hunter, M; James, P A; Kannu, P; McGillivray, G; Pachter, N; Peters, H; Rieubland, C; Savarirayan, R; Scheffer, I E; Sheffield, L; Tan, T; White, S M; Yeung, A; Bowman, Z; Ngo, C; Choy, K W; Cacheux, V; Wong, L; Amor, D J; Slater, H R

2009-02-01

Microarray genome analysis is realising its promise for improving detection of genetic abnormalities in individuals with mental retardation and congenital abnormality. Copy number variations (CNVs) are now readily detectable using a variety of platforms and a major challenge is the distinction of pathogenic from ubiquitous, benign polymorphic CNVs. The aim of this study was to investigate replacement of time consuming, locus specific testing for specific microdeletion and microduplication syndromes with microarray analysis, which theoretically should detect all known syndromes with CNV aetiologies as well as new ones. Genome wide copy number analysis was performed on 117 patients using Affymetrix 250K microarrays. 434 CNVs (195 losses and 239 gains) were found, including 18 pathogenic CNVs and 9 identified as "potentially pathogenic". Almost all pathogenic CNVs were larger than 500 kb, significantly larger than the median size of all CNVs detected. Segmental regions of loss of heterozygosity larger than 5 Mb were found in 5 patients. Genome microarray analysis has improved diagnostic success in this group of patients. Several examples of recently discovered "new syndromes" were found suggesting they are more common than previously suspected and collectively are likely to be a major cause of mental retardation. The findings have several implications for clinical practice. The study revealed the potential to make genetic diagnoses that were not evident in the clinical presentation, with implications for pretest counselling and the consent process. The importance of contributing novel CNVs to high quality databases for genotype-phenotype analysis and review of guidelines for selection of individuals for microarray analysis is emphasised.

Influence of tidal range on the stability of coastal marshland

USGS Publications Warehouse

Kirwan, Matthew L.; Guntenspergen, Glenn R.

2010-01-01

Early comparisons between rates of vertical accretion and sea level rise across marshes in different tidal ranges inspired a paradigm that marshes in high tidal range environments are more resilient to sea level rise than marshes in low tidal range environments. We use field-based observations to propose a relationship between vegetation growth and tidal range and to adapt two numerical models of marsh evolution to explicitly consider the effect of tidal range on the response of the marsh platform channel network system to accelerating rates of sea level rise. We find that the stability of both the channel network and vegetated platform increases with increasing tidal range. Our results support earlier hypotheses that suggest enhanced stability can be directly attributable to a vegetation growth range that expands with tidal range. Accretion rates equilibrate to the rate of sea level rise in all experiments regardless of tidal range, suggesting that comparisons between accretion rate and tidal range will not likely produce a significant relationship. Therefore, our model results offer an explanation to widely inconsistent field-based attempts to quantify this relationship while still supporting the long-held paradigm that high tidal range marshes are indeed more stable.

Development of SSR Markers in Hickory (Carya cathayensis Sarg.) and Their Transferability to Other Species of Carya.

PubMed

Li, Juan; Zeng, Yanru; Shen, Dengfeng; Xia, Guohua; Huang, Yinzhi; Huang, Youjun; Chang, Jun; Huang, Jianqin; Wang, Zhengjia

2014-10-01

Hickory (Carya cathayensis Sarg.), an important nut-producing species in Southeastern China, has high economic value, but so far there has been no cultivar bred under species although it is mostly propagated by seeding and some elite individuals have been found. It has been found recently that this species has a certain rate of apomixis and poor knowledge of its genetic background has influenced development of a feasible breeding strategy. Here in this paper we first release SSR (Simple sequence repeat) markers developed in this species and their transferability to other three species of the same genus, Carya. A total of 311 pairs of SSR primers in hickory were developed based on sequenced cDNAs of a fruit development-associated cDNA library and RNA-seq data of developing female floral buds and could be used to distinguish hickory, C. hunanensis Cheng et R. H. Chang ex R. H. Chang et Lu, C. illinoensis K. Koch (pecan) and C. dabieshanensis M. C. Liu et Z. J. Li, but they were monomorphic in both hickory and C. hunanensis although multi-alleles have been identified in all the four species. There is a transferability rate of 63.02% observed between hickory and pecan and the markers can be applied to study genetic diversity of accessions in pecan. When used in C. dabieshanensis, it was revealed that C. dabieshanensis had the number of alleles per locus ranging from 2 to 4, observed heterozygosity from 0 to 0.6667 and expected heterozygosity from 0.333 to 0.8667, respectively, which supports the existence of C. dabieshanensis as a separate species different from hickory and indicates that there is potential for selection and breeding in this species.

Development of SSR Markers in Hickory (Carya cathayensis Sarg.) and Their Transferability to Other Species of Carya

PubMed Central

Li, Juan; Zeng, Yanru; Shen, Dengfeng; Xia, Guohua; Huang, Yinzhi; Huang, Youjun; Chang, Jun; Huang, Jianqin; Wang, Zhengjia

2014-01-01

Hickory (Carya cathayensis Sarg.), an important nut-producing species in Southeastern China, has high economic value, but so far there has been no cultivar bred under species although it is mostly propagated by seeding and some elite individuals have been found. It has been found recently that this species has a certain rate of apomixis and poor knowledge of its genetic background has influenced development of a feasible breeding strategy. Here in this paper we first release SSR (Simple sequence repeat) markers developed in this species and their transferability to other three species of the same genus, Carya. A total of 311 pairs of SSR primers in hickory were developed based on sequenced cDNAs of a fruit development-associated cDNA library and RNA-seq data of developing female floral buds and could be used to distinguish hickory, C. hunanensis Cheng et R. H. Chang ex R. H. Chang et Lu, C. illinoensis K. Koch (pecan) and C. dabieshanensis M. C. Liu et Z. J. Li, but they were monomorphic in both hickory and C. hunanensis although multi-alleles have been identified in all the four species. There is a transferability rate of 63.02% observed between hickory and pecan and the markers can be applied to study genetic diversity of accessions in pecan. When used in C. dabieshanensis, it was revealed that C. dabieshanensis had the number of alleles per locus ranging from 2 to 4, observed heterozygosity from 0 to 0.6667 and expected heterozygosity from 0.333 to 0.8667, respectively, which supports the existence of C. dabieshanensis as a separate species different from hickory and indicates that there is potential for selection and breeding in this species. PMID:25435799

Eighteen microsatellite loci in Salix arbutifolia (Salicaceae) and cross-species amplification in Salix and Populus species.

PubMed

Hoshikawa, Takeshi; Kikuchi, Satoshi; Nagamitsu, Teruyoshi; Tomaru, Nobuhiro

2009-07-01

Salix arbutifolia is a riparian dioecious tree species that is of conservation concern in Japan because of its highly restricted distribution. Eighteen polymorphic loci of dinucleotide microsatellites were isolated and characterized. Among these, estimates of the expected heterozygosity ranged from 0.350 to 0.879. Cross-species amplification was successful at 9-13 loci among six Salix species and at three loci in one Populus species. © 2009 Blackwell Publishing Ltd.

International Observe the Moon Night

NASA Image and Video Library

2010-09-19

Double beams shoot into the night sky during the Internation Observe the Moon night event. Goddard's Laser Ranging Facility directs a laser toward the Lunar Reconassaince Orbiter on International Observe the Moon Night. (Sept 18, 2010) Background on laser ranging: www.nasa.gov/mission_pages/LRO/news/LRO_lr.html Credit: NASA/GSFC/Debbie Mccallum On September 18, 2010 the world joined the NASA Goddard Space Flight Center's Visitor Center in Greenbelt, Md., as well as other NASA Centers to celebrate the first annual International Observe the Moon Night (InOMN). To read more go to: www.nasa.gov/centers/goddard/news/features/2010/moon-nigh... NASA Goddard Space Flight Center contributes to NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s endeavors by providing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Join us on Facebook

Home range, social behavior, and dominance relationships in the African unstriped ground squirrel, Xerus rutilus

USGS Publications Warehouse

O'Shea, Thomas J.

1976-01-01

A field study of home range, social behavior, and dominance relationships in the African unstriped ground squirrel, Xerus rutilus, was conducted in semi-arid bushland near Kibwezi, Kenya. Ground squirrels lived alone or in small groups in isolated burrow systems and had broadly overlapping home ranges. They were neither territorial or colonial. Home ranges were estimated by visual observation of marked animals and those of males were considerably larger (mean=7.01 hectares (ha); n=4) than those of females (mean=1.37 ha; n-6). A continuum of agonistic behavior ranging from threat to combat is described, although actual combat was rarely observed. Sexual behavior includes a stereotypical tail display by adult males. Dominance relationships, based on 542 observed encounters between marked individuals, include a consistent male dominance over females and a fairly constant linear hierarchy among all individuals with shared home ranges. Similarities in the behavior of African ground squirrels and tree squirrels (Sciurus) are discussed.

Genetic variation and population structure in Jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes.

PubMed

Rout, P K; Thangraj, K; Mandal, A; Roy, R

2012-01-01

Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation

Genetic Variation and Population Structure in Jamunapari Goats Using Microsatellites, Mitochondrial DNA, and Milk Protein Genes